| Customer Name | ####### | Customer Institutaion | ####### | Customer Email | ####### | Project ID | ####### |
|---|---|
| Salesperson | Kyle Navel | knavel@lcsciences.com |
Your reliable partner in genomics, transcriptomics and proteomics
RNA-Seq (RNA sequencing), also called whole transcriptome shotgun sequencing (WTSS), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time.
RNA-Seq is used to analyze the continuously changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression over time, or differences in gene expression in different groups or treatments. In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. RNA-Seq can also be used to determine exon/intron boundaries and verify or amend previously annotated 5' and 3' gene boundaries
Prior to RNA-Seq, gene expression studies were done with hybridization-based microarrays. Issues with microarrays include cross-hybridization artifacts, poor quantification of lowly and highly expressed genes, and needing to know the sequence a priori. Because of these technical issues, transcriptomics transitioned to sequencing-based methods. These progressed from Sanger sequencing of Expressed Sequence Tag libraries, to chemical tag-based methods (e.g., serial analysis of gene expression), and finally to the current technology, next-gen sequencing of cDNA (notably RNA-Seq).
Fig.1 Summary of RNA-Seq
As shown in Fig.1, within the organisms, genes are transcribed and spliced (in eukaryotes) to produce mature mRNA transcripts (red). The mRNA is extracted from the organism, fragmented and copied into stable ds-cDNA (blue). The ds-cDNA is sequenced using high-throughput, short-read sequencing methods. These sequences can then be aligned to a reference genome sequence to reconstruct which genome regions were being transcribed. This data can be used to annotate where expressed genes are, their relative expression levels, and any alternative splice variants.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the poly(A) mRNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with a strand-specific library preparation by dUTP method. The average insert size for the paired-end libraries was 300±50 bp. And then we performed the paired-end 2×150bp sequencing on an Illumina Hiseq 4000 at LC Sciences following the vendor's recommended protocol.
Transcripts Assembly:
Firstly, Cutadapt[1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2[2] to map reads to the genome of Oryza sativa (Version: RGAP 7). The mapped reads of each sample were assembled using StringTie[3]. Then, all transcriptomes from 6 Samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie[3] and Ballgown[4] was used to estimate the expression levels of all transcripts.
Different expression analysis of mRNAs:
StringTie[3] was used to perform expression level for mRNAs by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown[4].
Bioinformatics pipeline for RNA sequencing (polyA)
Reference:
[1] Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet Journal 17 (2011).
[2] Kim, D., Langmead, B. & Salzberg, S.L. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12, 357–360 (2015).
[3] Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology. 33, 290–295 (2015).
[4] Frazee, A.C. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology. 33, 243–246 (2015).
Species name: Rice
Latin name: Oryza sativa
Specimens: ovule
| Sample | COND1 |
| Lo7_1 | Lo7 |
| Lo7_2 | Lo7 |
| Lo7_3 | Lo7 |
| Lo8_1 | Lo8 |
| Lo8_2 | Lo8 |
| Lo8_3 | Lo8 |
| Dababase | Web links | Version/date |
|---|---|---|
| Genome | http://rice.plantbiology.msu.edu/ | RGAP 7 | Gene Orthology (GO) | https://www.ncbi.nlm.nih.gov/projects/SNP/ | 2016.12 | KEGG | http://www.kegg.jp/ | 2017.06 |
| Analysis item | Software | Version/date | Quality control | FastQC | 0.10.1 | Adapter remove | Cutadapt | 1.10 | Mapping | HISAT | 2.0 | Transcripts assembly | StringTie | 1.3 | Differential expression analysis | Ballgown | 2016.09.29 | GO and KEGG enrichment analysis | Perl scripts in house | NA | SNP/Indel analysis | samtools | 0.7 | SNP/Indel annotation | ANNOVAR | 2017.09 | Alternative splicing | ASprofile | 1.0 |
|---|---|---|
Statistics of reads from 6 libraries was shown below. Results of FastQC, PCA analysis and sample correlation were deposited in summary/8_Quality_Control.
| Sample | Raw Data | Valid Data | Valid Ratio(reads) | Q20% | Q30% | GC content% | ||
| Read | Base | Read | Base | |||||
| Lo7_1 | 43988286 | 6.60G | 43668242 | 6.55G | 99.27 | 98.99 | 91.45 | 51 |
| Lo7_2 | 47347712 | 7.10G | 46996072 | 7.05G | 99.26 | 99.12 | 92.34 | 51.50 |
| Lo7_3 | 44763428 | 6.71G | 44422680 | 6.66G | 99.24 | 99.23 | 92.64 | 51.50 |
| Lo8_1 | 43991088 | 6.60G | 43671866 | 6.55G | 99.27 | 99.21 | 92.97 | 51.50 |
| Lo8_2 | 45642984 | 6.85G | 45340074 | 6.80G | 99.34 | 99.34 | 92.74 | 52 |
| Lo8_3 | 46678552 | 7.00G | 46354468 | 6.95G | 99.31 | 99.01 | 91.09 | 50.50 |
document location: summary/1_rawdata/ReadsQC.xlsx
| Sample | Valid reads | Mapped reads | Unique Mapped reads | Multi Mapped reads | PE Mapped reads | Reads map to sense strand | Reads map to antisense strand | Non-splice reads | Splice reads |
| Lo7_1 | 43668242 | 40525689(92.80%) | 32875835(75.29%) | 7649854(17.52%) | 37309218(85.44%) | 19379564(44.38%) | 19674393(45.05%) | 26202698(60.00%) | 12851259(29.43%) |
| Lo7_2 | 46996072 | 43804863(93.21%) | 34574453(73.57%) | 9230410(19.64%) | 40581704(86.35%) | 20715701(44.08%) | 21069668(44.83%) | 28516068(60.68%) | 13269301(28.23%) |
| Lo7_3 | 44422680 | 41579830(93.60%) | 32839571(73.93%) | 8740259(19.68%) | 38839830(87.43%) | 19721984(44.40%) | 20032131(45.09%) | 27193119(61.21%) | 12560996(28.28%) |
| Lo8_1 | 43671866 | 40934692(93.73%) | 32505589(74.43%) | 8429103(19.30%) | 37878490(86.73%) | 19392874(44.41%) | 19689746(45.09%) | 26159989(59.90%) | 12922631(29.59%) |
| Lo8_2 | 45340074 | 42486373(93.71%) | 33664651(74.25%) | 8821722(19.46%) | 39600686(87.34%) | 20152040(44.45%) | 20470043(45.15%) | 26981136(59.51%) | 13640947(30.09%) |
| Lo8_3 | 46354468 | 42647519(92.00%) | 35043515(75.60%) | 7604004(16.40%) | 39000572(84.14%) | 20342722(43.89%) | 20631931(44.51%) | 26992873(58.23%) | 13981780(30.16%) |
document location: summary/1_rawdata/2_mapped_stat.xlsx
document location: summary/2_reference_mapping/3_mapped_region_stat.png
document location: summary/2_reference_mapping/4_DensityDistribution/*_chromosome.jpeg
Those transcripts assembled by StringTie which are not annotated in genome annotation database are belong to novel transcripts with class code (i, j, o, u ,x).
Class code typies and definitions:
| class code | Description |
|---|---|
| j | Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript |
| i | A transfrag falling entirely within a reference intron |
| o | Generic exonic overlap with a reference transcript |
| u | Unknown, intergenic transcript |
| x | Exonic overlap with reference on the opposite strand |
document location:
summary/3_novel_transcripts/novel_merged.fa
summary/3_novel_transcripts/novel_merged.gtf
Tips: The Gene transfer format (GTF) is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format (GFF), but contains some additional conventions specific to gene information. A significant feature of the GTF that can be validated: given a sequence and a GTF file, one can check that the format is correct. This significantly reduces problems with the interchange of data between groups. We recommend you to open files with gtf and fa format by using several text editors such as Notepad++ (https://notepad-plus-plus.org/) and Vim (http://www.vim.org/).
StringTie was utilized to assemble all trascripts from mapped reads (bam format) by mapping software Tophat or HISAT2. Also both gene level and transcript level were estimated by StringTie using FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)×exon_length(kB)]).
Statistics of gene expression:
| Sample | Exp gene | Min. | 1st Qu. | Median | Mean | 3rd Qu. | Max. | Sd. | Sum. |
| Lo7_1 | 28592 | 0.00 | 0.65 | 3.09 | 12.72 | 10.66 | 3829.04 | 53.06 | 363662.40 |
| Lo7_2 | 28870 | 0.00 | 0.60 | 2.87 | 12.18 | 9.92 | 2509.16 | 48.10 | 351604.59 |
| Lo7_3 | 28638 | 0.00 | 0.60 | 2.86 | 12.52 | 9.88 | 3423.92 | 52.08 | 358608.39 |
| Lo8_1 | 28521 | 0.00 | 0.67 | 3.09 | 12.66 | 10.19 | 2672.82 | 49.89 | 361048.01 |
| Lo8_2 | 28718 | 0.00 | 0.67 | 3.00 | 12.90 | 10.04 | 3714.39 | 54.64 | 370343.89 |
| Lo8_3 | 28810 | 0.00 | 0.65 | 3.22 | 12.65 | 10.66 | 2940.30 | 49.43 | 364377.26 |
Statistics of transcript expression:
| Sample | Exp transcript | Min. | 1st Qu. | Median | Mean | 3rd Qu. | Max. | Sd. | Sum. |
| Lo7_1 | 57681 | 0.00 | 0.40 | 1.42 | 7.44 | 4.62 | 3829.04 | 40.37 | 429233.78 |
| Lo7_2 | 57848 | 0.00 | 0.37 | 1.34 | 7.25 | 4.31 | 5038.26 | 41.32 | 419308.11 |
| Lo7_3 | 57461 | 0.00 | 0.36 | 1.32 | 7.44 | 4.38 | 4606.14 | 43.58 | 427365.34 |
| Lo8_1 | 56912 | 0.00 | 0.37 | 1.33 | 7.54 | 4.41 | 3468.64 | 41.59 | 429105.86 |
| Lo8_2 | 57311 | 0.00 | 0.37 | 1.32 | 7.69 | 4.36 | 5177.10 | 47.30 | 440912.61 |
| Lo8_3 | 58177 | 0.00 | 0.39 | 1.41 | 7.39 | 4.61 | 2940.30 | 38.04 | 429953.33 |
document location:
summary/4_transcript_expression/1_gene_expression_statistics.xlsx
summary/4_transcript_expression/*_gene_expression_boxplot.png
summary/4_transcript_expression/1_gene_expression_statistics.xlsx
summary/4_transcript_expression/*_transcript_expression_boxplot.png
FI of gene expression:
| Sample | 0-0.1 FI | 0.1-0.3 FI | 0.3-3.57 FI | 3.57-15 FI | 15-60 FI | >60 FI |
| Lo7_1 | 2431(8.50%) | 2419(8.46%) | 10182(35.61%) | 8318(29.09%) | 4173(14.59%) | 1069(3.74%) |
| Lo7_2 | 2595(8.99%) | 2541(8.80%) | 10469(36.26%) | 8247(28.57%) | 4016(13.91%) | 1002(3.47%) |
| Lo7_3 | 2628(9.18%) | 2411(8.42%) | 10482(36.60%) | 8127(28.38%) | 3930(13.72%) | 1060(3.70%) |
| Lo8_1 | 2377(8.33%) | 2309(8.10%) | 10355(36.31%) | 8456(29.65%) | 3997(14.01%) | 1027(3.60%) |
| Lo8_2 | 2305(8.03%) | 2373(8.26%) | 10639(37.05%) | 8441(29.39%) | 3858(13.43%) | 1102(3.84%) |
| Lo8_3 | 2597(9.01%) | 2351(8.16%) | 9958(34.56%) | 8627(29.94%) | 4226(14.67%) | 1051(3.65%) |
FI of transcripts expression:
| Sample | 0-0.1 FI | 0.1-0.3 FI | 0.3-3.57 FI | 3.57-15 FI | 15-60 FI | >60 FI |
| Lo7_1 | 6003(10.41%) | 6183(10.72%) | 28415(49.26%) | 11528(19.99%) | 4423(7.67%) | 1129(1.96%) |
| Lo7_2 | 6312(10.91%) | 6545(11.31%) | 28570(49.39%) | 11113(19.21%) | 4225(7.30%) | 1083(1.87%) |
| Lo7_3 | 6455(11.23%) | 6346(11.04%) | 28269(49.20%) | 11068(19.26%) | 4220(7.34%) | 1103(1.92%) |
| Lo8_1 | 6191(10.88%) | 6362(11.18%) | 28023(49.24%) | 10994(19.32%) | 4207(7.39%) | 1135(1.99%) |
| Lo8_2 | 6154(10.74%) | 6429(11.22%) | 28430(49.61%) | 10925(19.06%) | 4195(7.32%) | 1178(2.06%) |
| Lo8_3 | 6302(10.83%) | 6215(10.68%) | 28457(48.91%) | 11654(20.03%) | 4435(7.62%) | 1114(1.91%) |
document location:
summary/4_transcript_expression/2_gene_expression_interval.xlsx
summary/4_transcript_expression/2_transcript_expression_interval.xlsx
document location:
summary/4_transcript_expression/*_gene_expression_density.png
summary/4_transcript_expression/*_transcript_expression_density.png
Gene expression profiling:
| gene_id | gene_name | transcript_id | GO | KEGG | KO_ENTRY | EC | Description | FPKM.Lo7_1 | FPKM.Lo7_2 | FPKM.Lo7_3 | FPKM.Lo8_1 | FPKM.Lo8_2 | FPKM.Lo8_3 |
| LOC_Os01g01090 | LOC_Os01g01090 | LOC_Os01g01090.1 | GO:0003755(peptidyl-prolyl cis-trans isomerase activity);GO:0005528(FK506 binding);GO:0005789(endoplasmic reticulum membrane);GO:0061077(chaperone-mediated protein folding) | NA | NA | NA | retrotransposon protein, putative, unclassified, expressed | 0 | 0 | 0 | 0 | 0.02 | 0 |
| LOC_Os01g01110 | LOC_Os01g01110 | LOC_Os01g01110.1 | GO:0004672(protein kinase activity);GO:0004674(protein serine/threonine kinase activity);GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation);GO:0007169(transmembrane receptor protein tyrosine kinase signaling pathway);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04075(Plant hormone signal transduction);04626(Plant-pathogen interaction) | K13416 | EC:2.7.10.1 2.7.11.1 | expressed protein | 0 | 0 | 0 | 0.59 | 0 | 0 |
| LOC_Os01g01290 | LOC_Os01g01290 | LOC_Os01g01290.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005515(protein binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0009738(abscisic acid-activated signaling pathway);GO:0010468(regulation of gene expression);GO:0046982(protein heterodimerization activity);GO:0048586(regulation of long-day photoperiodism, flowering);GO:0051247(positive regulation of protein metabolic process);GO:2000905(negative regulation of starch metabolic process) | NA | NA | NA | histone-like transcription factor and archaeal histone, putative, expressed | 0 | 0.11 | 0 | 0 | 0 | 0 |
| LOC_Os01g01360 | LOC_Os01g01360 | LOC_Os01g01360.1 | GO:0005215(transporter activity);GO:0005886(plasma membrane);GO:0006857(oligopeptide transport);GO:0016020(membrane);GO:0016021(integral component of membrane) | NA | NA | NA | peptide transporter PTR2, putative, expressed | 0 | 0.33 | 0.25 | 0.98 | 0.47 | 0.78 |
| LOC_Os01g01470 | LOC_Os01g01470 | LOC_Os01g01470.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0007275(multicellular organism development) | 03018(RNA degradation) | K12581 | NA | no apical meristem protein, putative, expressed | 0 | 0 | 0 | 0.08 | 0.06 | 0 |
| LOC_Os01g01730 | LOC_Os01g01730 | LOC_Os01g01730.1 | NA | NA | NA | NA | serine/arginine repetitive matrix protein 2, putative, expressed | 0 | 0 | 0 | 0 | 0 | 0.04 |
| LOC_Os01g01770 | LOC_Os01g01770 | LOC_Os01g01770.1 | GO:0003676(nucleic acid binding);GO:0004527(exonuclease activity);GO:0005622(intracellular);GO:0005634(nucleus);GO:0046872(metal ion binding) | 03008(Ribosome biogenesis in eukaryotes) | K14570 | EC:3.1.-.- | ZOS1-01 - C2H2 zinc finger protein, expressed | 0.26 | 0.04 | 0.07 | 0.27 | 0.05 | 0 |
| LOC_Os01g01840 | LOC_Os01g01840 | LOC_Os01g01840.1 | GO:0000977(RNA polymerase II regulatory region sequence-specific DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0006357(regulation of transcription from RNA polymerase II promoter);GO:0090575(RNA polymerase II transcription factor complex) | NA | NA | NA | helix-loop-helix DNA-binding domain containing protein, expressed | 0.02 | 0.02 | 0 | 0 | 0.05 | 0 |
| LOC_Os01g01950 | LOC_Os01g01950 | LOC_Os01g01950.1 | NA | NA | NA | NA | expressed protein | 0 | 0.07 | 0.07 | 0 | 0.21 | 0 |
| LOC_Os01g01980 | LOC_Os01g01980 | LOC_Os01g01980.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.16 | 0 | 0 |
| LOC_Os01g01990 | LOC_Os01g01990 | LOC_Os01g01990.1 | NA | NA | NA | NA | expressed protein | 0.29 | 0 | 0 | 0 | 0 | 0 |
| LOC_Os01g02110 | LOC_Os01g02110 | LOC_Os01g02110.1 | GO:0001046(core promoter sequence-specific DNA binding);GO:0001228(transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding);GO:0005634(nucleus);GO:0006366(transcription from RNA polymerase II promoter) | 04075(Plant hormone signal transduction);04712(Circadian rhythm - plant) | K12126 | NA | helix-loop-helix DNA-binding domain containing protein, expressed | 0 | 0.03 | 0 | 0 | 0 | 0.08 |
| LOC_Os01g02120 | LOC_Os01g02120 | LOC_Os01g02120.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0008429(phosphatidylethanolamine binding);GO:0009737(response to abscisic acid);GO:0009738(abscisic acid-activated signaling pathway);GO:0010030(positive regulation of seed germination) | 04712(Circadian rhythm - plant) | K16223 | NA | osMFT2 MFT-Like2 homologous to Mother of FT and TFL1 gene; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein, expressed | 0 | 0 | 0 | 0 | 0 | 0.05 |
| LOC_Os01g02190 | LOC_Os01g02190 | LOC_Os01g02190.1 | GO:0005887(integral component of plasma membrane);GO:0009992(cellular water homeostasis);GO:0015250(water channel activity);GO:0015254(glycerol channel activity);GO:0034220(ion transmembrane transport) | NA | NA | NA | aquaporin protein, putative, expressed | 0.17 | 0 | 0.17 | 0.12 | 0.08 | 0.19 |
| LOC_Os01g02210 | LOC_Os01g02210 | LOC_Os01g02210.1 | GO:0003755(peptidyl-prolyl cis-trans isomerase activity);GO:0005528(FK506 binding);GO:0005789(endoplasmic reticulum membrane);GO:0061077(chaperone-mediated protein folding) | NA | NA | NA | retrotransposon protein, putative, Ty3-gypsy subclass | 0 | 0 | 0.00 | 0 | 0 | 0 |
| LOC_Os01g02250 | LOC_Os01g02250 | LOC_Os01g02250.1 | GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005576(extracellular region);GO:0006952(defense response);GO:0043531(ADP binding) | 04626(Plant-pathogen interaction) | K13457 | NA | RGA-1, putative, expressed | 0 | 0 | 0.01 | 0 | 0 | 0.06 |
| LOC_Os01g02310 | LOC_Os01g02310 | LOC_Os01g02310.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation) | 04626(Plant-pathogen interaction) | K13430 | EC:2.7.11.1 | expressed protein | 0 | 0.03 | 0 | 0 | 0 | 0 |
| LOC_Os01g02370 | LOC_Os01g02370 | LOC_Os01g02370.1 | GO:0005886(plasma membrane) | 00520(Amino sugar and nucleotide sugar metabolism) | K01183 | EC:3.2.1.14 | receptor-like kinase ARK1AS, putative, expressed | 0.02 | 0.01 | 0.01 | 0.09 | 0 | 0.04 |
| LOC_Os01g02710 | LOC_Os01g02710 | LOC_Os01g02710.1 | GO:0005886(plasma membrane) | NA | NA | NA | LRk-type protein, putative, expressed | 0.07 | 0.03 | 0 | 0.03 | 0 | 0.08 |
| LOC_Os01g02950 | LOC_Os01g02950 | LOC_Os01g02950.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0.08 | 0 |
| LOC_Os01g03260 | LOC_Os01g03260 | LOC_Os01g03260.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.03 | 0 | 0 | 0 |
| LOC_Os01g03270 | LOC_Os01g03270 | LOC_Os01g03270.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | expressed protein | 0.12 | 0.10 | 0.02 | 0.49 | 0.27 | 0.20 |
| LOC_Os01g03290 | LOC_Os01g03290 | LOC_Os01g03290.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | seven in absentia protein family domain containing protein, expressed | 0 | 0 | 0 | 0 | 0.17 | 0 |
| LOC_Os01g03300 | LOC_Os01g03300 | LOC_Os01g03300.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | seven in absentia protein family protein, expressed | 0.02 | 0.06 | 0.17 | 0 | 0 | 0 |
| LOC_Os01g03320 | LOC_Os01g03320 | LOC_Os01g03320.1 | NA | NA | NA | NA | BBTI2 - Bowman-Birk type bran trypsin inhibitor precursor, expressed | 0.74 | 0.81 | 0.78 | 0.87 | 0.20 | 0.70 |
| LOC_Os01g03380 | LOC_Os01g03380 | LOC_Os01g03380.1 | NA | NA | NA | NA | BBTI6 - Bowman-Birk type bran trypsin inhibitor precursor, putative, expressed | 0 | 0 | 0.32 | 0 | 0.06 | 0.12 |
| LOC_Os01g03429 | LOC_Os01g03429 | LOC_Os01g03429.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | expressed protein | 0.10 | 0.04 | 0 | 0.06 | 0 | 0.12 |
| LOC_Os01g03464 | LOC_Os01g03464 | LOC_Os01g03464.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | expressed protein | 0 | 0.04 | 0 | 0 | 0 | 0.03 |
| LOC_Os01g03620 | LOC_Os01g03620 | LOC_Os01g03620.1 | GO:0005507(copper ion binding);GO:0016722(oxidoreductase activity, oxidizing metal ions) | NA | NA | NA | multicopper oxidase domain containing protein, expressed | 0.38 | 0.28 | 0.49 | 0.11 | 0.14 | 0.47 |
| LOC_Os01g03670 | LOC_Os01g03670 | LOC_Os01g03670.1 | GO:0003824(catalytic activity);GO:0005829(cytosol);GO:0010584(pollen exine formation);GO:0016491(oxidoreductase activity);GO:0050662(coenzyme binding);GO:0055114(oxidation-reduction process);GO:0080110(sporopollenin biosynthetic process) | 00940(Phenylpropanoid biosynthesis) | K09753 | EC:1.2.1.44 | dihydroflavonol-4-reductase, putative, expressed | 0.05 | 0.15 | 0.08 | 0.07 | 0.04 | 0.04 |
| LOC_Os01g03840 | LOC_Os01g03840 | LOC_Os01g03840.1 | GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0008285(negative regulation of cell proliferation);GO:0010094(specification of carpel identity);GO:0010097(specification of stamen identity);GO:0043565(sequence-specific DNA binding);GO:0044212(transcription regulatory region DNA binding);GO:0048437(floral organ development) | 03410(Base excision repair) | K10773 | EC:4.2.99.18 | ZOS1-02 - C2H2 zinc finger protein, expressed | 0.13 | 0.14 | 0.48 | 0.71 | 0.64 | 0.19 |
| LOC_Os01g03890 | LOC_Os01g03890 | LOC_Os01g03890.1 | GO:0009739(response to gibberellin) | NA | NA | NA | DUF260 domain containing protein, putative, expressed | 0.00 | 0.22 | 0 | 0 | 0.02 | 0.07 |
| LOC_Os01g03900 | LOC_Os01g03900 | LOC_Os01g03900.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 1.58 | 0 | 0 | 0 |
| LOC_Os01g03930 | LOC_Os01g03930 | LOC_Os01g03930.1 | NA | NA | NA | NA | expressed protein | 0 | 0.47 | 0 | 0 | 0 | 0 |
| LOC_Os01g03960 | LOC_Os01g03960 | LOC_Os01g03960.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.12 | 0 | 0 |
| LOC_Os01g04005 | LOC_Os01g04005 | LOC_Os01g04005.1 | NA | NA | NA | NA | expressed protein | 0.01 | 0.01 | 0 | 0 | 0 | 0 |
| LOC_Os01g04090 | LOC_Os01g04090 | LOC_Os01g04090.1 | NA | NA | NA | NA | expressed protein | 0.37 | 0.63 | 0.60 | 0.43 | 0.43 | 0.51 |
| LOC_Os01g04210 | LOC_Os01g04210 | LOC_Os01g04210.1 | GO:0008375(acetylglucosaminyltransferase activity);GO:0016021(integral component of membrane);GO:0016757(transferase activity, transferring glycosyl groups) | 04144(Endocytosis) | K12471 | NA | DNA binding protein, putative, expressed | 0.38 | 0.06 | 0 | 0.21 | 0.12 | 0.25 |
| LOC_Os01g04220 | LOC_Os01g04220 | LOC_Os01g04220.1 | GO:0008375(acetylglucosaminyltransferase activity);GO:0016021(integral component of membrane);GO:0016757(transferase activity, transferring glycosyl groups) | 04144(Endocytosis) | K12471 | NA | DNA binding protein, putative, expressed | 0.06 | 0.16 | 0.12 | 0.04 | 0.20 | 0.19 |
| LOC_Os01g04250 | LOC_Os01g04250 | LOC_Os01g04250.1 | GO:0007165(signal transduction);GO:0016020(membrane) | NA | NA | NA | expressed protein | 0 | 0.21 | 0.26 | 0.56 | 0 | 0 |
| LOC_Os01g04540 | LOC_Os01g04540 | LOC_Os01g04540.1 | NA | NA | NA | NA | serine/threonine-protein kinase At1g18390 precursor, putative, expressed | 0.28 | 0.13 | 0.55 | 0.12 | 0.40 | 0.04 |
| LOC_Os01g04550 | LOC_Os01g04550 | LOC_Os01g04550.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation);GO:0016021(integral component of membrane);GO:0016301(kinase activity);GO:0016310(phosphorylation) | 00520(Amino sugar and nucleotide sugar metabolism) | K01183 | EC:3.2.1.14 | expressed protein | 0.22 | 0.33 | 0.31 | 0.17 | 0.21 | 0.35 |
| LOC_Os01g04560 | LOC_Os01g04560 | LOC_Os01g04560.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane);GO:0007166(cell surface receptor signaling pathway) | NA | NA | NA | expressed protein | 0.05 | 0.20 | 0.02 | 0 | 0 | 0 |
| LOC_Os01g04640 | LOC_Os01g04640 | LOC_Os01g04640.1 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | reticulon domain containing protein, putative, expressed | 0.51 | 0.52 | 0.23 | 0.85 | 0.49 | 0.48 |
| LOC_Os01g04699 | LOC_Os01g04699 | LOC_Os01g04699.1 | NA | NA | NA | NA | expressed protein | 0.15 | 0.24 | 0 | 0.21 | 0.20 | 0.13 |
| LOC_Os01g04750 | LOC_Os01g04750 | LOC_Os01g04750.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0009873(ethylene-activated signaling pathway);GO:0045892(negative regulation of transcription, DNA-templated) | NA | NA | NA | B3 DNA binding domain containing protein, expressed | 0 | 0 | 0 | 0.03 | 0 | 0.09 |
| LOC_Os01g04800 | LOC_Os01g04800 | LOC_Os01g04800.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0009873(ethylene-activated signaling pathway);GO:0048573(photoperiodism, flowering) | 04075(Plant hormone signal transduction) | K14486 | NA | B3 DNA binding domain containing protein, expressed | 0.77 | 0.47 | 0.26 | 0.25 | 0.23 | 0.63 |
| LOC_Os01g05050 | LOC_Os01g05050 | LOC_Os01g05050.1 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0005759(mitochondrial matrix);GO:0008150(biological_process) | NA | NA | NA | mitochondrial glycoprotein, putative, expressed | 0 | 0 | 0 | 0 | 0 | 0.06 |
| LOC_Os01g05120 | LOC_Os01g05120 | LOC_Os01g05120.1 | GO:0003674(molecular_function);GO:0005829(cytosol);GO:0006511(ubiquitin-dependent protein catabolic process);GO:0009507(chloroplast) | 04141(Protein processing in endoplasmic reticulum) | K14016 | NA | ubiquitin fusion degradation protein, putative, expressed | 0.21 | 0 | 0 | 0.12 | 0.13 | 0.18 |
| LOC_Os01g05340 | LOC_Os01g05340 | LOC_Os01g05340.1 | NA | NA | NA | NA | expressed protein | 0.17 | 0.08 | 0.18 | 0.19 | 0.19 | 0.08 |
| LOC_Os01g05360 | LOC_Os01g05360 | LOC_Os01g05360.1 | GO:0009834(plant-type secondary cell wall biogenesis);GO:0010417(glucuronoxylan biosynthetic process);GO:0042285(xylosyltransferase activity) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0.25 | 0 |
| LOC_Os01g05380 | LOC_Os01g05380 | LOC_Os01g05380.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.02 | 0 | 0 | 0 |
| LOC_Os01g05400 | LOC_Os01g05400 | LOC_Os01g05400.1 | GO:0009834(plant-type secondary cell wall biogenesis);GO:0010417(glucuronoxylan biosynthetic process);GO:0042285(xylosyltransferase activity) | NA | NA | NA | expressed protein | 0 | 0 | 0.05 | 0 | 0 | 0 |
| LOC_Os01g05440 | LOC_Os01g05440 | LOC_Os01g05440.1 | GO:0004526(ribonuclease P activity);GO:0005655(nucleolar ribonuclease P complex);GO:0090502(RNA phosphodiester bond hydrolysis, endonucleolytic) | NA | NA | NA | XH domain containing protein, expressed | 0.09 | 0.34 | 0.02 | 0.17 | 0.14 | 0.11 |
| LOC_Os01g05450 | LOC_Os01g05450 | LOC_Os01g05450.1 | NA | NA | NA | NA | expressed protein | 0.45 | 0.13 | 0.12 | 0.24 | 0.13 | 0 |
| LOC_Os01g05510 | LOC_Os01g05510 | LOC_Os01g05510.4 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.02 |
| LOC_Os01g05530 | LOC_Os01g05530 | LOC_Os01g05530.1 | GO:0000027(ribosomal large subunit assembly);GO:0003723(RNA binding);GO:0005730(nucleolus) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.06 |
| LOC_Os01g05580 | LOC_Os01g05580 | LOC_Os01g05580.1 | NA | NA | NA | NA | Exo70 exocyst complex subunit family, putative, expressed | 0 | 0 | 0 | 0.05 | 0 | 0 |
| LOC_Os01g05585 | LOC_Os01g05585 | LOC_Os01g05585.1 | NA | NA | NA | NA | metallothionein, putative, expressed | 0 | 0.10 | 0 | 0.37 | 0 | 0.25 |
| LOC_Os01g05600 | LOC_Os01g05600 | LOC_Os01g05600.1 | GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005576(extracellular region);GO:0006952(defense response);GO:0043531(ADP binding) | 04626(Plant-pathogen interaction) | K13457 | NA | NBS-LRR disease resistance protein, putative, expressed | 0 | 0 | 0 | 0.42 | 0 | 0 |
| LOC_Os01g06030 | LOC_Os01g06030 | LOC_Os01g06030.1 | GO:0005634(nucleus) | 00350(Tyrosine metabolism);00950(Isoquinoline alkaloid biosynthesis) | K01592 | EC:4.1.1.25 | expressed protein | 0 | 0 | 0 | 0.07 | 0 | 0 |
| LOC_Os01g06040 | LOC_Os01g06040 | LOC_Os01g06040.1 | NA | 00350(Tyrosine metabolism);00950(Isoquinoline alkaloid biosynthesis) | K01592 | EC:4.1.1.25 | expressed protein | 0 | 0.09 | 0 | 0 | 0 | 0.10 |
| LOC_Os01g06060 | LOC_Os01g06060 | LOC_Os01g06060.1 | GO:0005634(nucleus);GO:0008152(metabolic process);GO:0052689(carboxylic ester hydrolase activity) | 04075(Plant hormone signal transduction) | K14493 | EC:3.-.-.- | gibberellin receptor GID1L2, putative, expressed | 0.04 | 0.04 | 0.04 | 0 | 0 | 0 |
| LOC_Os01g06070 | LOC_Os01g06070 | LOC_Os01g06070.1 | NA | NA | NA | NA | expressed protein | 0.11 | 0.06 | 0 | 0 | 0 | 0 |
| LOC_Os01g06120 | LOC_Os01g06120 | LOC_Os01g06120.1 | NA | NA | NA | NA | expressed protein | 0.03 | 0 | 0 | 0 | 0 | 0 |
| LOC_Os01g06150 | LOC_Os01g06150 | LOC_Os01g06150.1 | GO:0005634(nucleus) | NA | NA | NA | expressed protein | 0.70 | 0.29 | 0.92 | 0.63 | 0.56 | 0.82 |
| LOC_Os01g06210 | LOC_Os01g06210 | LOC_Os01g06210.1 | GO:0005634(nucleus);GO:0008152(metabolic process);GO:0052689(carboxylic ester hydrolase activity) | 04075(Plant hormone signal transduction) | K14493 | EC:3.-.-.- | gibberellin receptor GID1L2, putative, expressed | 0 | 0 | 0 | 0.00 | 0 | 0 |
| LOC_Os01g06220 | LOC_Os01g06220 | LOC_Os01g06220.1 | GO:0005634(nucleus);GO:0008152(metabolic process);GO:0052689(carboxylic ester hydrolase activity) | 04075(Plant hormone signal transduction) | K14493 | EC:3.-.-.- | gibberellin receptor GID1L2, putative, expressed | 0.18 | 0 | 0.04 | 0.07 | 0.12 | 0.10 |
| LOC_Os01g06240 | LOC_Os01g06240 | LOC_Os01g06240.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation) | 00260(Glycine, serine and threonine metabolism);00350(Tyrosine metabolism);00360(Phenylalanine metabolism);00410(beta-Alanine metabolism);00950(Isoquinoline alkaloid biosynthesis);00960(Tropane, piperidine and pyridine alkaloid biosynthesis) | K00276 | EC:1.4.3.21 | protein kinase, putative, expressed | 0.08 | 0.06 | 0 | 0 | 0.06 | 0 |
| LOC_Os01g06370 | LOC_Os01g06370 | LOC_Os01g06370.1 | NA | NA | NA | NA | expressed protein | 0 | 0.34 | 0 | 0 | 0.08 | 0 |
| LOC_Os01g06390 | LOC_Os01g06390 | LOC_Os01g06390.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.08 |
| LOC_Os01g06400 | LOC_Os01g06400 | LOC_Os01g06400.1 | NA | NA | NA | NA | expressed protein | 0.03 | 0.11 | 0 | 0 | 0 | 0 |
| LOC_Os01g06420 | LOC_Os01g06420 | LOC_Os01g06420.1 | NA | NA | NA | NA | expressed protein | 0 | 0.15 | 0 | 0.24 | 0.46 | 0.15 |
| LOC_Os01g06430 | LOC_Os01g06430 | LOC_Os01g06430.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.25 | 0.06 | 0 |
| LOC_Os01g06540 | LOC_Os01g06540 | LOC_Os01g06540.1 | GO:0003677(DNA binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0008270(zinc ion binding);GO:0016036(cellular response to phosphate starvation);GO:0016568(chromatin modification);GO:0035064(methylated histone binding);GO:0042393(histone binding);GO:0048767(root hair elongation);GO:0055065(metal ion homeostasis) | NA | NA | NA | PHD finger protein, putative, expressed | 0.17 | 0.10 | 0 | 0 | 0.26 | 0 |
| LOC_Os01g06670 | LOC_Os01g06670 | LOC_Os01g06670.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13466 | NA | hcr2-5D, putative, expressed | 0 | 0 | 0 | 0.02 | 0 | 0 |
| LOC_Os01g06720 | LOC_Os01g06720 | LOC_Os01g06720.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | disease resistance protein SlVe2 precursor, putative, expressed | 0.14 | 0 | 0.09 | 0.04 | 0.02 | 0.01 |
| LOC_Os01g06750 | LOC_Os01g06750 | LOC_Os01g06750.1 | GO:0005886(plasma membrane);GO:0006952(defense response);GO:0007165(signal transduction);GO:0016301(kinase activity) | 04075(Plant hormone signal transduction) | K13415 | EC:2.7.10.1 2.7.11.1 | verticillium wilt disease resistance protein precursor, putative, expressed | 0.06 | 0.05 | 0.11 | 0 | 0.16 | 0.14 |
| LOC_Os01g06790 | LOC_Os01g06790 | LOC_Os01g06790.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | disease resistance protein, putative, expressed | 0.02 | 0.08 | 0.03 | 0.03 | 0 | 0.02 |
| LOC_Os01g06820 | LOC_Os01g06820 | LOC_Os01g06820.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | hcr2-0B, putative, expressed | 0.15 | 0 | 0.10 | 0.10 | 0.13 | 0.05 |
| LOC_Os01g06836 | LOC_Os01g06836 | LOC_Os01g06836.1 | GO:0005886(plasma membrane);GO:0006952(defense response);GO:0007165(signal transduction);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13466 | NA | disease resistance protein SlVe2 precursor, putative, expressed | 0.10 | 0.05 | 0 | 0.05 | 0.03 | 0 |
| LOC_Os01g06870 | LOC_Os01g06870 | LOC_Os01g06870.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | resistance protein SlVe1 precursor, putative, expressed | 0 | 0.03 | 0 | 0 | 0 | 0.05 |
| LOC_Os01g06920 | LOC_Os01g06920 | LOC_Os01g06920.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13466 | NA | resistance protein SlVe1 precursor, putative, expressed | 0.16 | 0.32 | 0 | 0.44 | 0.51 | 0.54 |
| LOC_Os01g07020 | LOC_Os01g07020 | LOC_Os01g07020.1 | GO:0005887(integral component of plasma membrane);GO:0015179(L-amino acid transmembrane transporter activity);GO:0015297(antiporter activity) | NA | NA | NA | POEI39 - Pollen Ole e I allergen and extensin family protein precursor, putative, expressed | 0.09 | 0 | 0.04 | 0 | 0 | 0 |
| LOC_Os01g07030 | LOC_Os01g07030 | LOC_Os01g07030.1 | GO:0005887(integral component of plasma membrane);GO:0015179(L-amino acid transmembrane transporter activity);GO:0015297(antiporter activity) | NA | NA | NA | POEI40 - Pollen Ole e I allergen and extensin family protein precursor, expressed | 0.03 | 0.12 | 0.21 | 0.09 | 0.18 | 0.32 |
| LOC_Os01g07040 | LOC_Os01g07040 | LOC_Os01g07040.1 | GO:0005887(integral component of plasma membrane);GO:0015179(L-amino acid transmembrane transporter activity);GO:0015297(antiporter activity) | NA | NA | NA | POEI41 - Pollen Ole e I allergen and extensin family protein precursor, expressed | 0 | 0 | 0 | 0 | 0 | 0.12 |
| LOC_Os01g07150 | LOC_Os01g07150 | LOC_Os01g07150.1 | GO:0003674(molecular_function);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0.08 | 0 |
| LOC_Os01g07160 | LOC_Os01g07160 | LOC_Os01g07160.1 | GO:0004842(ubiquitin-protein transferase activity);GO:0019005(SCF ubiquitin ligase complex);GO:0031146(SCF-dependent proteasomal ubiquitin-dependent protein catabolic process) | NA | NA | NA | OsFBX3 - F-box domain containing protein, expressed | 0.21 | 0.28 | 0 | 0 | 0.04 | 0 |
| LOC_Os01g07180 | LOC_Os01g07180 | LOC_Os01g07180.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.10 | 0.15 | 0 | 0.10 |
| LOC_Os01g07364 | LOC_Os01g07364 | LOC_Os01g07364.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.11 |
| LOC_Os01g07430 | LOC_Os01g07430 | LOC_Os01g07430.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006355(regulation of transcription, DNA-templated);GO:0009651(response to salt stress);GO:0009723(response to ethylene);GO:0009737(response to abscisic acid);GO:0009753(response to jasmonic acid) | 00190(Oxidative phosphorylation);00860(Porphyrin and chlorophyll metabolism) | K02259 | NA | myb-like DNA-binding domain containing protein, putative, expressed | 0.03 | 0.06 | 0.05 | 0.07 | 0.35 | 0.29 |
| LOC_Os01g07450 | LOC_Os01g07450 | LOC_Os01g07450.1 | GO:0003677(DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0045892(negative regulation of transcription, DNA-templated) | 00190(Oxidative phosphorylation);00860(Porphyrin and chlorophyll metabolism) | K02259 | NA | MYB family transcription factor, putative, expressed | 0.13 | 0 | 0.13 | 0.06 | 0.06 | 0.03 |
| LOC_Os01g07460 | LOC_Os01g07460 | LOC_Os01g07460.1 | NA | NA | NA | NA | conserved hypothetical protein | 0 | 0 | 0 | 0.14 | 0 | 0 |
| LOC_Os01g07550 | LOC_Os01g07550 | LOC_Os01g07550.1 | NA | NA | NA | NA | hypothetical protein | 0 | 0 | 0 | 0 | 0 | 0.06 |
| LOC_Os01g07640 | LOC_Os01g07640 | LOC_Os01g07640.1 | GO:0005575(cellular_component);GO:0008150(biological_process) | 04075(Plant hormone signal transduction) | K14500 | EC:2.7.11.1 | ankyrin, putative, expressed | 0.17 | 0.04 | 0.07 | 0.21 | 0.12 | 0.15 |
| LOC_Os01g07660 | LOC_Os01g07660 | LOC_Os01g07660.1 | NA | NA | NA | NA | expressed protein | 0 | 0.05 | 0 | 0 | 0 | 0 |
| LOC_Os01g07710 | LOC_Os01g07710 | LOC_Os01g07710.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.06 | 0.04 | 0.23 | 0.14 |
| LOC_Os01g07770 | LOC_Os01g07770 | LOC_Os01g07770.1 | GO:0004601(peroxidase activity);GO:0009505(plant-type cell wall);GO:0009664(plant-type cell wall organization) | 00940(Phenylpropanoid biosynthesis) | K00430 | EC:1.11.1.7 | peroxidase precursor, putative, expressed | 0.38 | 0.69 | 0.56 | 0.27 | 0.45 | 0.63 |
| LOC_Os01g08070 | LOC_Os01g08070 | LOC_Os01g08070.1 | GO:0000147(actin cortical patch assembly);GO:0005884(actin filament);GO:0006897(endocytosis);GO:0008360(regulation of cell shape);GO:0030048(actin filament-based movement);GO:0030479(actin cortical patch);GO:0051015(actin filament binding);GO:0051127(positive regulation of actin nucleation);GO:0051666(actin cortical patch localization) | NA | NA | NA | transposon protein, putative, CACTA, En/Spm sub-class, expressed | 0 | 0.02 | 0 | 0 | 0 | 0 |
Transcript expression profiling:
| t_id | class_code | chr | strand | start | end | t_name | num_exons | length | gene_id | gene_name | GO | KEGG | KO_ENTRY | EC | Description | cov.Lo7_1 | FPKM.Lo7_1 | cov.Lo7_2 | FPKM.Lo7_2 | cov.Lo7_3 | FPKM.Lo7_3 | cov.Lo8_1 | FPKM.Lo8_1 | cov.Lo8_2 | FPKM.Lo8_2 | cov.Lo8_3 | FPKM.Lo8_3 |
| 1 | 0 | chr1 | + | 2903 | 10817 | LOC_Os01g01010.1 | 12 | 3017 | MSTRG.3 | LOC_Os01g01010 | GO:0005096(GTPase activator activity);GO:0005622(intracellular);GO:0006886(intracellular protein transport);GO:0012505(endomembrane system);GO:0017137(Rab GTPase binding);GO:0031338(regulation of vesicle fusion) | 03040(Spliceosome) | K12840 | NA | TBC domain containing protein, expressed | 15.39 | 2.59 | 33.21 | 5.20 | 22.18 | 3.65 | 22.48 | 3.76 | 32.34 | 5.20 | 30.97 | 4.95 |
| 2 | j | chr1 | + | 2926 | 10822 | MSTRG.3.2 | 12 | 2986 | MSTRG.3 | LOC_Os01g01010 | NA | NA | NA | NA | NA | 36.84 | 6.20 | 26.39 | 4.13 | 19.53 | 3.21 | 20.50 | 3.43 | 26.73 | 4.30 | 38.23 | 6.12 |
| 3 | j | chr1 | + | 2938 | 10822 | MSTRG.3.3 | 12 | 2923 | MSTRG.3 | LOC_Os01g01010 | NA | NA | NA | NA | NA | 5.83 | 0.98 | 1.41 | 0.22 | 0.59 | 0.10 | 0.53 | 0.09 | 0 | 0 | 0 | 0 |
| 4 | j | chr1 | + | 2968 | 10811 | MSTRG.3.4 | 13 | 2857 | MSTRG.3 | LOC_Os01g01010 | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0 | 0.87 | 0.14 | 0 | 0 | 0 | 0 | 0 | 0 |
| 5 | 0 | chr1 | + | 2984 | 10562 | LOC_Os01g01010.2 | 12 | 2218 | MSTRG.3 | LOC_Os01g01010 | GO:0005096(GTPase activator activity);GO:0005622(intracellular);GO:0006886(intracellular protein transport);GO:0012505(endomembrane system);GO:0017137(Rab GTPase binding);GO:0031338(regulation of vesicle fusion) | 03040(Spliceosome) | K12840 | NA | TBC domain containing protein, expressed | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 0.01 | 0.00 | 0 | 0 | 0.07 | 0.01 |
| 6 | j | chr1 | + | 11086 | 20323 | MSTRG.4.1 | 13 | 6352 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 0 | 0 | 31.28 | 4.90 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 7 | j | chr1 | + | 11086 | 20323 | MSTRG.4.2 | 13 | 6775 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 0 | 0 | 5.51 | 0.86 | 6.01 | 0.99 | 2.24 | 0.37 | 0 | 0 | 4.06 | 0.65 |
| 8 | 0 | chr1 | + | 11218 | 12435 | LOC_Os01g01019.1 | 2 | 1127 | MSTRG.4 | LOC_Os01g01019 | NA | NA | NA | NA | expressed protein | 0.75 | 0.13 | 0 | 0 | 0.40 | 0.07 | 0 | 0 | 0 | 0 | 0 | 0 |
| 9 | j | chr1 | + | 12627 | 20377 | MSTRG.4.4 | 11 | 5478 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 20.38 | 3.43 | 0 | 0 | 9.41 | 1.55 | 7.62 | 1.27 | 0 | 0 | 0 | 0 |
| 10 | j | chr1 | + | 12627 | 20377 | MSTRG.4.5 | 12 | 5285 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 16.70 | 2.81 | 0 | 0 | 0 | 0 | 21.45 | 3.59 | 0 | 0 | 17.34 | 2.77 |
| 11 | 0 | chr1 | + | 12648 | 15915 | LOC_Os01g01030.1 | 5 | 2464 | MSTRG.4 | LOC_Os01g01030 | GO:0005507(copper ion binding);GO:0009505(plant-type cell wall);GO:0009506(plasmodesma);GO:0016722(oxidoreductase activity, oxidizing metal ions) | 00053(Ascorbate and aldarate metabolism) | K00423 | EC:1.10.3.3 | monocopper oxidase, putative, expressed | 0 | 0 | 1.18 | 0.18 | 0 | 0 | 0 | 0 | 0 | 0 | 4.37 | 0.70 |
| 12 | j | chr1 | + | 12655 | 20323 | MSTRG.4.7 | 10 | 5494 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 4.53 | 0.76 | 0.57 | 0.09 | 0 | 0 | 2.19 | 0.37 | 17.79 | 2.86 | 32.29 | 5.16 |
| 13 | j | chr1 | + | 16024 | 20323 | MSTRG.4.8 | 9 | 2685 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 2.26 | 0.38 | 0.82 | 0.13 | 0 | 0 | 4.49 | 0.75 | 8.14 | 1.31 | 0 | 0 |
| 14 | j | chr1 | + | 16029 | 20320 | MSTRG.4.9 | 9 | 2674 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 3.05 | 0.51 | 1.67 | 0.26 | 0 | 0 | 4.06 | 0.68 | 9.14 | 1.47 | 0 | 0 |
| 15 | 0 | chr1 | + | 16292 | 18304 | LOC_Os01g01040.4 | 3 | 1524 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 0.06 | 0.01 | 2.11 | 0.33 | 0.71 | 0.12 | 0 | 0 | 0 | 0 | 0.20 | 0.03 |
| 16 | 0 | chr1 | + | 16292 | 20323 | LOC_Os01g01040.1 | 8 | 2508 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 1.65 | 0.28 | 8.44 | 1.32 | 11.14 | 1.83 | 2.70 | 0.45 | 8.96 | 1.44 | 0.40 | 0.06 |
| 17 | 0 | chr1 | + | 16321 | 20323 | LOC_Os01g01040.2 | 8 | 2482 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 1.15 | 0.19 | 4.18 | 0.65 | 19.03 | 3.13 | 3.07 | 0.51 | 8.02 | 1.29 | 0.29 | 0.05 |
| 18 | 0 | chr1 | + | 16321 | 20323 | LOC_Os01g01040.3 | 7 | 2583 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 1.16 | 0.20 | 2.92 | 0.46 | 19.45 | 3.20 | 3.29 | 0.55 | 9.61 | 1.54 | 2.79 | 0.45 |
| 19 | 0 | chr1 | + | 22841 | 26971 | LOC_Os01g01050.1 | 6 | 2039 | MSTRG.1 | LOC_Os01g01050 | NA | NA | NA | NA | R3H domain containing protein, expressed | 16.81 | 2.83 | 3.31 | 0.52 | 6.55 | 1.08 | 6.47 | 1.08 | 8.23 | 1.32 | 0.85 | 0.14 |
| 20 | 0 | chr1 | + | 22841 | 26971 | LOC_Os01g01050.2 | 6 | 1996 | MSTRG.1 | LOC_Os01g01050 | NA | NA | NA | NA | R3H domain containing protein, expressed | 18.74 | 3.16 | 11.28 | 1.77 | 22.15 | 3.65 | 21.03 | 3.52 | 13.28 | 2.14 | 27.27 | 4.36 |
| 21 | j | chr1 | + | 22850 | 26978 | MSTRG.1.3 | 5 | 2327 | MSTRG.1 | LOC_Os01g01050 | NA | NA | NA | NA | NA | 12.34 | 2.08 | 5.70 | 0.89 | 13.12 | 2.16 | 2.09 | 0.35 | 12.00 | 1.93 | 26.44 | 4.23 |
| 22 | 0 | chr1 | + | 27136 | 28651 | LOC_Os01g01060.1 | 4 | 920 | MSTRG.2 | LOC_Os01g01060 | GO:0000028(ribosomal small subunit assembly);GO:0003729(mRNA binding);GO:0003735(structural constituent of ribosome);GO:0006412(translation);GO:0019843(rRNA binding);GO:0022627(cytosolic small ribosomal subunit) | 03010(Ribosome) | K02989 | NA | 40S ribosomal protein S5, putative, expressed | 535.27 | 90.14 | 624.36 | 97.77 | 532.58 | 87.67 | 893.89 | 149.45 | 729.34 | 117.29 | 878.38 | 140.51 |
| 23 | j | chr1 | + | 29773 | 34495 | MSTRG.5.1 | 13 | 2115 | MSTRG.5 | LOC_Os01g01070 | NA | NA | NA | NA | NA | 8.02 | 1.35 | 8.85 | 1.39 | 26.32 | 4.33 | 23.84 | 3.99 | 10.42 | 1.68 | 10.81 | 1.73 |
| 24 | j | chr1 | + | 29789 | 34480 | MSTRG.5.2 | 12 | 1994 | MSTRG.5 | LOC_Os01g01070 | NA | NA | NA | NA | NA | 9.22 | 1.55 | 10.44 | 1.64 | 7.97 | 1.31 | 6.52 | 1.09 | 8.14 | 1.31 | 13.22 | 2.12 |
| 25 | 0 | chr1 | + | 29818 | 33943 | LOC_Os01g01070.3 | 13 | 1369 | MSTRG.5 | LOC_Os01g01070 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane);GO:0031307(integral component of mitochondrial outer membrane) | NA | NA | NA | expressed protein | 8.29 | 1.40 | 10.25 | 1.60 | 6.70 | 1.10 | 8.34 | 1.39 | 8.65 | 1.39 | 5.19 | 0.83 |
| 26 | 0 | chr1 | + | 29818 | 34493 | LOC_Os01g01070.1 | 14 | 1568 | MSTRG.5 | LOC_Os01g01070 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane);GO:0031307(integral component of mitochondrial outer membrane) | NA | NA | NA | expressed protein | 5.53 | 0.93 | 6.78 | 1.06 | 0.55 | 0.09 | 2.77 | 0.46 | 5.62 | 0.90 | 3.87 | 0.62 |
| 27 | 0 | chr1 | + | 29818 | 34493 | LOC_Os01g01070.2 | 14 | 1562 | MSTRG.5 | LOC_Os01g01070 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane);GO:0031307(integral component of mitochondrial outer membrane) | NA | NA | NA | expressed protein | 78.91 | 13.29 | 69.35 | 10.86 | 42.81 | 7.05 | 42.56 | 7.12 | 46.44 | 7.47 | 59.99 | 9.60 |
| 28 | j | chr1 | + | 35392 | 41235 | MSTRG.6.2 | 13 | 2562 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 3.70 | 0.62 | 20.49 | 3.21 | 4.22 | 0.69 | 0 | 0 | 3.23 | 0.52 | 4.66 | 0.75 |
| 29 | j | chr1 | + | 35392 | 41235 | MSTRG.6.3 | 13 | 2814 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 0.98 | 0.17 | 3.29 | 0.52 | 2.22 | 0.36 | 1.39 | 0.23 | 1.40 | 0.22 | 1.51 | 0.24 |
| 30 | j | chr1 | + | 35392 | 41253 | MSTRG.6.1 | 14 | 2324 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 9.09 | 1.53 | 18.91 | 2.96 | 45.71 | 7.52 | 12.15 | 2.03 | 48.93 | 7.87 | 12.56 | 2.01 |
| 31 | j | chr1 | + | 35450 | 41253 | MSTRG.6.4 | 14 | 2266 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 12.74 | 2.15 | 26.78 | 4.19 | 3.61 | 0.59 | 1.64 | 0.27 | 8.75 | 1.41 | 8.54 | 1.37 |
| 32 | j | chr1 | + | 35579 | 41188 | MSTRG.6.5 | 14 | 2231 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 29.60 | 4.98 | 17.97 | 2.81 | 18.91 | 3.11 | 29.44 | 4.92 | 18.18 | 2.92 | 42.95 | 6.87 |
| 33 | j | chr1 | + | 35579 | 41188 | MSTRG.6.6 | 12 | 2466 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 1.65 | 0.28 | 0.65 | 0.10 | 2.13 | 0.35 | 8.52 | 1.42 | 1.37 | 0.22 | 9.94 | 1.59 |
| 34 | 0 | chr1 | + | 35581 | 41180 | LOC_Os01g01080.1 | 15 | 1955 | MSTRG.6 | LOC_Os01g01080 | GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0006520(cellular amino acid metabolic process);GO:0008117(sphinganine-1-phosphate aldolase activity);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016831(carboxy-lyase activity);GO:0019752(carboxylic acid metabolic process);GO:0030149(sphingolipid catabolic process);GO:0030170(pyridoxal phosphate binding) | 00600(Sphingolipid metabolism) | K01634 | EC:4.1.2.27 | decarboxylase, putative, expressed | 214.31 | 36.09 | 122.44 | 19.17 | 162.21 | 26.70 | 174.37 | 29.15 | 114.36 | 18.39 | 90.61 | 14.49 |
| 35 | 0 | chr1 | + | 35581 | 41180 | LOC_Os01g01080.2 | 15 | 1976 | MSTRG.6 | LOC_Os01g01080 | GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0006520(cellular amino acid metabolic process);GO:0008117(sphinganine-1-phosphate aldolase activity);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016831(carboxy-lyase activity);GO:0019752(carboxylic acid metabolic process);GO:0030149(sphingolipid catabolic process);GO:0030170(pyridoxal phosphate binding) | 00600(Sphingolipid metabolism) | K01634 | EC:4.1.2.27 | decarboxylase, putative, expressed | 0.32 | 0.05 | 0 | 0 | 0.26 | 0.04 | 2.12 | 0.35 | 0.27 | 0.04 | 8.33 | 1.33 |
| 36 | 0 | chr1 | + | 35581 | 41180 | LOC_Os01g01080.3 | 14 | 2042 | MSTRG.6 | LOC_Os01g01080 | GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0006520(cellular amino acid metabolic process);GO:0008117(sphinganine-1-phosphate aldolase activity);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016831(carboxy-lyase activity);GO:0019752(carboxylic acid metabolic process);GO:0030149(sphingolipid catabolic process);GO:0030170(pyridoxal phosphate binding) | 00600(Sphingolipid metabolism) | K01634 | EC:4.1.2.27 | decarboxylase, putative, expressed | 1.68 | 0.28 | 9.20 | 1.44 | 0.61 | 0.10 | 5.93 | 0.99 | 0.56 | 0.09 | 2.43 | 0.39 |
| 37 | 0 | chr1 | + | 44595 | 47526 | LOC_Os01g01090.1 | 8 | 2409 | LOC_Os01g01090 | LOC_Os01g01090 | GO:0003755(peptidyl-prolyl cis-trans isomerase activity);GO:0005528(FK506 binding);GO:0005789(endoplasmic reticulum membrane);GO:0061077(chaperone-mediated protein folding) | NA | NA | NA | retrotransposon protein, putative, unclassified, expressed | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.13 | 0.02 | 0 | 0 |
| 38 | 0 | chr1 | + | 57082 | 57972 | LOC_Os01g01110.1 | 1 | 891 | LOC_Os01g01110 | LOC_Os01g01110 | GO:0004672(protein kinase activity);GO:0004674(protein serine/threonine kinase activity);GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation);GO:0007169(transmembrane receptor protein tyrosine kinase signaling pathway);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04075(Plant hormone signal transduction);04626(Plant-pathogen interaction) | K13416 | EC:2.7.10.1 2.7.11.1 | expressed protein | 0 | 0 | 0 | 0 | 0 | 0 | 3.55 | 0.59 | 0 | 0 | 0 | 0 |
| 39 | j | chr1 | + | 58431 | 63576 | MSTRG.7.1 | 7 | 4147 | MSTRG.7 | LOC_Os01g01120 | NA | NA | NA | NA | NA | 5.80 | 0.98 | 7.88 | 1.23 | 4.57 | 0.75 | 14.38 | 2.40 | 18.27 | 2.94 | 11.23 | 1.80 |
| 41 | 0 | chr1 | + | 62059 | 63576 | LOC_Os01g01120.1 | 4 | 1206 | MSTRG.7 | LOC_Os01g01120 | GO:0000287(magnesium ion binding);GO:0005737(cytoplasm);GO:0005829(cytosol);GO:0008270(zinc ion binding);GO:0009507(chloroplast);GO:0009570(chloroplast stroma);GO:0016787(hydrolase activity);GO:0019284(L-methionine biosynthetic process from S-adenosylmethionine);GO:0019509(L-methionine biosynthetic process from methylthioadenosine);GO:0043715(2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity);GO:0043716(2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity);GO:0043874(acireductone synthase activity);GO:0046570(methylthioribulose 1-phosphate dehydratase activity) | 00270(Cysteine and methionine metabolism) | K09880 | EC:3.1.3.77 | enolase-phosphatase E1, putative, expressed | 16.52 | 2.78 | 8.60 | 1.35 | 6.60 | 1.09 | 16.68 | 2.79 | 17.54 | 2.82 | 25.99 | 4.16 |
| 42 | 0 | chr1 | - | 63244 | 66302 | LOC_Os01g01130.1 | 7 | 2002 | MSTRG.8 | LOC_Os01g01130 | GO:0005634(nucleus) | 03013(RNA transport) | K13151 | NA | snurportin-1, putative, expressed | 30.53 | 5.14 | 27.09 | 4.24 | 22.84 | 3.76 | 31.68 | 5.30 | 17.59 | 2.83 | 40.19 | 6.43 |
| 44 | 0 | chr1 | + | 72775 | 77699 | LOC_Os01g01150.1 | 3 | 3756 | MSTRG.10 | LOC_Os01g01150 | GO:0000166(nucleotide binding);GO:0003676(nucleic acid binding);GO:0003723(RNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046872(metal ion binding) | NA | NA | NA | RNA recognition motif, putative, expressed | 9.77 | 1.64 | 13.05 | 2.04 | 23.46 | 3.86 | 18.37 | 3.07 | 0 | 0 | 13.54 | 2.17 |
| 45 | 0 | chr1 | + | 72775 | 78702 | LOC_Os01g01150.2 | 4 | 4638 | MSTRG.10 | LOC_Os01g01150 | GO:0000166(nucleotide binding);GO:0003676(nucleic acid binding);GO:0003723(RNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046872(metal ion binding) | NA | NA | NA | RNA recognition motif, putative, expressed | 4.77 | 0.80 | 4.98 | 0.78 | 4.53 | 0.75 | 2.79 | 0.47 | 1.21 | 0.19 | 6.33 | 1.01 |
| 46 | 0 | chr1 | + | 72775 | 79938 | LOC_Os01g01150.3 | 5 | 4603 | MSTRG.10 | LOC_Os01g01150 | GO:0000166(nucleotide binding);GO:0003676(nucleic acid binding);GO:0003723(RNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046872(metal ion binding) | NA | NA | NA | RNA recognition motif, putative, expressed | 6.52 | 1.10 | 4.71 | 0.74 | 4.97 | 0.82 | 3.09 | 0.52 | 7.56 | 1.22 | 6.14 | 0.98 |
| 47 | j | chr1 | + | 72775 | 80049 | MSTRG.10.1 | 6 | 4241 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 16.72 | 2.82 | 14.04 | 2.20 | 7.22 | 1.19 | 12.96 | 2.17 | 21.34 | 3.43 | 14.08 | 2.25 |
| 48 | j | chr1 | + | 72786 | 79891 | MSTRG.10.6 | 6 | 3995 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 4.57 | 0.77 | 11.71 | 1.83 | 10.36 | 1.71 | 3.82 | 0.64 | 10.38 | 1.67 | 7.53 | 1.21 |
| 49 | j | chr1 | + | 72786 | 79891 | MSTRG.10.7 | 7 | 3951 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 7.51 | 1.27 | 11.36 | 1.78 | 10.46 | 1.72 | 5.71 | 0.95 | 16.77 | 2.70 | 13.71 | 2.19 |
| 50 | j | chr1 | + | 72786 | 80049 | MSTRG.10.5 | 6 | 4239 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 11.05 | 1.86 | 14.90 | 2.33 | 10.33 | 1.70 | 5.23 | 0.87 | 7.97 | 1.28 | 8.75 | 1.40 |
| 51 | j | chr1 | + | 72804 | 79846 | MSTRG.10.8 | 5 | 4385 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 6.68 | 1.12 | 3.04 | 0.48 | 0 | 0 | 23.87 | 3.99 | 1.43 | 0.23 | 7.19 | 1.15 |
| 52 | j | chr1 | + | 72817 | 80049 | MSTRG.10.10 | 7 | 4001 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 7.49 | 1.26 | 8.43 | 1.32 | 8.69 | 1.43 | 2.19 | 0.37 | 4.90 | 0.79 | 4.69 | 0.75 |
| 53 | j | chr1 | + | 72817 | 80049 | MSTRG.10.9 | 7 | 3990 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 13.70 | 2.31 | 8.74 | 1.37 | 6.59 | 1.09 | 3.53 | 0.59 | 6.97 | 1.12 | 2.43 | 0.39 |
| 54 | 0 | chr1 | + | 82428 | 84302 | LOC_Os01g01160.1 | 2 | 1090 | MSTRG.9 | LOC_Os01g01160 | GO:0005515(protein binding);GO:0005634(nucleus);GO:0006457(protein folding);GO:0009507(chloroplast);GO:0010322(regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway);GO:0061077(chaperone-mediated protein folding);GO:1902395(regulation of 1-deoxy-D-xylulose-5-phosphate synthase activity) | 04141(Protein processing in endoplasmic reticulum) | K09518 | NA | heat shock protein DnaJ, putative, expressed | 31.73 | 5.34 | 29.18 | 4.57 | 27.73 | 4.56 | 34.85 | 5.83 | 18.77 | 3.02 | 2.34 | 0.37 |
| 55 | 0 | chr1 | + | 85337 | 88844 | LOC_Os01g01170.1 | 7 | 2334 | MSTRG.12 | LOC_Os01g01170 | NA | NA | NA | NA | expressed protein | 3.59 | 0.60 | 7.64 | 1.20 | 3.71 | 0.61 | 11.93 | 1.99 | 25.35 | 4.08 | 15.25 | 2.44 |
| 56 | j | chr1 | + | 85340 | 88935 | MSTRG.12.2 | 7 | 2419 | MSTRG.12 | LOC_Os01g01170 | NA | NA | NA | NA | NA | 4.25 | 0.72 | 2.86 | 0.45 | 1.39 | 0.23 | 8.35 | 1.40 | 9.64 | 1.55 | 6.57 | 1.05 |
| 60 | 0 | chr1 | + | 134291 | 135685 | LOC_Os01g01280.1 | 3 | 1226 | MSTRG.11 | LOC_Os01g01280 | GO:0003674(molecular_function);GO:0008150(biological_process);GO:0009507(chloroplast);GO:0009543(chloroplast thylakoid lumen);GO:0009579(thylakoid);GO:0031977(thylakoid lumen) | NA | NA | NA | expressed protein | 9.52 | 1.60 | 12.17 | 1.91 | 12.45 | 2.05 | 7.22 | 1.21 | 5.42 | 0.87 | 13.00 | 2.08 |
| 61 | 0 | chr1 | + | 139820 | 141588 | LOC_Os01g01290.1 | 2 | 1556 | LOC_Os01g01290 | LOC_Os01g01290 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005515(protein binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0009738(abscisic acid-activated signaling pathway);GO:0010468(regulation of gene expression);GO:0046982(protein heterodimerization activity);GO:0048586(regulation of long-day photoperiodism, flowering);GO:0051247(positive regulation of protein metabolic process);GO:2000905(negative regulation of starch metabolic process) | NA | NA | NA | histone-like transcription factor and archaeal histone, putative, expressed | 0 | 0 | 0.67 | 0.11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 62 | 0 | chr1 | + | 141936 | 144554 | LOC_Os01g01295.1 | 4 | 1793 | MSTRG.15 | LOC_Os01g01295 | GO:0009507(chloroplast) | NA | NA | NA | expressed protein | 47.46 | 7.99 | 18.23 | 2.86 | 57.90 | 9.53 | 57.65 | 9.64 | 48.85 | 7.86 | 22.59 | 3.61 |
| 63 | j | chr1 | + | 142782 | 144556 | MSTRG.15.2 | 2 | 1644 | MSTRG.15 | LOC_Os01g01295 | NA | NA | NA | NA | NA | 8.71 | 1.47 | 7.81 | 1.22 | 7.22 | 1.19 | 7.18 | 1.20 | 5.97 | 0.96 | 2.50 | 0.40 |
| 64 | 0 | chr1 | + | 145577 | 147852 | LOC_Os01g01302.1 | 9 | 1155 | MSTRG.16 | LOC_Os01g01302 | GO:0000287(magnesium ion binding);GO:0004765(shikimate kinase activity);GO:0009073(aromatic amino acid family biosynthetic process);GO:0019632(shikimate metabolic process) | 01230(Biosynthesis of amino acids);00400(Phenylalanine, tyrosine and tryptophan biosynthesis) | K00891 | EC:2.7.1.71 | shikimate kinase, putative, expressed | 54.08 | 9.11 | 44.18 | 6.92 | 29.41 | 4.84 | 43.91 | 7.34 | 62.49 | 10.05 | 50.67 | 8.11 |
| 65 | j | chr1 | + | 145602 | 147854 | MSTRG.16.2 | 8 | 1228 | MSTRG.16 | LOC_Os01g01302 | NA | NA | NA | NA | NA | 1.32 | 0.22 | 6.23 | 0.98 | 11.30 | 1.86 | 13.63 | 2.28 | 0.27 | 0.04 | 17.74 | 2.84 |
| 66 | 0 | chr1 | + | 148045 | 150577 | LOC_Os01g01307.1 | 5 | 979 | MSTRG.17 | LOC_Os01g01307 | GO:0003674(molecular_function);GO:0005576(extracellular region);GO:0005774(vacuolar membrane);GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0005794(Golgi apparatus);GO:0008150(biological_process);GO:0009506(plasmodesma);GO:0016021(integral component of membrane) | 04141(Protein processing in endoplasmic reticulum) | K13250 | NA | translocon-associated protein beta domain containing protein, expressed | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 30.11 | 4.84 | 0 | 0 |
| 68 | j | chr1 | + | 148055 | 150610 | MSTRG.17.6 | 5 | 1004 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 38.59 | 6.50 | 104.89 | 16.43 | 53.90 | 8.87 | 28.36 | 4.74 | 74.35 | 11.96 | 13.47 | 2.16 |
| 69 | j | chr1 | + | 148055 | 150610 | MSTRG.17.7 | 5 | 988 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 1.55 | 0.26 | 7.51 | 1.18 | 6.51 | 1.07 | 22.20 | 3.71 | 2.03 | 0.33 | 1.45 | 0.23 |
| 70 | j | chr1 | + | 148055 | 150610 | MSTRG.17.8 | 6 | 1353 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 12.36 | 2.08 | 16.90 | 2.65 | 36.65 | 6.03 | 32.48 | 5.43 | 14.59 | 2.35 | 14.05 | 2.25 |
| 71 | j | chr1 | + | 148055 | 150643 | MSTRG.17.3 | 5 | 1037 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 127.45 | 21.46 | 32.25 | 5.05 | 43.83 | 7.22 | 154.07 | 25.76 | 101.63 | 16.34 | 157.66 | 25.22 |
| 72 | j | chr1 | + | 148055 | 150643 | MSTRG.17.4 | 6 | 1037 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 153.88 | 25.91 | 47.09 | 7.37 | 35.58 | 5.86 | 95.23 | 15.92 | 99.63 | 16.02 | 164.74 | 26.35 |
| 73 | j | chr1 | + | 148055 | 150643 | MSTRG.17.5 | 5 | 1386 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 22.53 | 3.79 | 25.68 | 4.02 | 25.34 | 4.17 | 10.11 | 1.69 | 11.20 | 1.80 | 21.84 | 3.49 |
| 74 | j | chr1 | + | 148068 | 150571 | MSTRG.17.9 | 5 | 1429 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 36.58 | 6.16 | 40.71 | 6.38 | 57.13 | 9.40 | 29.96 | 5.01 | 48.79 | 7.85 | 48.35 | 7.73 |
| 75 | j | chr1 | + | 148072 | 150567 | MSTRG.17.10 | 6 | 800 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 0.93 | 0.16 | 2.63 | 0.41 | 0.82 | 0.14 | 21.12 | 3.53 | 0 | 0 | 0.49 | 0.08 |
| 76 | 0 | chr1 | + | 151409 | 156500 | LOC_Os01g01312.1 | 7 | 4165 | MSTRG.14 | LOC_Os01g01312 | GO:0003677(DNA binding);GO:0004386(helicase activity);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0006281(DNA repair);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0006974(cellular response to DNA damage stimulus);GO:0010332(response to gamma radiation) | 03420(Nucleotide excision repair) | K10841 | NA | retrotransposon protein, putative, Ty1-copia subclass, expressed | 30.90 | 5.20 | 19.01 | 2.98 | 30.10 | 4.96 | 22.81 | 3.81 | 36.34 | 5.84 | 36.30 | 5.81 |
| 77 | x | chr1 | + | 163052 | 169672 | MSTRG.21.1 | 5 | 1539 | MSTRG.21 | LOC_Os01g01340 | NA | NA | NA | NA | NA | 14.81 | 2.49 | 14.51 | 2.27 | 7.94 | 1.31 | 19.49 | 3.26 | 24.84 | 3.99 | 17.76 | 2.84 |
| 78 | x | chr1 | + | 163052 | 169672 | MSTRG.21.2 | 4 | 1426 | MSTRG.21 | LOC_Os01g01340 | NA | NA | NA | NA | NA | 0 | 0 | 11.00 | 1.72 | 0 | 0 | 3.58 | 0.60 | 0 | 0 | 6.12 | 0.98 |
| 79 | x | chr1 | + | 163114 | 169672 | MSTRG.21.3 | 5 | 1480 | MSTRG.21 | LOC_Os01g01340 | NA | NA | NA | NA | NA | 9.40 | 1.58 | 0 | 0 | 13.35 | 2.20 | 1.84 | 0.31 | 10.24 | 1.65 | 6.40 | 1.02 |
| 80 | 0 | chr1 | - | 168470 | 170381 | LOC_Os01g01340.2 | 2 | 1731 | MSTRG.22 | LOC_Os01g01340 | GO:0003674(molecular_function);GO:0008150(biological_process);GO:0009507(chloroplast) | 04144(Endocytosis) | K12198 | NA | light-induced protein 1-like, putative, expressed | 3.09 | 0.52 | 0 | 0 | 18.78 | 3.09 | 84.06 | 14.05 | 1.05 | 0.17 | 0.57 | 0.09 |
| 81 | 0 | chr1 | - | 168470 | 170389 | LOC_Os01g01340.1 | 3 | 1645 | MSTRG.22 | LOC_Os01g01340 | GO:0003674(molecular_function);GO:0008150(biological_process);GO:0009507(chloroplast) | 04144(Endocytosis) | K12198 | NA | light-induced protein 1-like, putative, expressed | 360.56 | 60.72 | 263.54 | 41.27 | 145.25 | 23.91 | 42.25 | 7.06 | 89.58 | 14.41 | 221.03 | 35.36 |
| 82 | j | chr1 | - | 168581 | 173195 | MSTRG.22.3 | 8 | 3105 | MSTRG.22 | LOC_Os01g01350 | NA | NA | NA | NA | NA | 18.42 | 3.10 | 23.38 | 3.66 | 8.46 | 1.39 | 40.63 | 6.79 | 38.28 | 6.16 | 32.97 | 5.27 |
| 83 | 0 | chr1 | - | 170712 | 173191 | LOC_Os01g01350.1 | 7 | 1151 | MSTRG.22 | LOC_Os01g01350 | GO:0005515(protein binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0007034(vacuolar transport);GO:0016192(vesicle-mediated transport) | 04144(Endocytosis) | K12198 | NA | SNF7 domain containing protein, putative, expressed | 9.77 | 1.64 | 9.48 | 1.48 | 15.88 | 2.61 | 22.29 | 3.73 | 6.72 | 1.08 | 32.12 | 5.14 |
| 84 | 0 | chr1 | - | 170712 | 173434 | LOC_Os01g01350.2 | 5 | 1574 | MSTRG.22 | LOC_Os01g01350 | GO:0005515(protein binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0007034(vacuolar transport);GO:0016192(vesicle-mediated transport) | 04144(Endocytosis) | K12198 | NA | SNF7 domain containing protein, putative, expressed | 7.04 | 1.19 | 4.83 | 0.76 | 2.63 | 0.43 | 2.59 | 0.43 | 5.69 | 0.91 | 5.13 | 0.82 |
| 85 | 0 | chr1 | + | 178310 | 180812 | LOC_Os01g01360.1 | 1 | 2503 | LOC_Os01g01360 | LOC_Os01g01360 | GO:0005215(transporter activity);GO:0005886(plasma membrane);GO:0006857(oligopeptide transport);GO:0016020(membrane);GO:0016021(integral component of membrane) | NA | NA | NA | peptide transporter PTR2, putative, expressed | 0 | 0 | 2.11 | 0.33 | 1.51 | 0.25 | 5.87 | 0.98 | 2.93 | 0.47 | 4.88 | 0.78 |
| 86 | p | chr1 | - | 185073 | 185970 | MSTRG.18.1 | 1 | 898 | MSTRG.18 | LOC_Os01g01369 | NA | NA | NA | NA | NA | 16.04 | 2.70 | 20.41 | 3.20 | 15.95 | 2.63 | 22.10 | 3.69 | 19.09 | 3.07 | 20.89 | 3.34 |
| 87 | j | chr1 | - | 186138 | 190825 | MSTRG.19.1 | 5 | 1550 | MSTRG.19 | LOC_Os01g01369 | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 33.76 | 5.43 | 0 | 0 |
| 88 | j | chr1 | - | 186240 | 188981 | MSTRG.19.2 | 2 | 2082 | MSTRG.19 | LOC_Os01g01369 | NA | NA | NA | NA | NA | 2.03 | 0.34 | 8.64 | 1.35 | 10.81 | 1.78 | 0 | 0 | 7.54 | 1.21 | 11.07 | 1.77 |
| 89 | 0 | chr1 | - | 186246 | 190846 | LOC_Os01g01369.1 | 4 | 1545 | MSTRG.19 | LOC_Os01g01369 | GO:0000247(C-8 sterol isomerase activity);GO:0005789(endoplasmic reticulum membrane);GO:0005886(plasma membrane);GO:0016021(integral component of membrane);GO:0016126(sterol biosynthetic process);GO:0047750(cholestenol delta-isomerase activity) | 00100(Steroid biosynthesis) | K01824 | EC:5.3.3.5 | 3-beta-hydroxysteroid-Delta-isomerase, putative, expressed | 73.81 | 12.43 | 93.17 | 14.59 | 74.09 | 12.20 | 91.03 | 15.22 | 36.37 | 5.85 | 42.98 | 6.87 |
| 90 | 0 | chr1 | + | 191036 | 196287 | LOC_Os01g01380.1 | 6 | 3482 | MSTRG.20 | LOC_Os01g01380 | NA | NA | NA | NA | expressed protein | 3.89 | 0.65 | 4.22 | 0.66 | 4.75 | 0.78 | 2.60 | 0.44 | 4.12 | 0.66 | 5.40 | 0.86 |
| 91 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.1 | 4 | 2142 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 89.89 | 15.14 | 104.37 | 16.34 | 50.39 | 8.29 | 108.42 | 18.13 | 97.44 | 15.67 | 113.94 | 18.23 |
| 92 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.2 | 5 | 2175 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 0.06 | 0.01 | 0.09 | 0.01 | 0 | 0 | 0 | 0 | 0 | 0 | 9.65 | 1.54 |
| 93 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.3 | 5 | 2182 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 11.58 | 1.95 | 0.30 | 0.05 | 24.89 | 4.10 | 42.82 | 7.16 | 15.40 | 2.48 | 30.64 | 4.90 |
| 94 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.4 | 4 | 2261 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 0 | 0 | 9.01 | 1.41 | 12.36 | 2.03 | 0 | 0 | 8.73 | 1.40 | 17.49 | 2.80 |
| 95 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.5 | 3 | 1054 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 1.90 | 0.32 | 2.86 | 0.45 | 7.62 | 1.25 | 7.34 | 1.23 | 8.10 | 1.30 | 6.46 | 1.03 |
| 96 | 0 | chr1 | + | 201944 | 206743 | LOC_Os01g01400.1 | 12 | 2735 | MSTRG.26 | LOC_Os01g01400 | GO:0003674(molecular_function);GO:0005575(cellular_component);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 5.80 | 0.98 | 2.41 | 0.38 | 2.18 | 0.36 | 3.96 | 0.66 | 3.52 | 0.57 | 9.87 | 1.58 |
| 97 | 0 | chr1 | - | 205710 | 209606 | LOC_Os01g01410.1 | 4 | 2489 | MSTRG.27 | LOC_Os01g01410 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane) | 04626(Plant-pathogen interaction) | K13430 | EC:2.7.11.1 | TKL_IRAK_C-LEC.1 - TKL_IRAK_C-LEC has homology to C-type lectin receptors, expressed | 23.48 | 3.95 | 76.59 | 11.99 | 24.12 | 3.97 | 73.23 | 12.24 | 57.94 | 9.32 | 77.44 | 12.39 |
| 98 | 0 | chr1 | - | 205710 | 209606 | LOC_Os01g01410.2 | 4 | 2486 | MSTRG.27 | LOC_Os01g01410 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane) | 04626(Plant-pathogen interaction) | K13430 | EC:2.7.11.1 | TKL_IRAK_C-LEC.1 - TKL_IRAK_C-LEC has homology to C-type lectin receptors, expressed | 20.30 | 3.42 | 32.01 | 5.01 | 16.47 | 2.71 | 38.37 | 6.42 | 43.93 | 7.06 | 65.82 | 10.53 |
| 99 | j | chr1 | - | 205711 | 209582 | MSTRG.27.4 | 4 | 2528 | MSTRG.27 | LOC_Os01g01410 | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.09 | 0.18 | 0 | 0 |
| 100 | j | chr1 | - | 205711 | 209600 | MSTRG.27.3 | 3 | 2613 | MSTRG.27 | LOC_Os01g01410 | NA | NA | NA | NA | NA | 12.10 | 2.04 | 7.54 | 1.18 | 7.39 | 1.22 | 20.57 | 3.44 | 16.78 | 2.70 | 5.00 | 0.80 |
| 101 | j | chr1 | + | 209677 | 214224 | MSTRG.28.1 | 7 | 2891 | MSTRG.28 | LOC_Os01g01420 | NA | NA | NA | NA | NA | 43.78 | 7.37 | 10.71 | 1.68 | 26.69 | 4.39 | 3.11 | 0.52 | 6.93 | 1.11 | 25.93 | 4.15 |
| 102 | 0 | chr1 | + | 209771 | 214188 | LOC_Os01g01420.1 | 8 | 1657 | MSTRG.28 | LOC_Os01g01420 | GO:0005720(nuclear heterochromatin);GO:0010216(maintenance of DNA methylation);GO:0016567(protein ubiquitination);GO:0061630(ubiquitin protein ligase activity);GO:0090308(regulation of methylation-dependent chromatin silencing) | NA | NA | NA | expressed protein | 11.44 | 1.93 | 64.71 | 10.13 | 90.26 | 14.86 | 93.44 | 15.62 | 120.54 | 19.38 | 124.92 | 19.98 |
| 103 | 0 | chr1 | + | 209771 | 214188 | LOC_Os01g01420.3 | 8 | 1653 | MSTRG.28 | LOC_Os01g01420 | GO:0005720(nuclear heterochromatin);GO:0010216(maintenance of DNA methylation);GO:0016567(protein ubiquitination);GO:0061630(ubiquitin protein ligase activity);GO:0090308(regulation of methylation-dependent chromatin silencing) | NA | NA | NA | expressed protein | 13.57 | 2.28 | 22.60 | 3.54 | 43.15 | 7.10 | 14.21 | 2.38 | 12.21 | 1.96 | 35.67 | 5.71 |
| 104 | 0 | chr1 | + | 209903 | 214229 | LOC_Os01g01420.2 | 7 | 1913 | MSTRG.28 | LOC_Os01g01420 | GO:0005720(nuclear heterochromatin);GO:0010216(maintenance of DNA methylation);GO:0016567(protein ubiquitination);GO:0061630(ubiquitin protein ligase activity);GO:0090308(regulation of methylation-dependent chromatin silencing) | NA | NA | NA | expressed protein | 115.14 | 19.39 | 28.40 | 4.45 | 30.23 | 4.98 | 14.53 | 2.43 | 8.24 | 1.33 | 40.57 | 6.49 |
| 105 | 0 | chr1 | + | 216126 | 217664 | LOC_Os01g01430.1 | 2 | 1425 | MSTRG.24 | LOC_Os01g01430 | GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0007275(multicellular organism development);GO:0009753(response to jasmonic acid);GO:0044212(transcription regulatory region DNA binding);GO:0045995(regulation of embryonic development);GO:0048317(seed morphogenesis);GO:0080060(integument development) | 00561(Glycerolipid metabolism) | K01054 | EC:3.1.1.23 | No apical meristem protein, putative, expressed | 7.36 | 1.24 | 0 | 0 | 0.83 | 0.14 | 0.21 | 0.03 | 0 | 0 | 0 | 0 |
document location:
summary/4_transcript_expression/4_genes_fpkm_expression.xlsx
summary/4_transcript_expression/5_isoforms_fpkm_expression.xlsx
Class code typies and definitions:
| class code | Description |
|---|---|
| =/0 | Complete match (mRNA, lncRNA etc) |
| c | Contained |
| j | Potentially novel isoform (fragment): at least one splice junction is hared with a reference transcript |
| e | Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment. |
| i | A transfrag falling entirely within a reference intron |
| o | Generic exonic overlap with a reference transcript |
| p | Possible polymerase run-on fragment (within 2Kbases of a reference transcript) |
| r | Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the are lower casebases |
| u | Unknown, intergenic transcript |
| x | Exonic overlap with reference on the opposite strand |
| s | An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors) |
| . | (.tracking file only, indicates multiple classifications) |
Exploratory analysis, visualization and statistical modeling are the next steps after assembling and quantifying genes and transcripts from StringTie. The assembly of lncRNA-seq reads reconstructs the exon–intron structure of genes and their isoforms. R package ballgown takes both transcript and gene expression levels from StringTie and applies rigorous statistical methods to determine which transcripts and genes are differentially expressed between two or more experiments. Ballgown also includes plotting tools as part of the R/Bioconductor package that help visualize the results.
Differentially expressed genes:
| gene_id | gene_name | transcript_id | GO | KEGG | KO_ENTRY | EC | Description | FPKM.Lo8_1 | FPKM.Lo8_2 | FPKM.Lo8_3 | FPKM.Lo7_1 | FPKM.Lo7_2 | FPKM.Lo7_3 | fc | log2(fc) | pval | qval | regulation | significant |
| LOC_Os01g01090 | LOC_Os01g01090 | LOC_Os01g01090.1 | GO:0003755(peptidyl-prolyl cis-trans isomerase activity);GO:0005528(FK506 binding);GO:0005789(endoplasmic reticulum membrane);GO:0061077(chaperone-mediated protein folding) | NA | NA | NA | retrotransposon protein, putative, unclassified, expressed | 0 | 0.02 | 0 | 0 | 0 | 0 | 1.01 | 0.01 | 0.39 | 0.80 | up | no |
| LOC_Os01g01110 | LOC_Os01g01110 | LOC_Os01g01110.1 | GO:0004672(protein kinase activity);GO:0004674(protein serine/threonine kinase activity);GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation);GO:0007169(transmembrane receptor protein tyrosine kinase signaling pathway);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04075(Plant hormone signal transduction);04626(Plant-pathogen interaction) | K13416 | EC:2.7.10.1;EC:2.7.11.1 | expressed protein | 0.59 | 0 | 0 | 0 | 0 | 0 | 1.27 | 0.34 | 0.38 | 0.80 | up | no |
| LOC_Os01g01290 | LOC_Os01g01290 | LOC_Os01g01290.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005515(protein binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0009738(abscisic acid-activated signaling pathway);GO:0010468(regulation of gene expression);GO:0046982(protein heterodimerization activity);GO:0048586(regulation of long-day photoperiodism, flowering);GO:0051247(positive regulation of protein metabolic process);GO:2000905(negative regulation of starch metabolic process) | NA | NA | NA | histone-like transcription factor and archaeal histone, putative, expressed | 0 | 0 | 0 | 0 | 0.11 | 0 | 0.98 | -0.03 | 0.71 | 0.93 | down | no |
| LOC_Os01g01360 | LOC_Os01g01360 | LOC_Os01g01360.1 | GO:0005215(transporter activity);GO:0005886(plasma membrane);GO:0006857(oligopeptide transport);GO:0016020(membrane);GO:0016021(integral component of membrane) | NA | NA | NA | peptide transporter PTR2, putative, expressed | 0.98 | 0.47 | 0.78 | 0 | 0.33 | 0.25 | 1.62 | 0.69 | 0.06 | 0.53 | up | no |
| LOC_Os01g01470 | LOC_Os01g01470 | LOC_Os01g01470.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0007275(multicellular organism development) | 03018(RNA degradation) | K12581 | NA | no apical meristem protein, putative, expressed | 0.08 | 0.06 | 0 | 0 | 0 | 0 | 1.07 | 0.10 | 0.10 | 0.57 | up | no |
| LOC_Os01g01730 | LOC_Os01g01730 | LOC_Os01g01730.1 | NA | NA | NA | NA | serine/arginine repetitive matrix protein 2, putative, expressed | 0 | 0 | 0.04 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g01770 | LOC_Os01g01770 | LOC_Os01g01770.1 | GO:0003676(nucleic acid binding);GO:0004527(exonuclease activity);GO:0005622(intracellular);GO:0005634(nucleus);GO:0046872(metal ion binding) | 03008(Ribosome biogenesis in eukaryotes) | K14570 | EC:3.1.-.- | ZOS1-01 - C2H2 zinc finger protein, expressed | 0.27 | 0.05 | 0 | 0.26 | 0.04 | 0.07 | 0.95 | -0.07 | 0.77 | 0.95 | down | no |
| LOC_Os01g01840 | LOC_Os01g01840 | LOC_Os01g01840.1 | GO:0000977(RNA polymerase II regulatory region sequence-specific DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0006357(regulation of transcription from RNA polymerase II promoter);GO:0090575(RNA polymerase II transcription factor complex) | NA | NA | NA | helix-loop-helix DNA-binding domain containing protein, expressed | 0 | 0.05 | 0 | 0.02 | 0.02 | 0 | 1.01 | 0.01 | 0.83 | 0.98 | up | no |
| LOC_Os01g01950 | LOC_Os01g01950 | LOC_Os01g01950.1 | NA | NA | NA | NA | expressed protein | 0 | 0.21 | 0 | 0 | 0.07 | 0.07 | 1.08 | 0.12 | 0.43 | 0.82 | up | no |
| LOC_Os01g01980 | LOC_Os01g01980 | LOC_Os01g01980.1 | NA | NA | NA | NA | expressed protein | 0.16 | 0 | 0 | 0 | 0 | 0 | 1.08 | 0.11 | 0.38 | 0.80 | up | no |
| LOC_Os01g01990 | LOC_Os01g01990 | LOC_Os01g01990.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.29 | 0 | 0 | 0.82 | -0.29 | 0.08 | 0.53 | down | no |
| LOC_Os01g02110 | LOC_Os01g02110 | LOC_Os01g02110.1 | GO:0001046(core promoter sequence-specific DNA binding);GO:0001228(transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding);GO:0005634(nucleus);GO:0006366(transcription from RNA polymerase II promoter) | 04075(Plant hormone signal transduction);04712(Circadian rhythm - plant) | K12126 | NA | helix-loop-helix DNA-binding domain containing protein, expressed | 0 | 0 | 0.08 | 0 | 0.03 | 0 | 1.00 | -0.01 | 0.91 | 1.00 | down | no |
| LOC_Os01g02120 | LOC_Os01g02120 | LOC_Os01g02120.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0008429(phosphatidylethanolamine binding);GO:0009737(response to abscisic acid);GO:0009738(abscisic acid-activated signaling pathway);GO:0010030(positive regulation of seed germination) | 04712(Circadian rhythm - plant) | K16223 | NA | osMFT2 MFT-Like2 homologous to Mother of FT and TFL1 gene; contains Pfam profile PF01161: Phosphatidylethanolamine-binding protein, expressed | 0 | 0 | 0.05 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g02190 | LOC_Os01g02190 | LOC_Os01g02190.1 | GO:0005887(integral component of plasma membrane);GO:0009992(cellular water homeostasis);GO:0015250(water channel activity);GO:0015254(glycerol channel activity);GO:0034220(ion transmembrane transport) | NA | NA | NA | aquaporin protein, putative, expressed | 0.12 | 0.08 | 0.19 | 0.17 | 0 | 0.17 | 0.97 | -0.04 | 0.74 | 0.94 | down | no |
| LOC_Os01g02210 | LOC_Os01g02210 | LOC_Os01g02210.1 | GO:0003755(peptidyl-prolyl cis-trans isomerase activity);GO:0005528(FK506 binding);GO:0005789(endoplasmic reticulum membrane);GO:0061077(chaperone-mediated protein folding) | NA | NA | NA | retrotransposon protein, putative, Ty3-gypsy subclass | 0 | 0 | 0 | 0 | 0 | 0.00 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g02250 | LOC_Os01g02250 | LOC_Os01g02250.1 | GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005576(extracellular region);GO:0006952(defense response);GO:0043531(ADP binding) | 04626(Plant-pathogen interaction) | K13457 | NA | RGA-1, putative, expressed | 0 | 0 | 0.06 | 0 | 0 | 0.01 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g02310 | LOC_Os01g02310 | LOC_Os01g02310.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation) | 04626(Plant-pathogen interaction) | K13430 | EC:2.7.11.1 | expressed protein | 0 | 0 | 0 | 0 | 0.03 | 0 | 1.00 | -0.01 | 0.71 | 0.93 | down | no |
| LOC_Os01g02370 | LOC_Os01g02370 | LOC_Os01g02370.1 | GO:0005886(plasma membrane) | 00520(Amino sugar and nucleotide sugar metabolism) | K01183 | EC:3.2.1.14 | receptor-like kinase ARK1AS, putative, expressed | 0.09 | 0 | 0.04 | 0.02 | 0.01 | 0.01 | 1.02 | 0.03 | 0.58 | 0.90 | up | no |
| LOC_Os01g02710 | LOC_Os01g02710 | LOC_Os01g02710.1 | GO:0005886(plasma membrane) | NA | NA | NA | LRk-type protein, putative, expressed | 0.03 | 0 | 0.08 | 0.07 | 0.03 | 0 | 0.96 | -0.06 | 0.12 | 0.60 | down | no |
| LOC_Os01g02950 | LOC_Os01g02950 | LOC_Os01g02950.1 | NA | NA | NA | NA | expressed protein | 0 | 0.08 | 0 | 0 | 0 | 0 | 1.04 | 0.06 | 0.39 | 0.80 | up | no |
| LOC_Os01g03260 | LOC_Os01g03260 | LOC_Os01g03260.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.03 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g03270 | LOC_Os01g03270 | LOC_Os01g03270.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | expressed protein | 0.49 | 0.27 | 0.20 | 0.12 | 0.10 | 0.02 | 1.23 | 0.30 | 0.15 | 0.63 | up | no |
| LOC_Os01g03290 | LOC_Os01g03290 | LOC_Os01g03290.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | seven in absentia protein family domain containing protein, expressed | 0 | 0.17 | 0 | 0 | 0 | 0 | 1.08 | 0.11 | 0.39 | 0.80 | up | no |
| LOC_Os01g03300 | LOC_Os01g03300 | LOC_Os01g03300.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | seven in absentia protein family protein, expressed | 0 | 0 | 0 | 0.02 | 0.06 | 0.17 | 0.97 | -0.04 | 0.61 | 0.91 | down | no |
| LOC_Os01g03320 | LOC_Os01g03320 | LOC_Os01g03320.1 | NA | NA | NA | NA | BBTI2 - Bowman-Birk type bran trypsin inhibitor precursor, expressed | 0.87 | 0.20 | 0.70 | 0.74 | 0.81 | 0.78 | 0.86 | -0.22 | 0.51 | 0.86 | down | no |
| LOC_Os01g03380 | LOC_Os01g03380 | LOC_Os01g03380.1 | NA | NA | NA | NA | BBTI6 - Bowman-Birk type bran trypsin inhibitor precursor, putative, expressed | 0 | 0.06 | 0.12 | 0 | 0 | 0.32 | 1.03 | 0.04 | 0.84 | 0.98 | up | no |
| LOC_Os01g03429 | LOC_Os01g03429 | LOC_Os01g03429.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | expressed protein | 0.06 | 0 | 0.12 | 0.10 | 0.04 | 0 | 0.95 | -0.08 | 0.16 | 0.65 | down | no |
| LOC_Os01g03464 | LOC_Os01g03464 | LOC_Os01g03464.1 | GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0006915(apoptotic process);GO:0042787(protein ubiquitination involved in ubiquitin-dependent protein catabolic process);GO:0043161(proteasome-mediated ubiquitin-dependent protein catabolic process);GO:0061630(ubiquitin protein ligase activity) | 04120(Ubiquitin mediated proteolysis) | K04506 | EC:2.3.2.27 | expressed protein | 0 | 0 | 0.03 | 0 | 0.04 | 0 | 0.99 | -0.01 | 0.77 | 0.95 | down | no |
| LOC_Os01g03620 | LOC_Os01g03620 | LOC_Os01g03620.1 | GO:0005507(copper ion binding);GO:0016722(oxidoreductase activity, oxidizing metal ions) | NA | NA | NA | multicopper oxidase domain containing protein, expressed | 0.11 | 0.14 | 0.47 | 0.38 | 0.28 | 0.49 | 0.82 | -0.28 | 0.26 | 0.76 | down | no |
| LOC_Os01g03670 | LOC_Os01g03670 | LOC_Os01g03670.1 | GO:0003824(catalytic activity);GO:0005829(cytosol);GO:0010584(pollen exine formation);GO:0016491(oxidoreductase activity);GO:0050662(coenzyme binding);GO:0055114(oxidation-reduction process);GO:0080110(sporopollenin biosynthetic process) | 00940(Phenylpropanoid biosynthesis) | K09753 | EC:1.2.1.44 | dihydroflavonol-4-reductase, putative, expressed | 0.07 | 0.04 | 0.04 | 0.05 | 0.15 | 0.08 | 0.99 | -0.02 | 0.75 | 0.95 | down | no |
| LOC_Os01g03840 | LOC_Os01g03840 | LOC_Os01g03840.1 | GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0008285(negative regulation of cell proliferation);GO:0010094(specification of carpel identity);GO:0010097(specification of stamen identity);GO:0043565(sequence-specific DNA binding);GO:0044212(transcription regulatory region DNA binding);GO:0048437(floral organ development) | 03410(Base excision repair) | K10773 | EC:4.2.99.18 | ZOS1-02 - C2H2 zinc finger protein, expressed | 0.71 | 0.64 | 0.19 | 0.13 | 0.14 | 0.48 | 1.48 | 0.57 | 0.06 | 0.53 | up | no |
| LOC_Os01g03890 | LOC_Os01g03890 | LOC_Os01g03890.1 | GO:0009739(response to gibberellin) | NA | NA | NA | DUF260 domain containing protein, putative, expressed | 0 | 0.02 | 0.07 | 0.00 | 0.22 | 0 | 0.97 | -0.04 | 0.81 | 0.97 | down | no |
| LOC_Os01g03900 | LOC_Os01g03900 | LOC_Os01g03900.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 1.58 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g03930 | LOC_Os01g03930 | LOC_Os01g03930.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0.47 | 0 | 0.93 | -0.11 | 0.71 | 0.93 | down | no |
| LOC_Os01g03960 | LOC_Os01g03960 | LOC_Os01g03960.1 | NA | NA | NA | NA | expressed protein | 0.12 | 0 | 0 | 0 | 0 | 0 | 1.06 | 0.08 | 0.38 | 0.80 | up | no |
| LOC_Os01g04005 | LOC_Os01g04005 | LOC_Os01g04005.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.01 | 0.01 | 0 | 0.99 | -0.01 | 0.04 | 0.52 | down | no |
| LOC_Os01g04090 | LOC_Os01g04090 | LOC_Os01g04090.1 | NA | NA | NA | NA | expressed protein | 0.43 | 0.43 | 0.51 | 0.37 | 0.63 | 0.60 | 1.01 | 0.01 | 0.90 | 1.00 | up | no |
| LOC_Os01g04210 | LOC_Os01g04210 | LOC_Os01g04210.1 | GO:0008375(acetylglucosaminyltransferase activity);GO:0016021(integral component of membrane);GO:0016757(transferase activity, transferring glycosyl groups) | 04144(Endocytosis) | K12471 | NA | DNA binding protein, putative, expressed | 0.21 | 0.12 | 0.25 | 0.38 | 0.06 | 0 | 0.89 | -0.17 | 0.18 | 0.67 | down | no |
| LOC_Os01g04220 | LOC_Os01g04220 | LOC_Os01g04220.1 | GO:0008375(acetylglucosaminyltransferase activity);GO:0016021(integral component of membrane);GO:0016757(transferase activity, transferring glycosyl groups) | 04144(Endocytosis) | K12471 | NA | DNA binding protein, putative, expressed | 0.04 | 0.20 | 0.19 | 0.06 | 0.16 | 0.12 | 1.03 | 0.05 | 0.71 | 0.93 | up | no |
| LOC_Os01g04250 | LOC_Os01g04250 | LOC_Os01g04250.1 | GO:0007165(signal transduction);GO:0016020(membrane) | NA | NA | NA | expressed protein | 0.56 | 0 | 0 | 0 | 0.21 | 0.26 | 1.21 | 0.27 | 0.41 | 0.81 | up | no |
| LOC_Os01g04540 | LOC_Os01g04540 | LOC_Os01g04540.1 | NA | NA | NA | NA | serine/threonine-protein kinase At1g18390 precursor, putative, expressed | 0.12 | 0.40 | 0.04 | 0.28 | 0.13 | 0.55 | 1.00 | 0.00 | 0.99 | 1.00 | up | no |
| LOC_Os01g04550 | LOC_Os01g04550 | LOC_Os01g04550.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation);GO:0016021(integral component of membrane);GO:0016301(kinase activity);GO:0016310(phosphorylation) | 00520(Amino sugar and nucleotide sugar metabolism) | K01183 | EC:3.2.1.14 | expressed protein | 0.17 | 0.21 | 0.35 | 0.22 | 0.33 | 0.31 | 0.96 | -0.07 | 0.59 | 0.90 | down | no |
| LOC_Os01g04560 | LOC_Os01g04560 | LOC_Os01g04560.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane);GO:0007166(cell surface receptor signaling pathway) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.05 | 0.20 | 0.02 | 0.93 | -0.11 | 0.39 | 0.80 | down | no |
| LOC_Os01g04640 | LOC_Os01g04640 | LOC_Os01g04640.1 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | reticulon domain containing protein, putative, expressed | 0.85 | 0.49 | 0.48 | 0.51 | 0.52 | 0.23 | 1.10 | 0.13 | 0.59 | 0.90 | up | no |
| LOC_Os01g04699 | LOC_Os01g04699 | LOC_Os01g04699.1 | NA | NA | NA | NA | expressed protein | 0.21 | 0.20 | 0.13 | 0.15 | 0.24 | 0 | 1.03 | 0.04 | 0.80 | 0.96 | up | no |
| LOC_Os01g04750 | LOC_Os01g04750 | LOC_Os01g04750.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0009873(ethylene-activated signaling pathway);GO:0045892(negative regulation of transcription, DNA-templated) | NA | NA | NA | B3 DNA binding domain containing protein, expressed | 0.03 | 0 | 0.09 | 0 | 0 | 0 | 1.02 | 0.02 | 0.66 | 0.93 | up | no |
| LOC_Os01g04800 | LOC_Os01g04800 | LOC_Os01g04800.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0009873(ethylene-activated signaling pathway);GO:0048573(photoperiodism, flowering) | 04075(Plant hormone signal transduction) | K14486 | NA | B3 DNA binding domain containing protein, expressed | 0.25 | 0.23 | 0.63 | 0.77 | 0.47 | 0.26 | 0.73 | -0.46 | 0.01 | 0.40 | down | no |
| LOC_Os01g05050 | LOC_Os01g05050 | LOC_Os01g05050.1 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0005759(mitochondrial matrix);GO:0008150(biological_process) | NA | NA | NA | mitochondrial glycoprotein, putative, expressed | 0 | 0 | 0.06 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g05120 | LOC_Os01g05120 | LOC_Os01g05120.1 | GO:0003674(molecular_function);GO:0005829(cytosol);GO:0006511(ubiquitin-dependent protein catabolic process);GO:0009507(chloroplast) | 04141(Protein processing in endoplasmic reticulum) | K14016 | NA | ubiquitin fusion degradation protein, putative, expressed | 0.12 | 0.13 | 0.18 | 0.21 | 0 | 0 | 0.97 | -0.05 | 0.45 | 0.83 | down | no |
| LOC_Os01g05340 | LOC_Os01g05340 | LOC_Os01g05340.1 | NA | NA | NA | NA | expressed protein | 0.19 | 0.19 | 0.08 | 0.17 | 0.08 | 0.18 | 1.04 | 0.05 | 0.62 | 0.91 | up | no |
| LOC_Os01g05360 | LOC_Os01g05360 | LOC_Os01g05360.1 | GO:0009834(plant-type secondary cell wall biogenesis);GO:0010417(glucuronoxylan biosynthetic process);GO:0042285(xylosyltransferase activity) | NA | NA | NA | expressed protein | 0 | 0.25 | 0 | 0 | 0 | 0 | 1.11 | 0.16 | 0.39 | 0.80 | up | no |
| LOC_Os01g05380 | LOC_Os01g05380 | LOC_Os01g05380.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.02 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g05400 | LOC_Os01g05400 | LOC_Os01g05400.1 | GO:0009834(plant-type secondary cell wall biogenesis);GO:0010417(glucuronoxylan biosynthetic process);GO:0042285(xylosyltransferase activity) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0.05 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g05440 | LOC_Os01g05440 | LOC_Os01g05440.1 | GO:0004526(ribonuclease P activity);GO:0005655(nucleolar ribonuclease P complex);GO:0090502(RNA phosphodiester bond hydrolysis, endonucleolytic) | NA | NA | NA | XH domain containing protein, expressed | 0.17 | 0.14 | 0.11 | 0.09 | 0.34 | 0.02 | 1.01 | 0.02 | 0.92 | 1.00 | up | no |
| LOC_Os01g05450 | LOC_Os01g05450 | LOC_Os01g05450.1 | NA | NA | NA | NA | expressed protein | 0.24 | 0.13 | 0 | 0.45 | 0.13 | 0.12 | 0.85 | -0.23 | 0.37 | 0.80 | down | no |
| LOC_Os01g05510 | LOC_Os01g05510 | LOC_Os01g05510.4 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.02 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g05530 | LOC_Os01g05530 | LOC_Os01g05530.1 | GO:0000027(ribosomal large subunit assembly);GO:0003723(RNA binding);GO:0005730(nucleolus) | NA | NA | NA | expressed protein | 0 | 0 | 0.06 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g05580 | LOC_Os01g05580 | LOC_Os01g05580.1 | NA | NA | NA | NA | Exo70 exocyst complex subunit family, putative, expressed | 0.05 | 0 | 0 | 0 | 0 | 0 | 1.02 | 0.03 | 0.38 | 0.80 | up | no |
| LOC_Os01g05585 | LOC_Os01g05585 | LOC_Os01g05585.1 | NA | NA | NA | NA | metallothionein, putative, expressed | 0.37 | 0 | 0.25 | 0 | 0.10 | 0 | 1.15 | 0.21 | 0.42 | 0.81 | up | no |
| LOC_Os01g05600 | LOC_Os01g05600 | LOC_Os01g05600.1 | GO:0005515(protein binding);GO:0005524(ATP binding);GO:0005576(extracellular region);GO:0006952(defense response);GO:0043531(ADP binding) | 04626(Plant-pathogen interaction) | K13457 | NA | NBS-LRR disease resistance protein, putative, expressed | 0.42 | 0 | 0 | 0 | 0 | 0 | 1.20 | 0.26 | 0.38 | 0.80 | up | no |
| LOC_Os01g06030 | LOC_Os01g06030 | LOC_Os01g06030.1 | GO:0005634(nucleus) | 00350(Tyrosine metabolism);00950(Isoquinoline alkaloid biosynthesis) | K01592 | EC:4.1.1.25 | expressed protein | 0.07 | 0 | 0 | 0 | 0 | 0 | 1.03 | 0.05 | 0.38 | 0.80 | up | no |
| LOC_Os01g06040 | LOC_Os01g06040 | LOC_Os01g06040.1 | NA | 00350(Tyrosine metabolism);00950(Isoquinoline alkaloid biosynthesis) | K01592 | EC:4.1.1.25 | expressed protein | 0 | 0 | 0.10 | 0 | 0.09 | 0 | 0.98 | -0.03 | 0.81 | 0.97 | down | no |
| LOC_Os01g06060 | LOC_Os01g06060 | LOC_Os01g06060.1 | GO:0005634(nucleus);GO:0008152(metabolic process);GO:0052689(carboxylic ester hydrolase activity) | 04075(Plant hormone signal transduction) | K14493 | EC:3.-.-.- | gibberellin receptor GID1L2, putative, expressed | 0 | 0 | 0 | 0.04 | 0.04 | 0.04 | 0.96 | -0.06 | 0.00 | 0.11 | down | no |
| LOC_Os01g06070 | LOC_Os01g06070 | LOC_Os01g06070.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.11 | 0.06 | 0 | 0.91 | -0.14 | 0.05 | 0.53 | down | no |
| LOC_Os01g06120 | LOC_Os01g06120 | LOC_Os01g06120.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.03 | 0 | 0 | 0.97 | -0.04 | 0.08 | 0.53 | down | no |
| LOC_Os01g06150 | LOC_Os01g06150 | LOC_Os01g06150.1 | GO:0005634(nucleus) | NA | NA | NA | expressed protein | 0.63 | 0.56 | 0.82 | 0.70 | 0.29 | 0.92 | 0.99 | -0.01 | 0.97 | 1.00 | down | no |
| LOC_Os01g06210 | LOC_Os01g06210 | LOC_Os01g06210.1 | GO:0005634(nucleus);GO:0008152(metabolic process);GO:0052689(carboxylic ester hydrolase activity) | 04075(Plant hormone signal transduction) | K14493 | EC:3.-.-.- | gibberellin receptor GID1L2, putative, expressed | 0.00 | 0 | 0 | 0 | 0 | 0 | 1.00 | 0.00 | 0.38 | 0.80 | up | no |
| LOC_Os01g06220 | LOC_Os01g06220 | LOC_Os01g06220.1 | GO:0005634(nucleus);GO:0008152(metabolic process);GO:0052689(carboxylic ester hydrolase activity) | 04075(Plant hormone signal transduction) | K14493 | EC:3.-.-.- | gibberellin receptor GID1L2, putative, expressed | 0.07 | 0.12 | 0.10 | 0.18 | 0 | 0.04 | 0.96 | -0.06 | 0.50 | 0.86 | down | no |
| LOC_Os01g06240 | LOC_Os01g06240 | LOC_Os01g06240.1 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation) | 00260(Glycine, serine and threonine metabolism);00350(Tyrosine metabolism);00360(Phenylalanine metabolism);00410(beta-Alanine metabolism);00950(Isoquinoline alkaloid biosynthesis);00960(Tropane, piperidine and pyridine alkaloid biosynthesis) | K00276 | EC:1.4.3.21 | protein kinase, putative, expressed | 0 | 0.06 | 0 | 0.08 | 0.06 | 0 | 0.96 | -0.07 | 0.36 | 0.80 | down | no |
| LOC_Os01g06370 | LOC_Os01g06370 | LOC_Os01g06370.1 | NA | NA | NA | NA | expressed protein | 0 | 0.08 | 0 | 0 | 0.34 | 0 | 0.98 | -0.03 | 0.91 | 1.00 | down | no |
| LOC_Os01g06390 | LOC_Os01g06390 | LOC_Os01g06390.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.08 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g06400 | LOC_Os01g06400 | LOC_Os01g06400.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0.03 | 0.11 | 0 | 0.95 | -0.07 | 0.38 | 0.80 | down | no |
| LOC_Os01g06420 | LOC_Os01g06420 | LOC_Os01g06420.1 | NA | NA | NA | NA | expressed protein | 0.24 | 0.46 | 0.15 | 0 | 0.15 | 0 | 1.31 | 0.38 | 0.10 | 0.57 | up | no |
| LOC_Os01g06430 | LOC_Os01g06430 | LOC_Os01g06430.1 | NA | NA | NA | NA | expressed protein | 0.25 | 0.06 | 0 | 0 | 0 | 0 | 1.15 | 0.20 | 0.23 | 0.73 | up | no |
| LOC_Os01g06540 | LOC_Os01g06540 | LOC_Os01g06540.1 | GO:0003677(DNA binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0008270(zinc ion binding);GO:0016036(cellular response to phosphate starvation);GO:0016568(chromatin modification);GO:0035064(methylated histone binding);GO:0042393(histone binding);GO:0048767(root hair elongation);GO:0055065(metal ion homeostasis) | NA | NA | NA | PHD finger protein, putative, expressed | 0 | 0.26 | 0 | 0.17 | 0.10 | 0 | 0.97 | -0.04 | 0.85 | 0.98 | down | no |
| LOC_Os01g06670 | LOC_Os01g06670 | LOC_Os01g06670.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13466 | NA | hcr2-5D, putative, expressed | 0.02 | 0 | 0 | 0 | 0 | 0 | 1.01 | 0.01 | 0.38 | 0.80 | up | no |
| LOC_Os01g06720 | LOC_Os01g06720 | LOC_Os01g06720.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | disease resistance protein SlVe2 precursor, putative, expressed | 0.04 | 0.02 | 0.01 | 0.14 | 0 | 0.09 | 0.93 | -0.11 | 0.26 | 0.76 | down | no |
| LOC_Os01g06750 | LOC_Os01g06750 | LOC_Os01g06750.1 | GO:0005886(plasma membrane);GO:0006952(defense response);GO:0007165(signal transduction);GO:0016301(kinase activity) | 04075(Plant hormone signal transduction) | K13415 | EC:2.7.10.1;EC:2.7.11.1 | verticillium wilt disease resistance protein precursor, putative, expressed | 0 | 0.16 | 0.14 | 0.06 | 0.05 | 0.11 | 1.02 | 0.02 | 0.84 | 0.98 | up | no |
| LOC_Os01g06790 | LOC_Os01g06790 | LOC_Os01g06790.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | disease resistance protein, putative, expressed | 0.03 | 0 | 0.02 | 0.02 | 0.08 | 0.03 | 0.98 | -0.03 | 0.59 | 0.90 | down | no |
| LOC_Os01g06820 | LOC_Os01g06820 | LOC_Os01g06820.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | hcr2-0B, putative, expressed | 0.10 | 0.13 | 0.05 | 0.15 | 0 | 0.10 | 0.99 | -0.01 | 0.93 | 1.00 | down | no |
| LOC_Os01g06836 | LOC_Os01g06836 | LOC_Os01g06836.1 | GO:0005886(plasma membrane);GO:0006952(defense response);GO:0007165(signal transduction);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13466 | NA | disease resistance protein SlVe2 precursor, putative, expressed | 0.05 | 0.03 | 0 | 0.10 | 0.05 | 0 | 0.96 | -0.06 | 0.36 | 0.80 | down | no |
| LOC_Os01g06870 | LOC_Os01g06870 | LOC_Os01g06870.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane) | 04626(Plant-pathogen interaction) | K13420 | EC:2.7.11.1 | resistance protein SlVe1 precursor, putative, expressed | 0 | 0 | 0.05 | 0 | 0.03 | 0 | 0.99 | -0.01 | 0.84 | 0.98 | down | no |
| LOC_Os01g06920 | LOC_Os01g06920 | LOC_Os01g06920.1 | GO:0006952(defense response);GO:0007165(signal transduction);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04626(Plant-pathogen interaction) | K13466 | NA | resistance protein SlVe1 precursor, putative, expressed | 0.44 | 0.51 | 0.54 | 0.16 | 0.32 | 0 | 1.24 | 0.31 | 0.17 | 0.66 | up | no |
| LOC_Os01g07020 | LOC_Os01g07020 | LOC_Os01g07020.1 | GO:0005887(integral component of plasma membrane);GO:0015179(L-amino acid transmembrane transporter activity);GO:0015297(antiporter activity) | NA | NA | NA | POEI39 - Pollen Ole e I allergen and extensin family protein precursor, putative, expressed | 0 | 0 | 0 | 0.09 | 0 | 0.04 | 0.93 | -0.10 | 0.11 | 0.58 | down | no |
| LOC_Os01g07030 | LOC_Os01g07030 | LOC_Os01g07030.1 | GO:0005887(integral component of plasma membrane);GO:0015179(L-amino acid transmembrane transporter activity);GO:0015297(antiporter activity) | NA | NA | NA | POEI40 - Pollen Ole e I allergen and extensin family protein precursor, expressed | 0.09 | 0.18 | 0.32 | 0.03 | 0.12 | 0.21 | 1.08 | 0.11 | 0.53 | 0.87 | up | no |
| LOC_Os01g07040 | LOC_Os01g07040 | LOC_Os01g07040.1 | GO:0005887(integral component of plasma membrane);GO:0015179(L-amino acid transmembrane transporter activity);GO:0015297(antiporter activity) | NA | NA | NA | POEI41 - Pollen Ole e I allergen and extensin family protein precursor, expressed | 0 | 0 | 0.12 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g07150 | LOC_Os01g07150 | LOC_Os01g07150.1 | GO:0003674(molecular_function);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 0 | 0.08 | 0 | 0 | 0 | 0 | 1.04 | 0.05 | 0.39 | 0.80 | up | no |
| LOC_Os01g07160 | LOC_Os01g07160 | LOC_Os01g07160.1 | GO:0004842(ubiquitin-protein transferase activity);GO:0019005(SCF ubiquitin ligase complex);GO:0031146(SCF-dependent proteasomal ubiquitin-dependent protein catabolic process) | NA | NA | NA | OsFBX3 - F-box domain containing protein, expressed | 0 | 0.04 | 0 | 0.21 | 0.28 | 0 | 0.83 | -0.27 | 0.19 | 0.68 | down | no |
| LOC_Os01g07180 | LOC_Os01g07180 | LOC_Os01g07180.1 | NA | NA | NA | NA | expressed protein | 0.15 | 0 | 0.10 | 0 | 0 | 0.10 | 1.07 | 0.10 | 0.43 | 0.81 | up | no |
| LOC_Os01g07364 | LOC_Os01g07364 | LOC_Os01g07364.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0.11 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g07430 | LOC_Os01g07430 | LOC_Os01g07430.1 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006355(regulation of transcription, DNA-templated);GO:0009651(response to salt stress);GO:0009723(response to ethylene);GO:0009737(response to abscisic acid);GO:0009753(response to jasmonic acid) | 00190(Oxidative phosphorylation);00860(Porphyrin and chlorophyll metabolism) | K02259 | NA | myb-like DNA-binding domain containing protein, putative, expressed | 0.07 | 0.35 | 0.29 | 0.03 | 0.06 | 0.05 | 1.15 | 0.21 | 0.28 | 0.78 | up | no |
| LOC_Os01g07450 | LOC_Os01g07450 | LOC_Os01g07450.1 | GO:0003677(DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0045892(negative regulation of transcription, DNA-templated) | 00190(Oxidative phosphorylation);00860(Porphyrin and chlorophyll metabolism) | K02259 | NA | MYB family transcription factor, putative, expressed | 0.06 | 0.06 | 0.03 | 0.13 | 0 | 0.13 | 0.96 | -0.06 | 0.59 | 0.90 | down | no |
| LOC_Os01g07460 | LOC_Os01g07460 | LOC_Os01g07460.1 | NA | NA | NA | NA | conserved hypothetical protein | 0.14 | 0 | 0 | 0 | 0 | 0 | 1.07 | 0.10 | 0.38 | 0.80 | up | no |
| LOC_Os01g07550 | LOC_Os01g07550 | LOC_Os01g07550.1 | NA | NA | NA | NA | hypothetical protein | 0 | 0 | 0.06 | 0 | 0 | 0 | 1.00 | 0.00 | 1.00 | 1.00 | up | no |
| LOC_Os01g07640 | LOC_Os01g07640 | LOC_Os01g07640.1 | GO:0005575(cellular_component);GO:0008150(biological_process) | 04075(Plant hormone signal transduction) | K14500 | EC:2.7.11.1 | ankyrin, putative, expressed | 0.21 | 0.12 | 0.15 | 0.17 | 0.04 | 0.07 | 1.02 | 0.03 | 0.71 | 0.93 | up | no |
| LOC_Os01g07660 | LOC_Os01g07660 | LOC_Os01g07660.1 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0.05 | 0 | 0.99 | -0.01 | 0.71 | 0.93 | down | no |
| LOC_Os01g07710 | LOC_Os01g07710 | LOC_Os01g07710.1 | NA | NA | NA | NA | expressed protein | 0.04 | 0.23 | 0.14 | 0 | 0 | 0.06 | 1.13 | 0.18 | 0.21 | 0.71 | up | no |
| LOC_Os01g07770 | LOC_Os01g07770 | LOC_Os01g07770.1 | GO:0004601(peroxidase activity);GO:0009505(plant-type cell wall);GO:0009664(plant-type cell wall organization) | 00940(Phenylpropanoid biosynthesis) | K00430 | EC:1.11.1.7 | peroxidase precursor, putative, expressed | 0.27 | 0.45 | 0.63 | 0.38 | 0.69 | 0.56 | 0.94 | -0.08 | 0.71 | 0.93 | down | no |
| LOC_Os01g08070 | LOC_Os01g08070 | LOC_Os01g08070.1 | GO:0000147(actin cortical patch assembly);GO:0005884(actin filament);GO:0006897(endocytosis);GO:0008360(regulation of cell shape);GO:0030048(actin filament-based movement);GO:0030479(actin cortical patch);GO:0051015(actin filament binding);GO:0051127(positive regulation of actin nucleation);GO:0051666(actin cortical patch localization) | NA | NA | NA | transposon protein, putative, CACTA, En/Spm sub-class, expressed | 0 | 0 | 0 | 0 | 0.02 | 0 | 1.00 | -0.00 | 0.71 | 0.93 | down | no |
Differentially expressed transcripts:
| t_id | class_code | chr | strand | start | end | t_name | num_exons | length | gene_id | gene_name | GO | KEGG | KO_ENTRY | EC | Description | cov.Lo8_1 | FPKM.Lo8_1 | cov.Lo8_2 | FPKM.Lo8_2 | cov.Lo8_3 | FPKM.Lo8_3 | cov.Lo7_1 | FPKM.Lo7_1 | cov.Lo7_2 | FPKM.Lo7_2 | cov.Lo7_3 | FPKM.Lo7_3 | fc | log2(fc) | pval | qval | regulation | significant |
| 1 | 0 | chr1 | + | 2903 | 10817 | LOC_Os01g01010.1 | 12 | 3017 | MSTRG.3 | LOC_Os01g01010 | GO:0005096(GTPase activator activity);GO:0005622(intracellular);GO:0006886(intracellular protein transport);GO:0012505(endomembrane system);GO:0017137(Rab GTPase binding);GO:0031338(regulation of vesicle fusion) | 03040(Spliceosome) | K12840 | NA | TBC domain containing protein, expressed | 22.48 | 3.76 | 32.34 | 5.20 | 30.97 | 4.95 | 15.39 | 2.59 | 33.21 | 5.20 | 22.18 | 3.65 | 1.18 | 0.24 | 0.47 | 0.78 | up | no |
| 2 | j | chr1 | + | 2926 | 10822 | MSTRG.3.2 | 12 | 2986 | MSTRG.3 | LOC_Os01g01010 | NA | NA | NA | NA | NA | 20.50 | 3.43 | 26.73 | 4.30 | 38.23 | 6.12 | 36.84 | 6.20 | 26.39 | 4.13 | 19.53 | 3.21 | 1.08 | 0.11 | 0.40 | 0.78 | up | no |
| 3 | j | chr1 | + | 2938 | 10822 | MSTRG.3.3 | 12 | 2923 | MSTRG.3 | LOC_Os01g01010 | NA | NA | NA | NA | NA | 0.53 | 0.09 | 0 | 0 | 0 | 0 | 5.83 | 0.98 | 1.41 | 0.22 | 0.59 | 0.10 | 0.76 | -0.39 | 0.23 | 0.76 | down | no |
| 4 | j | chr1 | + | 2968 | 10811 | MSTRG.3.4 | 13 | 2857 | MSTRG.3 | LOC_Os01g01010 | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.87 | 0.14 | 0.95 | -0.07 | 0.37 | 0.78 | down | no |
| 5 | 0 | chr1 | + | 2984 | 10562 | LOC_Os01g01010.2 | 12 | 2218 | MSTRG.3 | LOC_Os01g01010 | GO:0005096(GTPase activator activity);GO:0005622(intracellular);GO:0006886(intracellular protein transport);GO:0012505(endomembrane system);GO:0017137(Rab GTPase binding);GO:0031338(regulation of vesicle fusion) | 03040(Spliceosome) | K12840 | NA | TBC domain containing protein, expressed | 0.01 | 0.00 | 0 | 0 | 0.07 | 0.01 | 0.09 | 0.02 | 0.05 | 0.01 | 0.00 | 0.00 | 1.00 | -0.00 | 0.45 | 0.78 | down | no |
| 6 | j | chr1 | + | 11086 | 20323 | MSTRG.4.1 | 13 | 6352 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 31.28 | 4.90 | 0 | 0 | 0.53 | -0.90 | 0.42 | 0.78 | down | no |
| 7 | j | chr1 | + | 11086 | 20323 | MSTRG.4.2 | 13 | 6775 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 2.24 | 0.37 | 0 | 0 | 4.06 | 0.65 | 0 | 0 | 5.51 | 0.86 | 6.01 | 0.99 | 0.84 | -0.26 | 0.60 | 0.84 | down | no |
| 8 | 0 | chr1 | + | 11218 | 12435 | LOC_Os01g01019.1 | 2 | 1127 | MSTRG.4 | LOC_Os01g01019 | NA | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0 | 0 | 0.75 | 0.13 | 0 | 0 | 0.40 | 0.07 | 0.95 | -0.08 | 0.21 | 0.74 | down | no |
| 9 | j | chr1 | + | 12627 | 20377 | MSTRG.4.4 | 11 | 5478 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 7.62 | 1.27 | 0 | 0 | 0 | 0 | 20.38 | 3.43 | 0 | 0 | 9.41 | 1.55 | 0.60 | -0.75 | 0.45 | 0.78 | down | no |
| 10 | j | chr1 | + | 12627 | 20377 | MSTRG.4.5 | 12 | 5285 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 21.45 | 3.59 | 0 | 0 | 17.34 | 2.77 | 16.70 | 2.81 | 0 | 0 | 0 | 0 | 1.84 | 0.88 | 0.38 | 0.78 | up | no |
| 11 | 0 | chr1 | + | 12648 | 15915 | LOC_Os01g01030.1 | 5 | 2464 | MSTRG.4 | LOC_Os01g01030 | GO:0005507(copper ion binding);GO:0009505(plant-type cell wall);GO:0009506(plasmodesma);GO:0016722(oxidoreductase activity, oxidizing metal ions) | 00053(Ascorbate and aldarate metabolism) | K00423 | EC:1.10.3.3 | monocopper oxidase, putative, expressed | 0 | 0 | 0 | 0 | 4.37 | 0.70 | 0 | 0 | 1.18 | 0.18 | 0 | 0 | 1.17 | 0.22 | 0.41 | 0.78 | up | no |
| 12 | j | chr1 | + | 12655 | 20323 | MSTRG.4.7 | 10 | 5494 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 2.19 | 0.37 | 17.79 | 2.86 | 32.29 | 5.16 | 4.53 | 0.76 | 0.57 | 0.09 | 0 | 0 | 2.84 | 1.50 | 0.06 | 0.66 | up | no |
| 13 | j | chr1 | + | 16024 | 20323 | MSTRG.4.8 | 9 | 2685 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 4.49 | 0.75 | 8.14 | 1.31 | 0 | 0 | 2.26 | 0.38 | 0.82 | 0.13 | 0 | 0 | 1.33 | 0.41 | 0.37 | 0.78 | up | no |
| 14 | j | chr1 | + | 16029 | 20320 | MSTRG.4.9 | 9 | 2674 | MSTRG.4 | LOC_Os01g01040 | NA | NA | NA | NA | NA | 4.06 | 0.68 | 9.14 | 1.47 | 0 | 0 | 3.05 | 0.51 | 1.67 | 0.26 | 0 | 0 | 1.26 | 0.33 | 0.51 | 0.80 | up | no |
| 15 | 0 | chr1 | + | 16292 | 18304 | LOC_Os01g01040.4 | 3 | 1524 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 0.20 | 0.03 | 0.06 | 0.01 | 2.11 | 0.33 | 0.71 | 0.12 | 0.88 | -0.19 | 0.24 | 0.77 | down | no |
| 16 | 0 | chr1 | + | 16292 | 20323 | LOC_Os01g01040.1 | 8 | 2508 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 2.70 | 0.45 | 8.96 | 1.44 | 0.40 | 0.06 | 1.65 | 0.28 | 8.44 | 1.32 | 11.14 | 1.83 | 0.71 | -0.50 | 0.19 | 0.74 | down | no |
| 17 | 0 | chr1 | + | 16321 | 20323 | LOC_Os01g01040.2 | 8 | 2482 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 3.07 | 0.51 | 8.02 | 1.29 | 0.29 | 0.05 | 1.15 | 0.19 | 4.18 | 0.65 | 19.03 | 3.13 | 0.70 | -0.52 | 0.35 | 0.78 | down | no |
| 18 | 0 | chr1 | + | 16321 | 20323 | LOC_Os01g01040.3 | 7 | 2583 | MSTRG.4 | LOC_Os01g01040 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane) | NA | NA | NA | expressed protein | 3.29 | 0.55 | 9.61 | 1.54 | 2.79 | 0.45 | 1.16 | 0.20 | 2.92 | 0.46 | 19.45 | 3.20 | 0.86 | -0.22 | 0.73 | 0.90 | down | no |
| 19 | 0 | chr1 | + | 22841 | 26971 | LOC_Os01g01050.1 | 6 | 2039 | MSTRG.1 | LOC_Os01g01050 | NA | NA | NA | NA | R3H domain containing protein, expressed | 6.47 | 1.08 | 8.23 | 1.32 | 0.85 | 0.14 | 16.81 | 2.83 | 3.31 | 0.52 | 6.55 | 1.08 | 0.77 | -0.39 | 0.56 | 0.82 | down | no |
| 20 | 0 | chr1 | + | 22841 | 26971 | LOC_Os01g01050.2 | 6 | 1996 | MSTRG.1 | LOC_Os01g01050 | NA | NA | NA | NA | R3H domain containing protein, expressed | 21.03 | 3.52 | 13.28 | 2.14 | 27.27 | 4.36 | 18.74 | 3.16 | 11.28 | 1.77 | 22.15 | 3.65 | 1.15 | 0.21 | 0.58 | 0.83 | up | no |
| 21 | j | chr1 | + | 22850 | 26978 | MSTRG.1.3 | 5 | 2327 | MSTRG.1 | LOC_Os01g01050 | NA | NA | NA | NA | NA | 2.09 | 0.35 | 12.00 | 1.93 | 26.44 | 4.23 | 12.34 | 2.08 | 5.70 | 0.89 | 13.12 | 2.16 | 1.12 | 0.17 | 0.77 | 0.92 | up | no |
| 22 | 0 | chr1 | + | 27136 | 28651 | LOC_Os01g01060.1 | 4 | 920 | MSTRG.2 | LOC_Os01g01060 | GO:0000028(ribosomal small subunit assembly);GO:0003729(mRNA binding);GO:0003735(structural constituent of ribosome);GO:0006412(translation);GO:0019843(rRNA binding);GO:0022627(cytosolic small ribosomal subunit) | 03010(Ribosome) | K02989 | NA | 40S ribosomal protein S5, putative, expressed | 893.89 | 149.45 | 729.34 | 117.29 | 878.38 | 140.51 | 535.27 | 90.14 | 624.36 | 97.77 | 532.58 | 87.67 | 1.47 | 0.56 | 0.02 | 0.55 | up | no |
| 23 | j | chr1 | + | 29773 | 34495 | MSTRG.5.1 | 13 | 2115 | MSTRG.5 | LOC_Os01g01070 | NA | NA | NA | NA | NA | 23.84 | 3.99 | 10.42 | 1.68 | 10.81 | 1.73 | 8.02 | 1.35 | 8.85 | 1.39 | 26.32 | 4.33 | 1.01 | 0.02 | 0.97 | 0.99 | up | no |
| 24 | j | chr1 | + | 29789 | 34480 | MSTRG.5.2 | 12 | 1994 | MSTRG.5 | LOC_Os01g01070 | NA | NA | NA | NA | NA | 6.52 | 1.09 | 8.14 | 1.31 | 13.22 | 2.12 | 9.22 | 1.55 | 10.44 | 1.64 | 7.97 | 1.31 | 1.02 | 0.02 | 0.87 | 0.96 | up | no |
| 25 | 0 | chr1 | + | 29818 | 33943 | LOC_Os01g01070.3 | 13 | 1369 | MSTRG.5 | LOC_Os01g01070 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane);GO:0031307(integral component of mitochondrial outer membrane) | NA | NA | NA | expressed protein | 8.34 | 1.39 | 8.65 | 1.39 | 5.19 | 0.83 | 8.29 | 1.40 | 10.25 | 1.60 | 6.70 | 1.10 | 0.91 | -0.13 | 0.46 | 0.78 | down | no |
| 26 | 0 | chr1 | + | 29818 | 34493 | LOC_Os01g01070.1 | 14 | 1568 | MSTRG.5 | LOC_Os01g01070 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane);GO:0031307(integral component of mitochondrial outer membrane) | NA | NA | NA | expressed protein | 2.77 | 0.46 | 5.62 | 0.90 | 3.87 | 0.62 | 5.53 | 0.93 | 6.78 | 1.06 | 0.55 | 0.09 | 1.03 | 0.04 | 0.91 | 0.97 | up | no |
| 27 | 0 | chr1 | + | 29818 | 34493 | LOC_Os01g01070.2 | 14 | 1562 | MSTRG.5 | LOC_Os01g01070 | GO:0003674(molecular_function);GO:0005739(mitochondrion);GO:0008150(biological_process);GO:0016021(integral component of membrane);GO:0031307(integral component of mitochondrial outer membrane) | NA | NA | NA | expressed protein | 42.56 | 7.12 | 46.44 | 7.47 | 59.99 | 9.60 | 78.91 | 13.29 | 69.35 | 10.86 | 42.81 | 7.05 | 0.85 | -0.24 | 0.27 | 0.78 | down | no |
| 28 | j | chr1 | + | 35392 | 41235 | MSTRG.6.2 | 13 | 2562 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 0 | 0 | 3.23 | 0.52 | 4.66 | 0.75 | 3.70 | 0.62 | 20.49 | 3.21 | 4.22 | 0.69 | 0.61 | -0.70 | 0.32 | 0.78 | down | no |
| 29 | j | chr1 | + | 35392 | 41235 | MSTRG.6.3 | 13 | 2814 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 1.39 | 0.23 | 1.40 | 0.22 | 1.51 | 0.24 | 0.98 | 0.17 | 3.29 | 0.52 | 2.22 | 0.36 | 0.91 | -0.14 | 0.31 | 0.78 | down | no |
| 30 | j | chr1 | + | 35392 | 41253 | MSTRG.6.1 | 14 | 2324 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 12.15 | 2.03 | 48.93 | 7.87 | 12.56 | 2.01 | 9.09 | 1.53 | 18.91 | 2.96 | 45.71 | 7.52 | 0.90 | -0.15 | 0.83 | 0.94 | down | no |
| 31 | j | chr1 | + | 35450 | 41253 | MSTRG.6.4 | 14 | 2266 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 1.64 | 0.27 | 8.75 | 1.41 | 8.54 | 1.37 | 12.74 | 2.15 | 26.78 | 4.19 | 3.61 | 0.59 | 0.68 | -0.56 | 0.44 | 0.78 | down | no |
| 32 | j | chr1 | + | 35579 | 41188 | MSTRG.6.5 | 14 | 2231 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 29.44 | 4.92 | 18.18 | 2.92 | 42.95 | 6.87 | 29.60 | 4.98 | 17.97 | 2.81 | 18.91 | 3.11 | 1.32 | 0.40 | 0.18 | 0.74 | up | no |
| 33 | j | chr1 | + | 35579 | 41188 | MSTRG.6.6 | 12 | 2466 | MSTRG.6 | LOC_Os01g01080 | NA | NA | NA | NA | NA | 8.52 | 1.42 | 1.37 | 0.22 | 9.94 | 1.59 | 1.65 | 0.28 | 0.65 | 0.10 | 2.13 | 0.35 | 1.63 | 0.71 | 0.16 | 0.74 | up | no |
| 34 | 0 | chr1 | + | 35581 | 41180 | LOC_Os01g01080.1 | 15 | 1955 | MSTRG.6 | LOC_Os01g01080 | GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0006520(cellular amino acid metabolic process);GO:0008117(sphinganine-1-phosphate aldolase activity);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016831(carboxy-lyase activity);GO:0019752(carboxylic acid metabolic process);GO:0030149(sphingolipid catabolic process);GO:0030170(pyridoxal phosphate binding) | 00600(Sphingolipid metabolism) | K01634 | EC:4.1.2.27 | decarboxylase, putative, expressed | 174.37 | 29.15 | 114.36 | 18.39 | 90.61 | 14.49 | 214.31 | 36.09 | 122.44 | 19.17 | 162.21 | 26.70 | 0.75 | -0.41 | 0.42 | 0.78 | down | no |
| 35 | 0 | chr1 | + | 35581 | 41180 | LOC_Os01g01080.2 | 15 | 1976 | MSTRG.6 | LOC_Os01g01080 | GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0006520(cellular amino acid metabolic process);GO:0008117(sphinganine-1-phosphate aldolase activity);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016831(carboxy-lyase activity);GO:0019752(carboxylic acid metabolic process);GO:0030149(sphingolipid catabolic process);GO:0030170(pyridoxal phosphate binding) | 00600(Sphingolipid metabolism) | K01634 | EC:4.1.2.27 | decarboxylase, putative, expressed | 2.12 | 0.35 | 0.27 | 0.04 | 8.33 | 1.33 | 0.32 | 0.05 | 0 | 0 | 0.26 | 0.04 | 1.51 | 0.60 | 0.11 | 0.74 | up | no |
| 36 | 0 | chr1 | + | 35581 | 41180 | LOC_Os01g01080.3 | 14 | 2042 | MSTRG.6 | LOC_Os01g01080 | GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0006520(cellular amino acid metabolic process);GO:0008117(sphinganine-1-phosphate aldolase activity);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016831(carboxy-lyase activity);GO:0019752(carboxylic acid metabolic process);GO:0030149(sphingolipid catabolic process);GO:0030170(pyridoxal phosphate binding) | 00600(Sphingolipid metabolism) | K01634 | EC:4.1.2.27 | decarboxylase, putative, expressed | 5.93 | 0.99 | 0.56 | 0.09 | 2.43 | 0.39 | 1.68 | 0.28 | 9.20 | 1.44 | 0.61 | 0.10 | 0.94 | -0.08 | 0.88 | 0.96 | down | no |
| 37 | 0 | chr1 | + | 44595 | 47526 | LOC_Os01g01090.1 | 8 | 2409 | LOC_Os01g01090 | LOC_Os01g01090 | GO:0003755(peptidyl-prolyl cis-trans isomerase activity);GO:0005528(FK506 binding);GO:0005789(endoplasmic reticulum membrane);GO:0061077(chaperone-mediated protein folding) | NA | NA | NA | retrotransposon protein, putative, unclassified, expressed | 0 | 0 | 0.13 | 0.02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.01 | 0.01 | 0.47 | 0.78 | up | no |
| 38 | 0 | chr1 | + | 57082 | 57972 | LOC_Os01g01110.1 | 1 | 891 | LOC_Os01g01110 | LOC_Os01g01110 | GO:0004672(protein kinase activity);GO:0004674(protein serine/threonine kinase activity);GO:0005524(ATP binding);GO:0005886(plasma membrane);GO:0006468(protein phosphorylation);GO:0007169(transmembrane receptor protein tyrosine kinase signaling pathway);GO:0016020(membrane);GO:0016021(integral component of membrane);GO:0016301(kinase activity) | 04075(Plant hormone signal transduction);04626(Plant-pathogen interaction) | K13416 | EC:2.7.10.1;EC:2.7.11.1 | expressed protein | 3.55 | 0.59 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.15 | 0.20 | 0.46 | 0.78 | up | no |
| 39 | j | chr1 | + | 58431 | 63576 | MSTRG.7.1 | 7 | 4147 | MSTRG.7 | LOC_Os01g01120 | NA | NA | NA | NA | NA | 14.38 | 2.40 | 18.27 | 2.94 | 11.23 | 1.80 | 5.80 | 0.98 | 7.88 | 1.23 | 4.57 | 0.75 | 1.67 | 0.74 | 0.03 | 0.56 | up | no |
| 41 | 0 | chr1 | + | 62059 | 63576 | LOC_Os01g01120.1 | 4 | 1206 | MSTRG.7 | LOC_Os01g01120 | GO:0000287(magnesium ion binding);GO:0005737(cytoplasm);GO:0005829(cytosol);GO:0008270(zinc ion binding);GO:0009507(chloroplast);GO:0009570(chloroplast stroma);GO:0016787(hydrolase activity);GO:0019284(L-methionine biosynthetic process from S-adenosylmethionine);GO:0019509(L-methionine biosynthetic process from methylthioadenosine);GO:0043715(2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity);GO:0043716(2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity);GO:0043874(acireductone synthase activity);GO:0046570(methylthioribulose 1-phosphate dehydratase activity) | 00270(Cysteine and methionine metabolism) | K09880 | EC:3.1.3.77 | enolase-phosphatase E1, putative, expressed | 16.68 | 2.79 | 17.54 | 2.82 | 25.99 | 4.16 | 16.52 | 2.78 | 8.60 | 1.35 | 6.60 | 1.09 | 1.68 | 0.74 | 0.01 | 0.47 | up | no |
| 42 | 0 | chr1 | - | 63244 | 66302 | LOC_Os01g01130.1 | 7 | 2002 | MSTRG.8 | LOC_Os01g01130 | GO:0005634(nucleus) | 03013(RNA transport) | K13151 | NA | snurportin-1, putative, expressed | 31.68 | 5.30 | 17.59 | 2.83 | 40.19 | 6.43 | 30.53 | 5.14 | 27.09 | 4.24 | 22.84 | 3.76 | 1.10 | 0.13 | 0.65 | 0.86 | up | no |
| 44 | 0 | chr1 | + | 72775 | 77699 | LOC_Os01g01150.1 | 3 | 3756 | MSTRG.10 | LOC_Os01g01150 | GO:0000166(nucleotide binding);GO:0003676(nucleic acid binding);GO:0003723(RNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046872(metal ion binding) | NA | NA | NA | RNA recognition motif, putative, expressed | 18.37 | 3.07 | 0 | 0 | 13.54 | 2.17 | 9.77 | 1.64 | 13.05 | 2.04 | 23.46 | 3.86 | 0.69 | -0.53 | 0.55 | 0.81 | down | no |
| 45 | 0 | chr1 | + | 72775 | 78702 | LOC_Os01g01150.2 | 4 | 4638 | MSTRG.10 | LOC_Os01g01150 | GO:0000166(nucleotide binding);GO:0003676(nucleic acid binding);GO:0003723(RNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046872(metal ion binding) | NA | NA | NA | RNA recognition motif, putative, expressed | 2.79 | 0.47 | 1.21 | 0.19 | 6.33 | 1.01 | 4.77 | 0.80 | 4.98 | 0.78 | 4.53 | 0.75 | 0.88 | -0.18 | 0.38 | 0.78 | down | no |
| 46 | 0 | chr1 | + | 72775 | 79938 | LOC_Os01g01150.3 | 5 | 4603 | MSTRG.10 | LOC_Os01g01150 | GO:0000166(nucleotide binding);GO:0003676(nucleic acid binding);GO:0003723(RNA binding);GO:0005634(nucleus);GO:0008150(biological_process);GO:0046872(metal ion binding) | NA | NA | NA | RNA recognition motif, putative, expressed | 3.09 | 0.52 | 7.56 | 1.22 | 6.14 | 0.98 | 6.52 | 1.10 | 4.71 | 0.74 | 4.97 | 0.82 | 1.02 | 0.02 | 0.91 | 0.97 | up | no |
| 47 | j | chr1 | + | 72775 | 80049 | MSTRG.10.1 | 6 | 4241 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 12.96 | 2.17 | 21.34 | 3.43 | 14.08 | 2.25 | 16.72 | 2.82 | 14.04 | 2.20 | 7.22 | 1.19 | 1.21 | 0.28 | 0.44 | 0.78 | up | no |
| 48 | j | chr1 | + | 72786 | 79891 | MSTRG.10.6 | 6 | 3995 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 3.82 | 0.64 | 10.38 | 1.67 | 7.53 | 1.21 | 4.57 | 0.77 | 11.71 | 1.83 | 10.36 | 1.71 | 0.88 | -0.19 | 0.60 | 0.84 | down | no |
| 49 | j | chr1 | + | 72786 | 79891 | MSTRG.10.7 | 7 | 3951 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 5.71 | 0.95 | 16.77 | 2.70 | 13.71 | 2.19 | 7.51 | 1.27 | 11.36 | 1.78 | 10.46 | 1.72 | 1.11 | 0.15 | 0.69 | 0.88 | up | no |
| 50 | j | chr1 | + | 72786 | 80049 | MSTRG.10.5 | 6 | 4239 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 5.23 | 0.87 | 7.97 | 1.28 | 8.75 | 1.40 | 11.05 | 1.86 | 14.90 | 2.33 | 10.33 | 1.70 | 0.74 | -0.43 | 0.07 | 0.68 | down | no |
| 51 | j | chr1 | + | 72804 | 79846 | MSTRG.10.8 | 5 | 4385 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 23.87 | 3.99 | 1.43 | 0.23 | 7.19 | 1.15 | 6.68 | 1.12 | 3.04 | 0.48 | 0 | 0 | 1.65 | 0.72 | 0.42 | 0.78 | up | no |
| 52 | j | chr1 | + | 72817 | 80049 | MSTRG.10.10 | 7 | 4001 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 2.19 | 0.37 | 4.90 | 0.79 | 4.69 | 0.75 | 7.49 | 1.26 | 8.43 | 1.32 | 8.69 | 1.43 | 0.70 | -0.52 | 0.04 | 0.62 | down | no |
| 53 | j | chr1 | + | 72817 | 80049 | MSTRG.10.9 | 7 | 3990 | MSTRG.10 | LOC_Os01g01150 | NA | NA | NA | NA | NA | 3.53 | 0.59 | 6.97 | 1.12 | 2.43 | 0.39 | 13.70 | 2.31 | 8.74 | 1.37 | 6.59 | 1.09 | 0.66 | -0.59 | 0.15 | 0.74 | down | no |
| 54 | 0 | chr1 | + | 82428 | 84302 | LOC_Os01g01160.1 | 2 | 1090 | MSTRG.9 | LOC_Os01g01160 | GO:0005515(protein binding);GO:0005634(nucleus);GO:0006457(protein folding);GO:0009507(chloroplast);GO:0010322(regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway);GO:0061077(chaperone-mediated protein folding);GO:1902395(regulation of 1-deoxy-D-xylulose-5-phosphate synthase activity) | 04141(Protein processing in endoplasmic reticulum) | K09518 | NA | heat shock protein DnaJ, putative, expressed | 34.85 | 5.83 | 18.77 | 3.02 | 2.34 | 0.37 | 31.73 | 5.34 | 29.18 | 4.57 | 27.73 | 4.56 | 0.53 | -0.92 | 0.21 | 0.74 | down | no |
| 55 | 0 | chr1 | + | 85337 | 88844 | LOC_Os01g01170.1 | 7 | 2334 | MSTRG.12 | LOC_Os01g01170 | NA | NA | NA | NA | expressed protein | 11.93 | 1.99 | 25.35 | 4.08 | 15.25 | 2.44 | 3.59 | 0.60 | 7.64 | 1.20 | 3.71 | 0.61 | 2.07 | 1.05 | 0.04 | 0.63 | up | yes |
| 56 | j | chr1 | + | 85340 | 88935 | MSTRG.12.2 | 7 | 2419 | MSTRG.12 | LOC_Os01g01170 | NA | NA | NA | NA | NA | 8.35 | 1.40 | 9.64 | 1.55 | 6.57 | 1.05 | 4.25 | 0.72 | 2.86 | 0.45 | 1.39 | 0.23 | 1.61 | 0.68 | 0.04 | 0.62 | up | no |
| 60 | 0 | chr1 | + | 134291 | 135685 | LOC_Os01g01280.1 | 3 | 1226 | MSTRG.11 | LOC_Os01g01280 | GO:0003674(molecular_function);GO:0008150(biological_process);GO:0009507(chloroplast);GO:0009543(chloroplast thylakoid lumen);GO:0009579(thylakoid);GO:0031977(thylakoid lumen) | NA | NA | NA | expressed protein | 7.22 | 1.21 | 5.42 | 0.87 | 13.00 | 2.08 | 9.52 | 1.60 | 12.17 | 1.91 | 12.45 | 2.05 | 0.84 | -0.26 | 0.34 | 0.78 | down | no |
| 61 | 0 | chr1 | + | 139820 | 141588 | LOC_Os01g01290.1 | 2 | 1556 | LOC_Os01g01290 | LOC_Os01g01290 | GO:0003677(DNA binding);GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005515(protein binding);GO:0005634(nucleus);GO:0005829(cytosol);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0009738(abscisic acid-activated signaling pathway);GO:0010468(regulation of gene expression);GO:0046982(protein heterodimerization activity);GO:0048586(regulation of long-day photoperiodism, flowering);GO:0051247(positive regulation of protein metabolic process);GO:2000905(negative regulation of starch metabolic process) | NA | NA | NA | histone-like transcription factor and archaeal histone, putative, expressed | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.67 | 0.11 | 0 | 0 | 0.97 | -0.05 | 0.42 | 0.78 | down | no |
| 62 | 0 | chr1 | + | 141936 | 144554 | LOC_Os01g01295.1 | 4 | 1793 | MSTRG.15 | LOC_Os01g01295 | GO:0009507(chloroplast) | NA | NA | NA | expressed protein | 57.65 | 9.64 | 48.85 | 7.86 | 22.59 | 3.61 | 47.46 | 7.99 | 18.23 | 2.86 | 57.90 | 9.53 | 1.02 | 0.03 | 0.97 | 0.99 | up | no |
| 63 | j | chr1 | + | 142782 | 144556 | MSTRG.15.2 | 2 | 1644 | MSTRG.15 | LOC_Os01g01295 | NA | NA | NA | NA | NA | 7.18 | 1.20 | 5.97 | 0.96 | 2.50 | 0.40 | 8.71 | 1.47 | 7.81 | 1.22 | 7.22 | 1.19 | 0.78 | -0.36 | 0.16 | 0.74 | down | no |
| 64 | 0 | chr1 | + | 145577 | 147852 | LOC_Os01g01302.1 | 9 | 1155 | MSTRG.16 | LOC_Os01g01302 | GO:0000287(magnesium ion binding);GO:0004765(shikimate kinase activity);GO:0009073(aromatic amino acid family biosynthetic process);GO:0019632(shikimate metabolic process) | 01230(Biosynthesis of amino acids);00400(Phenylalanine, tyrosine and tryptophan biosynthesis) | K00891 | EC:2.7.1.71 | shikimate kinase, putative, expressed | 43.91 | 7.34 | 62.49 | 10.05 | 50.67 | 8.11 | 54.08 | 9.11 | 44.18 | 6.92 | 29.41 | 4.84 | 1.24 | 0.31 | 0.33 | 0.78 | up | no |
| 65 | j | chr1 | + | 145602 | 147854 | MSTRG.16.2 | 8 | 1228 | MSTRG.16 | LOC_Os01g01302 | NA | NA | NA | NA | NA | 13.63 | 2.28 | 0.27 | 0.04 | 17.74 | 2.84 | 1.32 | 0.22 | 6.23 | 0.98 | 11.30 | 1.86 | 1.25 | 0.32 | 0.72 | 0.89 | up | no |
| 66 | 0 | chr1 | + | 148045 | 150577 | LOC_Os01g01307.1 | 5 | 979 | MSTRG.17 | LOC_Os01g01307 | GO:0003674(molecular_function);GO:0005576(extracellular region);GO:0005774(vacuolar membrane);GO:0005783(endoplasmic reticulum);GO:0005789(endoplasmic reticulum membrane);GO:0005794(Golgi apparatus);GO:0008150(biological_process);GO:0009506(plasmodesma);GO:0016021(integral component of membrane) | 04141(Protein processing in endoplasmic reticulum) | K13250 | NA | translocon-associated protein beta domain containing protein, expressed | 0 | 0 | 30.11 | 4.84 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.71 | 0.77 | 0.47 | 0.78 | up | no |
| 68 | j | chr1 | + | 148055 | 150610 | MSTRG.17.6 | 5 | 1004 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 28.36 | 4.74 | 74.35 | 11.96 | 13.47 | 2.16 | 38.59 | 6.50 | 104.89 | 16.43 | 53.90 | 8.87 | 0.52 | -0.95 | 0.18 | 0.74 | down | no |
| 69 | j | chr1 | + | 148055 | 150610 | MSTRG.17.7 | 5 | 988 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 22.20 | 3.71 | 2.03 | 0.33 | 1.45 | 0.23 | 1.55 | 0.26 | 7.51 | 1.18 | 6.51 | 1.07 | 1.02 | 0.03 | 0.96 | 0.99 | up | no |
| 70 | j | chr1 | + | 148055 | 150610 | MSTRG.17.8 | 6 | 1353 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 32.48 | 5.43 | 14.59 | 2.35 | 14.05 | 2.25 | 12.36 | 2.08 | 16.90 | 2.65 | 36.65 | 6.03 | 0.91 | -0.14 | 0.76 | 0.91 | down | no |
| 71 | j | chr1 | + | 148055 | 150643 | MSTRG.17.3 | 5 | 1037 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 154.07 | 25.76 | 101.63 | 16.34 | 157.66 | 25.22 | 127.45 | 21.46 | 32.25 | 5.05 | 43.83 | 7.22 | 2.39 | 1.25 | 0.10 | 0.74 | up | no |
| 72 | j | chr1 | + | 148055 | 150643 | MSTRG.17.4 | 6 | 1037 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 95.23 | 15.92 | 99.63 | 16.02 | 164.74 | 26.35 | 153.88 | 25.91 | 47.09 | 7.37 | 35.58 | 5.86 | 1.91 | 0.93 | 0.09 | 0.74 | up | no |
| 73 | j | chr1 | + | 148055 | 150643 | MSTRG.17.5 | 5 | 1386 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 10.11 | 1.69 | 11.20 | 1.80 | 21.84 | 3.49 | 22.53 | 3.79 | 25.68 | 4.02 | 25.34 | 4.17 | 0.67 | -0.58 | 0.06 | 0.68 | down | no |
| 74 | j | chr1 | + | 148068 | 150571 | MSTRG.17.9 | 5 | 1429 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 29.96 | 5.01 | 48.79 | 7.85 | 48.35 | 7.73 | 36.58 | 6.16 | 40.71 | 6.38 | 57.13 | 9.40 | 0.95 | -0.08 | 0.80 | 0.93 | down | no |
| 75 | j | chr1 | + | 148072 | 150567 | MSTRG.17.10 | 6 | 800 | MSTRG.17 | LOC_Os01g01307 | NA | NA | NA | NA | NA | 21.12 | 3.53 | 0 | 0 | 0.49 | 0.08 | 0.93 | 0.16 | 2.63 | 0.41 | 0.82 | 0.14 | 1.31 | 0.39 | 0.64 | 0.86 | up | no |
| 76 | 0 | chr1 | + | 151409 | 156500 | LOC_Os01g01312.1 | 7 | 4165 | MSTRG.14 | LOC_Os01g01312 | GO:0003677(DNA binding);GO:0004386(helicase activity);GO:0005524(ATP binding);GO:0005634(nucleus);GO:0006281(DNA repair);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0006974(cellular response to DNA damage stimulus);GO:0010332(response to gamma radiation) | 03420(Nucleotide excision repair) | K10841 | NA | retrotransposon protein, putative, Ty1-copia subclass, expressed | 22.81 | 3.81 | 36.34 | 5.84 | 36.30 | 5.81 | 30.90 | 5.20 | 19.01 | 2.98 | 30.10 | 4.96 | 1.18 | 0.24 | 0.45 | 0.78 | up | no |
| 77 | x | chr1 | + | 163052 | 169672 | MSTRG.21.1 | 5 | 1539 | MSTRG.21 | LOC_Os01g01340 | NA | NA | NA | NA | NA | 19.49 | 3.26 | 24.84 | 3.99 | 17.76 | 2.84 | 14.81 | 2.49 | 14.51 | 2.27 | 7.94 | 1.31 | 1.46 | 0.55 | 0.12 | 0.74 | up | no |
| 78 | x | chr1 | + | 163052 | 169672 | MSTRG.21.2 | 4 | 1426 | MSTRG.21 | LOC_Os01g01340 | NA | NA | NA | NA | NA | 3.58 | 0.60 | 0 | 0 | 6.12 | 0.98 | 0 | 0 | 11.00 | 1.72 | 0 | 0 | 1.06 | 0.09 | 0.90 | 0.97 | up | no |
| 79 | x | chr1 | + | 163114 | 169672 | MSTRG.21.3 | 5 | 1480 | MSTRG.21 | LOC_Os01g01340 | NA | NA | NA | NA | NA | 1.84 | 0.31 | 10.24 | 1.65 | 6.40 | 1.02 | 9.40 | 1.58 | 0 | 0 | 13.35 | 2.20 | 0.96 | -0.05 | 0.94 | 0.98 | down | no |
| 80 | 0 | chr1 | - | 168470 | 170381 | LOC_Os01g01340.2 | 2 | 1731 | MSTRG.22 | LOC_Os01g01340 | GO:0003674(molecular_function);GO:0008150(biological_process);GO:0009507(chloroplast) | 04144(Endocytosis) | K12198 | NA | light-induced protein 1-like, putative, expressed | 84.06 | 14.05 | 1.05 | 0.17 | 0.57 | 0.09 | 3.09 | 0.52 | 0 | 0 | 18.78 | 3.09 | 1.28 | 0.36 | 0.81 | 0.93 | up | no |
| 81 | 0 | chr1 | - | 168470 | 170389 | LOC_Os01g01340.1 | 3 | 1645 | MSTRG.22 | LOC_Os01g01340 | GO:0003674(molecular_function);GO:0008150(biological_process);GO:0009507(chloroplast) | 04144(Endocytosis) | K12198 | NA | light-induced protein 1-like, putative, expressed | 42.25 | 7.06 | 89.58 | 14.41 | 221.03 | 35.36 | 360.56 | 60.72 | 263.54 | 41.27 | 145.25 | 23.91 | 0.46 | -1.11 | 0.05 | 0.65 | down | no |
| 82 | j | chr1 | - | 168581 | 173195 | MSTRG.22.3 | 8 | 3105 | MSTRG.22 | LOC_Os01g01350 | NA | NA | NA | NA | NA | 40.63 | 6.79 | 38.28 | 6.16 | 32.97 | 5.27 | 18.42 | 3.10 | 23.38 | 3.66 | 8.46 | 1.39 | 1.98 | 0.99 | 0.07 | 0.69 | up | no |
| 83 | 0 | chr1 | - | 170712 | 173191 | LOC_Os01g01350.1 | 7 | 1151 | MSTRG.22 | LOC_Os01g01350 | GO:0005515(protein binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0007034(vacuolar transport);GO:0016192(vesicle-mediated transport) | 04144(Endocytosis) | K12198 | NA | SNF7 domain containing protein, putative, expressed | 22.29 | 3.73 | 6.72 | 1.08 | 32.12 | 5.14 | 9.77 | 1.64 | 9.48 | 1.48 | 15.88 | 2.61 | 1.41 | 0.50 | 0.43 | 0.78 | up | no |
| 84 | 0 | chr1 | - | 170712 | 173434 | LOC_Os01g01350.2 | 5 | 1574 | MSTRG.22 | LOC_Os01g01350 | GO:0005515(protein binding);GO:0005634(nucleus);GO:0005737(cytoplasm);GO:0007034(vacuolar transport);GO:0016192(vesicle-mediated transport) | 04144(Endocytosis) | K12198 | NA | SNF7 domain containing protein, putative, expressed | 2.59 | 0.43 | 5.69 | 0.91 | 5.13 | 0.82 | 7.04 | 1.19 | 4.83 | 0.76 | 2.63 | 0.43 | 0.99 | -0.01 | 0.97 | 0.99 | down | no |
| 85 | 0 | chr1 | + | 178310 | 180812 | LOC_Os01g01360.1 | 1 | 2503 | LOC_Os01g01360 | LOC_Os01g01360 | GO:0005215(transporter activity);GO:0005886(plasma membrane);GO:0006857(oligopeptide transport);GO:0016020(membrane);GO:0016021(integral component of membrane) | NA | NA | NA | peptide transporter PTR2, putative, expressed | 5.87 | 0.98 | 2.93 | 0.47 | 4.88 | 0.78 | 0 | 0 | 2.11 | 0.33 | 1.51 | 0.25 | 1.45 | 0.53 | 0.07 | 0.69 | up | no |
| 86 | p | chr1 | - | 185073 | 185970 | MSTRG.18.1 | 1 | 898 | MSTRG.18 | LOC_Os01g01369 | NA | NA | NA | NA | NA | 22.10 | 3.69 | 19.09 | 3.07 | 20.89 | 3.34 | 16.04 | 2.70 | 20.41 | 3.20 | 15.95 | 2.63 | 1.13 | 0.18 | 0.17 | 0.74 | up | no |
| 87 | j | chr1 | - | 186138 | 190825 | MSTRG.19.1 | 5 | 1550 | MSTRG.19 | LOC_Os01g01369 | NA | NA | NA | NA | NA | 0 | 0 | 33.76 | 5.43 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.76 | 0.81 | 0.47 | 0.78 | up | no |
| 88 | j | chr1 | - | 186240 | 188981 | MSTRG.19.2 | 2 | 2082 | MSTRG.19 | LOC_Os01g01369 | NA | NA | NA | NA | NA | 0 | 0 | 7.54 | 1.21 | 11.07 | 1.77 | 2.03 | 0.34 | 8.64 | 1.35 | 10.81 | 1.78 | 0.89 | -0.16 | 0.82 | 0.93 | down | no |
| 89 | 0 | chr1 | - | 186246 | 190846 | LOC_Os01g01369.1 | 4 | 1545 | MSTRG.19 | LOC_Os01g01369 | GO:0000247(C-8 sterol isomerase activity);GO:0005789(endoplasmic reticulum membrane);GO:0005886(plasma membrane);GO:0016021(integral component of membrane);GO:0016126(sterol biosynthetic process);GO:0047750(cholestenol delta-isomerase activity) | 00100(Steroid biosynthesis) | K01824 | EC:5.3.3.5 | 3-beta-hydroxysteroid-Delta-isomerase, putative, expressed | 91.03 | 15.22 | 36.37 | 5.85 | 42.98 | 6.87 | 73.81 | 12.43 | 93.17 | 14.59 | 74.09 | 12.20 | 0.66 | -0.59 | 0.26 | 0.78 | down | no |
| 90 | 0 | chr1 | + | 191036 | 196287 | LOC_Os01g01380.1 | 6 | 3482 | MSTRG.20 | LOC_Os01g01380 | NA | NA | NA | NA | expressed protein | 2.60 | 0.44 | 4.12 | 0.66 | 5.40 | 0.86 | 3.89 | 0.65 | 4.22 | 0.66 | 4.75 | 0.78 | 0.98 | -0.03 | 0.80 | 0.93 | down | no |
| 91 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.1 | 4 | 2142 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 108.42 | 18.13 | 97.44 | 15.67 | 113.94 | 18.23 | 89.89 | 15.14 | 104.37 | 16.34 | 50.39 | 8.29 | 1.36 | 0.45 | 0.24 | 0.77 | up | no |
| 92 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.2 | 5 | 2175 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 0 | 0 | 0 | 0 | 9.65 | 1.54 | 0.06 | 0.01 | 0.09 | 0.01 | 0 | 0 | 1.44 | 0.53 | 0.21 | 0.74 | up | no |
| 93 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.3 | 5 | 2182 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 42.82 | 7.16 | 15.40 | 2.48 | 30.64 | 4.90 | 11.58 | 1.95 | 0.30 | 0.05 | 24.89 | 4.10 | 2.21 | 1.14 | 0.29 | 0.78 | up | no |
| 94 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.4 | 4 | 2261 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 0 | 0 | 8.73 | 1.40 | 17.49 | 2.80 | 0 | 0 | 9.01 | 1.41 | 12.36 | 2.03 | 1.08 | 0.12 | 0.90 | 0.97 | up | no |
| 95 | 0 | chr1 | + | 197647 | 200803 | LOC_Os01g01390.5 | 3 | 1054 | MSTRG.23 | LOC_Os01g01390 | GO:0003674(molecular_function);GO:0005634(nucleus);GO:0005886(plasma membrane);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 7.34 | 1.23 | 8.10 | 1.30 | 6.46 | 1.03 | 1.90 | 0.32 | 2.86 | 0.45 | 7.62 | 1.25 | 1.31 | 0.38 | 0.18 | 0.74 | up | no |
| 96 | 0 | chr1 | + | 201944 | 206743 | LOC_Os01g01400.1 | 12 | 2735 | MSTRG.26 | LOC_Os01g01400 | GO:0003674(molecular_function);GO:0005575(cellular_component);GO:0008150(biological_process) | NA | NA | NA | expressed protein | 3.96 | 0.66 | 3.52 | 0.57 | 9.87 | 1.58 | 5.80 | 0.98 | 2.41 | 0.38 | 2.18 | 0.36 | 1.28 | 0.36 | 0.01 | 0.43 | up | no |
| 97 | 0 | chr1 | - | 205710 | 209606 | LOC_Os01g01410.1 | 4 | 2489 | MSTRG.27 | LOC_Os01g01410 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane) | 04626(Plant-pathogen interaction) | K13430 | EC:2.7.11.1 | TKL_IRAK_C-LEC.1 - TKL_IRAK_C-LEC has homology to C-type lectin receptors, expressed | 73.23 | 12.24 | 57.94 | 9.32 | 77.44 | 12.39 | 23.48 | 3.95 | 76.59 | 11.99 | 24.12 | 3.97 | 1.77 | 0.82 | 0.23 | 0.76 | up | no |
| 98 | 0 | chr1 | - | 205710 | 209606 | LOC_Os01g01410.2 | 4 | 2486 | MSTRG.27 | LOC_Os01g01410 | GO:0004674(protein serine/threonine kinase activity);GO:0005886(plasma membrane) | 04626(Plant-pathogen interaction) | K13430 | EC:2.7.11.1 | TKL_IRAK_C-LEC.1 - TKL_IRAK_C-LEC has homology to C-type lectin receptors, expressed | 38.37 | 6.42 | 43.93 | 7.06 | 65.82 | 10.53 | 20.30 | 3.42 | 32.01 | 5.01 | 16.47 | 2.71 | 1.97 | 0.98 | 0.04 | 0.62 | up | no |
| 99 | j | chr1 | - | 205711 | 209582 | MSTRG.27.4 | 4 | 2528 | MSTRG.27 | LOC_Os01g01410 | NA | NA | NA | NA | NA | 0 | 0 | 1.09 | 0.18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1.05 | 0.07 | 0.47 | 0.78 | up | no |
| 100 | j | chr1 | - | 205711 | 209600 | MSTRG.27.3 | 3 | 2613 | MSTRG.27 | LOC_Os01g01410 | NA | NA | NA | NA | NA | 20.57 | 3.44 | 16.78 | 2.70 | 5.00 | 0.80 | 12.10 | 2.04 | 7.54 | 1.18 | 7.39 | 1.22 | 1.22 | 0.28 | 0.56 | 0.82 | up | no |
| 101 | j | chr1 | + | 209677 | 214224 | MSTRG.28.1 | 7 | 2891 | MSTRG.28 | LOC_Os01g01420 | NA | NA | NA | NA | NA | 3.11 | 0.52 | 6.93 | 1.11 | 25.93 | 4.15 | 43.78 | 7.37 | 10.71 | 1.68 | 26.69 | 4.39 | 0.58 | -0.80 | 0.17 | 0.74 | down | no |
| 102 | 0 | chr1 | + | 209771 | 214188 | LOC_Os01g01420.1 | 8 | 1657 | MSTRG.28 | LOC_Os01g01420 | GO:0005720(nuclear heterochromatin);GO:0010216(maintenance of DNA methylation);GO:0016567(protein ubiquitination);GO:0061630(ubiquitin protein ligase activity);GO:0090308(regulation of methylation-dependent chromatin silencing) | NA | NA | NA | expressed protein | 93.44 | 15.62 | 120.54 | 19.38 | 124.92 | 19.98 | 11.44 | 1.93 | 64.71 | 10.13 | 90.26 | 14.86 | 2.22 | 1.15 | 0.21 | 0.74 | up | no |
| 103 | 0 | chr1 | + | 209771 | 214188 | LOC_Os01g01420.3 | 8 | 1653 | MSTRG.28 | LOC_Os01g01420 | GO:0005720(nuclear heterochromatin);GO:0010216(maintenance of DNA methylation);GO:0016567(protein ubiquitination);GO:0061630(ubiquitin protein ligase activity);GO:0090308(regulation of methylation-dependent chromatin silencing) | NA | NA | NA | expressed protein | 14.21 | 2.38 | 12.21 | 1.96 | 35.67 | 5.71 | 13.57 | 2.28 | 22.60 | 3.54 | 43.15 | 7.10 | 0.83 | -0.27 | 0.69 | 0.88 | down | no |
| 104 | 0 | chr1 | + | 209903 | 214229 | LOC_Os01g01420.2 | 7 | 1913 | MSTRG.28 | LOC_Os01g01420 | GO:0005720(nuclear heterochromatin);GO:0010216(maintenance of DNA methylation);GO:0016567(protein ubiquitination);GO:0061630(ubiquitin protein ligase activity);GO:0090308(regulation of methylation-dependent chromatin silencing) | NA | NA | NA | expressed protein | 14.53 | 2.43 | 8.24 | 1.33 | 40.57 | 6.49 | 115.14 | 19.39 | 28.40 | 4.45 | 30.23 | 4.98 | 0.51 | -0.96 | 0.07 | 0.68 | down | no |
| 105 | 0 | chr1 | + | 216126 | 217664 | LOC_Os01g01430.1 | 2 | 1425 | MSTRG.24 | LOC_Os01g01430 | GO:0003700(transcription factor activity, sequence-specific DNA binding);GO:0005634(nucleus);GO:0006351(transcription, DNA-templated);GO:0006355(regulation of transcription, DNA-templated);GO:0007275(multicellular organism development);GO:0009753(response to jasmonic acid);GO:0044212(transcription regulatory region DNA binding);GO:0045995(regulation of embryonic development);GO:0048317(seed morphogenesis);GO:0080060(integument development) | 00561(Glycerolipid metabolism) | K01054 | EC:3.1.1.23 | No apical meristem protein, putative, expressed | 0.21 | 0.03 | 0 | 0 | 0 | 0 | 7.36 | 1.24 | 0 | 0 | 0.83 | 0.14 | 0.77 | -0.38 | 0.35 | 0.78 | down | no |
document location:
summary/5_differential_expression/*VS*/Gene_differential_expression.xlsx
summary/5_differential_expression/*VS*/Transcript_differential_expression.xlsx
document location:
summary/5_differential_expression/*VS*/*_Genes_volcano.png
summary/5_differential_expression/*VS*/*_Transcript_volcano.png
Heatmap is a graphical representation of data where the individual z values (repeated) or Log10 (non-repeated) contained in a matrix are represented as color scheme. Calculation formula of z value is shown below. Sample-i means expression level (fpkm value).
document location:
summary/5_differential_expression/*VS*/*_genes_heatmap.png
summary/5_differential_expression/*VS*/*_transcripts_heatmap.png
Gene ontology (GO) (http://www.geneontology.org) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis.
GO is part of a larger classification effort, the Open Biomedical Ontologies (OBO).
Although gene nomenclature itself aims to maintain and develop controlled vocabulary of gene and gene products, the Gene Ontology extends the effort by using markup language to make the data (not only of the genes and their products but also of all their attributes) machine readable, and to do so in a way that is unified across all species (whereas gene nomenclature conventions vary by biologic taxon).
Significant GO terms were calculated by Hypergeometric equation as shown below. TB gene number=number of total genes; TS gene number=number of differentially expressed genes in total genes; B gene number=total number of gene in all GO terms; S gene number=number of differentially expressed genes in this GO term. Those GO terms with p value<0.05 were defined as significant GO terms.
Significant GO terms::
| GO_ID | GO_Term | GO_function | GO_class | Genes | S gene number | TS gene number | B gene number | TB gene number | pvalue |
| GO:0003677 | DNA binding | molecular_function | 6 | LOC_Os01g11550;LOC_Os01g14720;LOC_Os01g36390;LOC_Os01g43230;LOC_Os01g44390;LOC_Os01g45090;LOC_Os01g64360;LOC_Os02g34970;LOC_Os02g49986;LOC_Os02g58440;LOC_Os03g03260;LOC_Os03g09170;LOC_Os03g20090;LOC_Os03g20900;LOC_Os03g53190;LOC_Os03g57260;LOC_Os03g60080;LOC_Os04g32590;LOC_Os04g34970;LOC_Os04g45330;LOC_Os05g02420;LOC_Os05g23700;LOC_Os05g32070;LOC_Os06g03670;LOC_Os06g22030;LOC_Os06g46560;LOC_Os08g33150;LOC_Os09g04440;LOC_Os09g28200;LOC_Os10g39150;LOC_Os11g03420;LOC_Os12g06200;LOC_Os12g29330;LOC_Os12g34510;LOC_Os12g37400 | 35 | 298 | 977 | 17883 | 0.00 |
| GO:0006268 | DNA unwinding involved in DNA replication | biological_process | 11 | LOC_Os01g36390;LOC_Os11g29380;LOC_Os12g37400 | 3 | 298 | 7 | 17883 | 0.00 |
| GO:0015979 | photosynthesis | biological_process | 5 | LOC_Os01g14410;LOC_Os01g41710;LOC_Os03g31750;LOC_Os04g59440;LOC_Os07g05365;LOC_Os07g05480 | 6 | 298 | 55 | 17883 | 0.00 |
| GO:0016168 | chlorophyll binding | molecular_function | 6 | LOC_Os01g14410;LOC_Os01g41710;LOC_Os04g59440;LOC_Os07g05480 | 4 | 298 | 23 | 17883 | 0.00 |
| GO:0009534 | chloroplast thylakoid | cellular_component | 12 | LOC_Os01g02880;LOC_Os01g31690;LOC_Os03g49720;LOC_Os04g59440;LOC_Os07g05365;LOC_Os07g05480;LOC_Os10g39150 | 7 | 298 | 89 | 17883 | 0.00 |
| GO:0010025 | wax biosynthetic process | biological_process | 5 | LOC_Os02g56920;LOC_Os03g14170;LOC_Os10g33250 | 3 | 298 | 12 | 17883 | 0.00 |
| GO:0015140 | malate transmembrane transporter activity | molecular_function | 10 | LOC_Os02g45150;LOC_Os04g34010;LOC_Os10g42180 | 3 | 298 | 12 | 17883 | 0.00 |
| GO:0043068 | positive regulation of programmed cell death | biological_process | 8 | LOC_Os02g07430;LOC_Os05g41670;LOC_Os06g46560 | 3 | 298 | 13 | 17883 | 0.00 |
| GO:0008094 | DNA-dependent ATPase activity | molecular_function | 11 | LOC_Os01g36390;LOC_Os12g31370;LOC_Os12g37400 | 3 | 298 | 14 | 17883 | 0.00 |
| GO:0009523 | photosystem II | cellular_component | 10 | LOC_Os01g14410;LOC_Os04g59440;LOC_Os07g05365 | 3 | 298 | 14 | 17883 | 0.00 |
| GO:0008453 | alanine-glyoxylate transaminase activity | molecular_function | 7 | LOC_Os03g21960;LOC_Os08g39300 | 2 | 298 | 4 | 17883 | 0.00 |
| GO:0042555 | MCM complex | cellular_component | 5 | LOC_Os01g36390;LOC_Os12g37400 | 2 | 298 | 4 | 17883 | 0.00 |
| GO:0007049 | cell cycle | biological_process | 5 | LOC_Os01g36390;LOC_Os09g02360;LOC_Os09g21450;LOC_Os12g06200;LOC_Os12g37400 | 5 | 298 | 57 | 17883 | 0.00 |
| GO:0043668 | exine | cellular_component | 6 | LOC_Os02g56920;LOC_Os10g33250 | 2 | 298 | 5 | 17883 | 0.00 |
| GO:0009737 | response to abscisic acid | biological_process | 6 | LOC_Os03g01320;LOC_Os03g20090;LOC_Os03g58790;LOC_Os04g34970;LOC_Os04g39110;LOC_Os04g43200;LOC_Os08g33150;LOC_Os09g25390;LOC_Os10g39150;LOC_Os11g06980;LOC_Os12g29330 | 11 | 298 | 251 | 17883 | 0.00 |
| GO:0010287 | plastoglobule | cellular_component | 13 | LOC_Os01g02880;LOC_Os01g31690;LOC_Os01g41710;LOC_Os03g49720 | 4 | 298 | 38 | 17883 | 0.00 |
| GO:0009651 | response to salt stress | biological_process | 6 | LOC_Os02g02870;LOC_Os03g01320;LOC_Os03g09170;LOC_Os03g20090;LOC_Os04g39110;LOC_Os04g40600;LOC_Os04g43200;LOC_Os06g08080;LOC_Os07g01020;LOC_Os11g06980;LOC_Os12g29330 | 11 | 298 | 256 | 17883 | 0.00 |
| GO:0000347 | THO complex | cellular_component | 11 | LOC_Os01g36390;LOC_Os12g37400 | 2 | 298 | 7 | 17883 | 0.01 |
| GO:0010207 | photosystem II assembly | biological_process | 7 | LOC_Os01g31690;LOC_Os06g24540 | 2 | 298 | 8 | 17883 | 0.01 |
| GO:0042127 | regulation of cell proliferation | biological_process | 5 | LOC_Os04g43300;LOC_Os09g02360 | 2 | 298 | 8 | 17883 | 0.01 |
| GO:0009522 | photosystem I | cellular_component | 10 | LOC_Os01g14410;LOC_Os07g05480 | 2 | 298 | 8 | 17883 | 0.01 |
| GO:0003727 | single-stranded RNA binding | molecular_function | 7 | LOC_Os02g02510;LOC_Os03g19560 | 2 | 298 | 8 | 17883 | 0.01 |
| GO:0009535 | chloroplast thylakoid membrane | cellular_component | 13 | LOC_Os01g14410;LOC_Os01g31690;LOC_Os01g41710;LOC_Os03g49720;LOC_Os04g59440;LOC_Os07g05365;LOC_Os07g05480;LOC_Os07g30670;LOC_Os10g39150 | 9 | 298 | 204 | 17883 | 0.01 |
| GO:0048653 | anther development | biological_process | 7 | LOC_Os02g30850;LOC_Os02g56920;LOC_Os10g33250 | 3 | 298 | 26 | 17883 | 0.01 |
| GO:0031072 | heat shock protein binding | molecular_function | 5 | LOC_Os02g30320;LOC_Os05g01530 | 2 | 298 | 9 | 17883 | 0.01 |
| GO:0009705 | plant-type vacuole membrane | cellular_component | 11 | LOC_Os02g45150;LOC_Os04g34010;LOC_Os06g08080;LOC_Os10g39220;LOC_Os10g42180 | 5 | 298 | 78 | 17883 | 0.01 |
| GO:0006270 | DNA replication initiation | biological_process | 11 | LOC_Os01g36390;LOC_Os12g37400 | 2 | 298 | 10 | 17883 | 0.01 |
| GO:0009269 | response to desiccation | biological_process | 6 | LOC_Os04g43200;LOC_Os11g06980 | 2 | 298 | 11 | 17883 | 0.01 |
| GO:0006351 | transcription, DNA-templated | biological_process | 10 | LOC_Os01g11550;LOC_Os01g43230;LOC_Os01g44390;LOC_Os01g45090;LOC_Os01g64360;LOC_Os02g34970;LOC_Os03g03260;LOC_Os03g09170;LOC_Os03g20090;LOC_Os03g20900;LOC_Os03g60080;LOC_Os04g32590;LOC_Os04g34970;LOC_Os05g02420;LOC_Os05g48650;LOC_Os05g49100;LOC_Os06g03670;LOC_Os06g22030;LOC_Os09g28200;LOC_Os11g03420;LOC_Os12g06200;LOC_Os12g29330;LOC_Os12g37400 | 23 | 298 | 850 | 17883 | 0.02 |
| GO:0009773 | photosynthetic electron transport in photosystem I | biological_process | 8 | LOC_Os07g30670;LOC_Os10g39150 | 2 | 298 | 12 | 17883 | 0.02 |
| GO:0003700 | transcription factor activity, sequence-specific DNA binding | molecular_function | 4 | LOC_Os01g02100;LOC_Os01g11550;LOC_Os01g44390;LOC_Os01g45090;LOC_Os01g64360;LOC_Os01g66290;LOC_Os02g34970;LOC_Os02g49986;LOC_Os03g03260;LOC_Os03g09170;LOC_Os03g20090;LOC_Os03g20900;LOC_Os03g41390;LOC_Os04g32590;LOC_Os04g34970;LOC_Os04g45330;LOC_Os05g02420;LOC_Os05g32070;LOC_Os05g49100;LOC_Os06g03670;LOC_Os06g46560;LOC_Os08g33150;LOC_Os09g28200;LOC_Os12g06200;LOC_Os12g29330 | 25 | 298 | 951 | 17883 | 0.02 |
| GO:0009607 | response to biotic stimulus | biological_process | 4 | LOC_Os04g39150 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0050281 | serine-glyoxylate transaminase activity | molecular_function | 7 | LOC_Os08g39300 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0004558 | alpha-1,4-glucosidase activity | molecular_function | 9 | LOC_Os01g16310 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0035304 | regulation of protein dephosphorylation | biological_process | 9 | LOC_Os01g31690 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0032450 | maltose alpha-glucosidase activity | molecular_function | 9 | LOC_Os01g16310 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0046498 | S-adenosylhomocysteine metabolic process | biological_process | 11 | LOC_Os03g55330 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0046906 | tetrapyrrole binding | molecular_function | 5 | LOC_Os11g16550 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0046521 | sphingoid catabolic process | biological_process | 8 | LOC_Os10g26700 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0006271 | DNA strand elongation involved in DNA replication | biological_process | 11 | LOC_Os01g10690 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0046922 | peptide-O-fucosyltransferase activity | molecular_function | 8 | LOC_Os07g38490 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:1901918 | negative regulation of exoribonuclease activity | biological_process | 12 | LOC_Os03g19560 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0045860 | positive regulation of protein kinase activity | biological_process | 11 | LOC_Os08g02340 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:1900033 | negative regulation of trichome patterning | biological_process | 10 | LOC_Os01g43230 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0010466 | negative regulation of peptidase activity | biological_process | 10 | LOC_Os04g22220 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0008618 | 7-methylguanosine metabolic process | biological_process | 12 | LOC_Os03g53530 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0005658 | alpha DNA polymerase:primase complex | cellular_component | 13 | LOC_Os01g64820 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0042493 | response to drug | biological_process | 5 | LOC_Os08g39550 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0050306 | sucrose 1F-fructosyltransferase activity | molecular_function | 8 | LOC_Os02g01590 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0010242 | oxygen evolving activity | molecular_function | 5 | LOC_Os01g31690 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0009173 | pyrimidine ribonucleoside monophosphate metabolic process | biological_process | 11 | LOC_Os06g02000 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0030054 | cell junction | cellular_component | 3 | LOC_Os05g30010 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0051446 | positive regulation of meiotic cell cycle | biological_process | 6 | LOC_Os12g06200 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0004760 | serine-pyruvate transaminase activity | molecular_function | 7 | LOC_Os08g39300 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0048629 | trichome patterning | biological_process | 8 | LOC_Os01g43230 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0042549 | photosystem II stabilization | biological_process | 8 | LOC_Os01g31690 | 1 | 298 | 1 | 17883 | 0.02 |
| GO:0033609 | oxalate metabolic process | biological_process | 9 | LOC_Os08g08970;LOC_Os08g08980;LOC_Os08g13440 | 3 | 298 | 33 | 17883 | 0.02 |
| GO:0046564 | oxalate decarboxylase activity | molecular_function | 7 | LOC_Os08g08970;LOC_Os08g08980;LOC_Os08g13440 | 3 | 298 | 33 | 17883 | 0.02 |
| GO:2000652 | regulation of secondary cell wall biogenesis | biological_process | 8 | LOC_Os02g49986;LOC_Os08g33150 | 2 | 298 | 13 | 17883 | 0.02 |
| GO:0000790 | nuclear chromatin | cellular_component | 13 | LOC_Os03g53190;LOC_Os12g34510 | 2 | 298 | 13 | 17883 | 0.02 |
| GO:0009579 | thylakoid | cellular_component | 7 | LOC_Os01g31690;LOC_Os04g59440;LOC_Os07g05365;LOC_Os07g05480;LOC_Os10g39150 | 5 | 298 | 93 | 17883 | 0.02 |
| GO:0022625 | cytosolic large ribosomal subunit | cellular_component | 11 | LOC_Os01g51020;LOC_Os02g32760;LOC_Os02g47140;LOC_Os07g33997;LOC_Os08g02340;LOC_Os09g32520 | 6 | 298 | 129 | 17883 | 0.02 |
| GO:0009654 | photosystem II oxygen evolving complex | cellular_component | 10 | LOC_Os01g31690;LOC_Os07g05365 | 2 | 298 | 14 | 17883 | 0.02 |
| GO:0003697 | single-stranded DNA binding | molecular_function | 8 | LOC_Os02g02510;LOC_Os02g02870;LOC_Os12g31370 | 3 | 298 | 37 | 17883 | 0.02 |
| GO:0006355 | regulation of transcription, DNA-templated | biological_process | 11 | LOC_Os01g11550;LOC_Os01g14720;LOC_Os01g44390;LOC_Os01g45090;LOC_Os01g64360;LOC_Os02g02870;LOC_Os02g34970;LOC_Os02g49986;LOC_Os03g03260;LOC_Os03g09170;LOC_Os03g20090;LOC_Os03g20900;LOC_Os03g60080;LOC_Os04g32590;LOC_Os04g34970;LOC_Os05g02420;LOC_Os05g23700;LOC_Os05g49100;LOC_Os06g03670;LOC_Os06g05890;LOC_Os06g22030;LOC_Os06g39680;LOC_Os06g46560;LOC_Os08g33150;LOC_Os09g28200;LOC_Os11g03420;LOC_Os12g06200;LOC_Os12g37400 | 28 | 298 | 1132 | 17883 | 0.02 |
| GO:0010427 | abscisic acid binding | molecular_function | 6 | LOC_Os02g15640;LOC_Os08g28670 | 2 | 298 | 15 | 17883 | 0.03 |
| GO:0080163 | regulation of protein serine/threonine phosphatase activity | biological_process | 11 | LOC_Os02g15640;LOC_Os08g28670 | 2 | 298 | 15 | 17883 | 0.03 |
| GO:0070180 | large ribosomal subunit rRNA binding | molecular_function | 8 | LOC_Os02g32760;LOC_Os08g02340 | 2 | 298 | 15 | 17883 | 0.03 |
| GO:0048481 | plant ovule development | biological_process | 8 | LOC_Os01g66290;LOC_Os03g03260 | 2 | 298 | 16 | 17883 | 0.03 |
| GO:0004864 | protein phosphatase inhibitor activity | molecular_function | 6 | LOC_Os02g15640;LOC_Os08g28670 | 2 | 298 | 16 | 17883 | 0.03 |
| GO:0009620 | response to fungus | biological_process | 7 | LOC_Os03g20090;LOC_Os03g60080;LOC_Os04g43200 | 3 | 298 | 41 | 17883 | 0.03 |
| GO:0005509 | calcium ion binding | molecular_function | 7 | LOC_Os01g31690;LOC_Os02g55880;LOC_Os04g43200;LOC_Os05g31620;LOC_Os09g25390;LOC_Os09g31040 | 6 | 298 | 141 | 17883 | 0.03 |
| GO:0048283 | indeterminate inflorescence morphogenesis | biological_process | 6 | LOC_Os01g66290 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0003917 | DNA topoisomerase type I activity | molecular_function | 6 | LOC_Os03g57260 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0006272 | leading strand elongation | biological_process | 12 | LOC_Os01g64820 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0031407 | oxylipin metabolic process | biological_process | 10 | LOC_Os04g43200 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0031990 | mRNA export from nucleus in response to heat stress | biological_process | 8 | LOC_Os02g02510 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0007051 | spindle organization | biological_process | 7 | LOC_Os05g28290 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0050242 | pyruvate, phosphate dikinase activity | molecular_function | 7 | LOC_Os03g31750 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0046500 | S-adenosylmethionine metabolic process | biological_process | 11 | LOC_Os03g55330 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0006090 | pyruvate metabolic process | biological_process | 9 | LOC_Os03g31750 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0051782 | negative regulation of cell division | biological_process | 7 | LOC_Os08g42600 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0030295 | protein kinase activator activity | molecular_function | 6 | LOC_Os08g02340 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0051091 | positive regulation of sequence-specific DNA binding transcription factor activity | biological_process | 13 | LOC_Os01g59410 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0070131 | positive regulation of mitochondrial translation | biological_process | 10 | LOC_Os05g01330 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0015099 | nickel cation transmembrane transporter activity | molecular_function | 11 | LOC_Os03g06090 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0071614 | linoleic acid epoxygenase activity | molecular_function | 6 | LOC_Os04g43200 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0004127 | cytidylate kinase activity | molecular_function | 9 | LOC_Os06g02000 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0032578 | aleurone grain membrane | cellular_component | 12 | LOC_Os03g26820 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0009517 | PSII associated light-harvesting complex II | cellular_component | 13 | LOC_Os04g59440 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0046604 | positive regulation of mitotic centrosome separation | biological_process | 12 | LOC_Os05g28290 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0034402 | recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex | biological_process | 12 | LOC_Os02g02510 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0009041 | uridylate kinase activity | molecular_function | 9 | LOC_Os06g02000 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0015675 | nickel cation transport | biological_process | 9 | LOC_Os03g06090 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0051738 | xanthophyll binding | molecular_function | 6 | LOC_Os04g59440 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0000082 | G1/S transition of mitotic cell cycle | biological_process | 8 | LOC_Os05g28290 | 1 | 298 | 2 | 17883 | 0.03 |
| GO:0010114 | response to red light | biological_process | 8 | LOC_Os01g44390;LOC_Os03g19560 | 2 | 298 | 18 | 17883 | 0.04 |
| GO:0009409 | response to cold | biological_process | 5 | LOC_Os01g14410;LOC_Os02g02870;LOC_Os03g01320;LOC_Os03g09170;LOC_Os03g14170;LOC_Os04g43200;LOC_Os06g03670 | 7 | 298 | 185 | 17883 | 0.04 |
| GO:0031969 | chloroplast membrane | cellular_component | 13 | LOC_Os03g19560;LOC_Os04g43200;LOC_Os11g16550 | 3 | 298 | 44 | 17883 | 0.04 |
document location: summary/5_differential_expression/*VS*/1_GO_Enrichment/*VS*_GO_enrichment_Gene.xlsx
Barplot of enriched GO terms:
document location: summary/5_differential_expression/*VS*/1_GO_Enrichment/*VS*_GO_enrichment.png
Scatterplot of enriched GO terms:
Number of differentially expressed genes enriched in GO terms, p value and rich factor are shown in scatterplot. Rich factor=(number of differentially expressed genes in GO term)/(total number of genes in GO term). The larger rich factor is, the higher enrichment is.
document location: summary/5_differential_expression/*VS*/1_GO_Enrichment/*VS*_GO_enrichment_scatterplot.png
KEGG (Kyoto Encyclopedia of Genes and Genomes) (http://www.kegg.jp/) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
Significant KEGG pathways were calculated by Hypergeometric equation as shown below. TB gene number=number of total genes; TS gene number=number of differentially expressed genes in total genes; B gene number=total number of genes in KEGG pathways; S gene number=number of differentially expressed genes in this KEGG pathway. Those KEGG pathways with p value<0.05 were defined as significant KEGG pathways.
Significant KEGG pathways::
| pathway_id | pathway_name | Genes | S gene number | TS gene number | B gene number | TB gene number | pvalue |
| ko03030 | DNA replication | LOC_Os01g10690;LOC_Os01g36390;LOC_Os01g64820;LOC_Os02g58220;LOC_Os03g57260;LOC_Os03g63870;LOC_Os11g29380;LOC_Os12g37400 | 8 | 162 | 101 | 9820 | 0.00 |
| ko03010 | Ribosome | LOC_Os01g08470;LOC_Os01g51020;LOC_Os01g73160;LOC_Os02g01540;LOC_Os02g32760;LOC_Os02g47140;LOC_Os03g01320;LOC_Os03g07290;LOC_Os03g59720;LOC_Os05g39960;LOC_Os07g33997;LOC_Os08g02340;LOC_Os09g32520 | 13 | 162 | 387 | 9820 | 0.01 |
| ko03060 | Protein export | LOC_Os02g54060;LOC_Os05g43540;LOC_Os10g37690;LOC_Os11g01300 | 4 | 162 | 67 | 9820 | 0.02 |
| ko00603 | Glycosphingolipid biosynthesis - globo series | LOC_Os10g35070;LOC_Os12g05550 | 2 | 162 | 17 | 9820 | 0.03 |
| ko00195 | Photosynthesis | LOC_Os01g31690;LOC_Os04g59440;LOC_Os07g05365;LOC_Os07g05480 | 4 | 162 | 74 | 9820 | 0.03 |
| ko00073 | Cutin, suberine and wax biosynthesis | LOC_Os01g42870;LOC_Os02g56920;LOC_Os04g43200;LOC_Os10g33250 | 4 | 162 | 75 | 9820 | 0.04 |
| ko03440 | Homologous recombination | LOC_Os01g10690;LOC_Os02g58220;LOC_Os03g57260;LOC_Os03g63870;LOC_Os12g31370 | 5 | 162 | 121 | 9820 | 0.05 |
| ko03430 | Mismatch repair | LOC_Os01g10690;LOC_Os02g58220;LOC_Os03g57260;LOC_Os03g63870 | 4 | 162 | 84 | 9820 | 0.05 |
| ko00280 | Valine, leucine and isoleucine degradation | LOC_Os03g10620;LOC_Os03g21960;LOC_Os06g50380 | 3 | 162 | 52 | 9820 | 0.05 |
| ko00040 | Pentose and glucuronate interconversions | LOC_Os01g44390;LOC_Os05g37060;LOC_Os06g01760;LOC_Os06g50380;LOC_Os08g12410;LOC_Os11g08750 | 6 | 162 | 165 | 9820 | 0.06 |
| ko00943 | Isoflavonoid biosynthesis | LOC_Os08g37040;LOC_Os09g28690 | 2 | 162 | 27 | 9820 | 0.07 |
| ko00750 | Vitamin B6 metabolism | LOC_Os02g13290;LOC_Os07g01020 | 2 | 162 | 38 | 9820 | 0.13 |
| ko00966 | Glucosinolate biosynthesis | LOC_Os04g08828;LOC_Os04g09430 | 2 | 162 | 40 | 9820 | 0.14 |
| ko00904 | Diterpenoid biosynthesis | LOC_Os05g48700;LOC_Os07g46852;LOC_Os09g07450 | 3 | 162 | 80 | 9820 | 0.15 |
| ko00860 | Porphyrin and chlorophyll metabolism | LOC_Os01g10930;LOC_Os02g49986;LOC_Os03g58790;LOC_Os08g33150 | 4 | 162 | 123 | 9820 | 0.15 |
| ko00250 | Alanine, aspartate and glutamate metabolism | LOC_Os03g21960;LOC_Os08g39300 | 2 | 162 | 42 | 9820 | 0.15 |
| ko00460 | Cyanoamino acid metabolism | LOC_Os04g08828;LOC_Os04g09430;LOC_Os04g32540;LOC_Os11g31980 | 4 | 162 | 127 | 9820 | 0.16 |
| ko00196 | Photosynthesis - antenna proteins | LOC_Os01g41710 | 1 | 162 | 11 | 9820 | 0.17 |
| ko00240 | Pyrimidine metabolism | LOC_Os01g10690;LOC_Os01g64820;LOC_Os02g02510;LOC_Os03g56310;LOC_Os06g02000 | 5 | 162 | 180 | 9820 | 0.18 |
| ko00510 | N-Glycan biosynthesis | LOC_Os01g16310;LOC_Os01g57840 | 2 | 162 | 49 | 9820 | 0.19 |
| ko03013 | RNA transport | LOC_Os01g03490;LOC_Os01g66290;LOC_Os02g02870;LOC_Os03g14030;LOC_Os03g20900;LOC_Os04g42140;LOC_Os05g28510;LOC_Os09g04440 | 8 | 162 | 345 | 9820 | 0.21 |
| ko00561 | Glycerolipid metabolism | LOC_Os02g34970;LOC_Os03g60080;LOC_Os06g50380;LOC_Os10g35070 | 4 | 162 | 150 | 9820 | 0.24 |
| ko00500 | Starch and sucrose metabolism | LOC_Os01g44390;LOC_Os01g71474;LOC_Os02g01590;LOC_Os03g14540;LOC_Os03g28330;LOC_Os03g30000;LOC_Os05g37060;LOC_Os06g01760;LOC_Os07g35480;LOC_Os08g02996;LOC_Os08g12410;LOC_Os11g08750 | 12 | 162 | 586 | 9820 | 0.26 |
| ko03420 | Nucleotide excision repair | LOC_Os01g10690;LOC_Os02g58220;LOC_Os03g57260;LOC_Os03g63870 | 4 | 162 | 169 | 9820 | 0.30 |
| ko00340 | Histidine metabolism | LOC_Os06g50380 | 1 | 162 | 23 | 9820 | 0.32 |
| ko00941 | Flavonoid biosynthesis | LOC_Os07g40986;LOC_Os08g43040;LOC_Os10g40934 | 3 | 162 | 122 | 9820 | 0.33 |
| ko00640 | Propanoate metabolism | LOC_Os03g10620 | 1 | 162 | 26 | 9820 | 0.35 |
| ko00760 | Nicotinate and nicotinamide metabolism | LOC_Os03g56310 | 1 | 162 | 26 | 9820 | 0.35 |
| ko04933 | AGE-RAGE signaling pathway in diabetic complications | LOC_Os02g02840;LOC_Os06g05890 | 2 | 162 | 75 | 9820 | 0.35 |
| ko03015 | mRNA surveillance pathway | LOC_Os01g66290;LOC_Os08g38880;LOC_Os09g04440;LOC_Os09g37790 | 4 | 162 | 183 | 9820 | 0.36 |
| ko00230 | Purine metabolism | LOC_Os01g10690;LOC_Os01g64820;LOC_Os02g02510;LOC_Os03g56310 | 4 | 162 | 188 | 9820 | 0.38 |
| ko00590 | Arachidonic acid metabolism | LOC_Os01g70430 | 1 | 162 | 30 | 9820 | 0.39 |
| ko04145 | Phagosome | LOC_Os02g02840;LOC_Os05g01810;LOC_Os11g01300 | 3 | 162 | 138 | 9820 | 0.40 |
| ko04141 | Protein processing in endoplasmic reticulum | LOC_Os01g16310;LOC_Os01g57840;LOC_Os02g54060;LOC_Os03g63520;LOC_Os04g46390;LOC_Os05g01520;LOC_Os11g01300 | 7 | 162 | 366 | 9820 | 0.40 |
| ko00902 | Monoterpenoid | LOC_Os03g52880 | 1 | 162 | 32 | 9820 | 0.41 |
| ko00052 | Galactose metabolism | LOC_Os02g01590;LOC_Os10g35070 | 2 | 162 | 87 | 9820 | 0.42 |
| ko00410 | beta-Alanine metabolism | LOC_Os03g10620;LOC_Os06g50380 | 2 | 162 | 88 | 9820 | 0.43 |
| ko04075 | Plant hormone signal transduction | LOC_Os02g15640;LOC_Os02g56120;LOC_Os04g22220;LOC_Os04g52000;LOC_Os04g55620;LOC_Os05g51660;LOC_Os06g22919;LOC_Os06g50380;LOC_Os08g41320;LOC_Os09g02360;LOC_Os09g21450;LOC_Os09g37500 | 12 | 162 | 682 | 9820 | 0.45 |
| ko00010 | Glycolysis / Gluconeogenesis | LOC_Os01g02880;LOC_Os05g39310;LOC_Os06g50380 | 3 | 162 | 151 | 9820 | 0.46 |
| ko00604 | Glycosphingolipid biosynthesis - ganglio series | LOC_Os12g05550 | 1 | 162 | 37 | 9820 | 0.46 |
| ko01210 | 2-Oxocarboxylic acid metabolism | LOC_Os04g08828;LOC_Os04g09430 | 2 | 162 | 94 | 9820 | 0.46 |
| ko00620 | Pyruvate metabolism | LOC_Os03g31750;LOC_Os06g50380 | 2 | 162 | 94 | 9820 | 0.46 |
| ko00071 | Fatty acid degradation | LOC_Os06g50380 | 1 | 162 | 38 | 9820 | 0.47 |
| ko00514 | Other types of O-glycan | LOC_Os07g38490 | 1 | 162 | 39 | 9820 | 0.48 |
| ko04931 | Insulin resistance | LOC_Os04g52000;LOC_Os06g50380;LOC_Os12g01140 | 3 | 162 | 158 | 9820 | 0.49 |
| ko00910 | Nitrogen metabolism | LOC_Os08g36630 | 1 | 162 | 42 | 9820 | 0.50 |
| ko00480 | Glutathione metabolism | LOC_Os01g27360;LOC_Os03g04220 | 2 | 162 | 102 | 9820 | 0.50 |
| ko04070 | Phosphatidylinositol signaling system | LOC_Os03g53190;LOC_Os12g34510 | 2 | 162 | 102 | 9820 | 0.50 |
| ko04626 | Plant-pathogen interaction | LOC_Os01g45090;LOC_Os01g53920;LOC_Os03g09170;LOC_Os03g20090;LOC_Os03g20450;LOC_Os03g53190;LOC_Os04g22220;LOC_Os04g34970;LOC_Os05g02420;LOC_Os05g07300;LOC_Os05g31620;LOC_Os05g49100;LOC_Os05g51660;LOC_Os06g46560;LOC_Os07g08750;LOC_Os08g34640;LOC_Os08g39550;LOC_Os09g39930;LOC_Os10g33080;LOC_Os12g34510 | 20 | 162 | 1194 | 9820 | 0.51 |
| ko00920 | Sulfur metabolism | LOC_Os02g55880 | 1 | 162 | 43 | 9820 | 0.51 |
| ko00310 | Lysine degradation | LOC_Os06g50380 | 1 | 162 | 45 | 9820 | 0.53 |
| ko04146 | Peroxisome | LOC_Os08g39300;LOC_Os12g32330 | 2 | 162 | 108 | 9820 | 0.53 |
| ko00100 | Steroid biosynthesis | LOC_Os01g53520 | 1 | 162 | 47 | 9820 | 0.54 |
| ko00563 | Glycosylphosphatidylinositol(GPI)-anchor biosynthesis | LOC_Os01g55110 | 1 | 162 | 48 | 9820 | 0.55 |
| ko00270 | Cysteine and methionine metabolism | LOC_Os03g21960;LOC_Os10g28350 | 2 | 162 | 115 | 9820 | 0.57 |
| ko00710 | Carbon fixation in photosynthetic organisms | LOC_Os01g02880;LOC_Os03g31750 | 2 | 162 | 118 | 9820 | 0.58 |
| ko00260 | Glycine, serine and threonine metabolism | LOC_Os03g21960;LOC_Os08g39300 | 2 | 162 | 118 | 9820 | 0.58 |
| ko00565 | Ether lipid metabolism | LOC_Os09g25390 | 1 | 162 | 53 | 9820 | 0.59 |
| ko00903 | Limonene and pinene | LOC_Os06g50380 | 1 | 162 | 56 | 9820 | 0.61 |
| ko00531 | Glycosaminoglycan degradation | LOC_Os02g44630 | 1 | 162 | 57 | 9820 | 0.61 |
| ko00330 | Arginine and proline metabolism | LOC_Os06g50380 | 1 | 162 | 60 | 9820 | 0.63 |
| ko03040 | Spliceosome | LOC_Os02g04950;LOC_Os03g19560;LOC_Os03g49200;LOC_Os06g50890;LOC_Os07g04150;LOC_Os07g10256 | 6 | 162 | 400 | 9820 | 0.65 |
| ko03050 | Proteasome | LOC_Os08g43640 | 1 | 162 | 73 | 9820 | 0.70 |
| ko03020 | RNA polymerase | LOC_Os02g02510 | 1 | 162 | 73 | 9820 | 0.70 |
| ko00630 | Glyoxylate and dicarboxylate metabolism | LOC_Os08g39300 | 1 | 162 | 76 | 9820 | 0.72 |
| ko00600 | Sphingolipid metabolism | LOC_Os10g35070 | 1 | 162 | 77 | 9820 | 0.72 |
| ko00030 | Pentose phosphate pathway | LOC_Os01g02880 | 1 | 162 | 79 | 9820 | 0.73 |
| ko01200 | Carbon metabolism | LOC_Os01g02880;LOC_Os03g10620;LOC_Os03g31750;LOC_Os08g39300 | 4 | 162 | 314 | 9820 | 0.77 |
| ko04140 | Regulation of autophagy | LOC_Os12g41180 | 1 | 162 | 90 | 9820 | 0.78 |
| ko03410 | Base excision repair | LOC_Os01g10690 | 1 | 162 | 91 | 9820 | 0.78 |
| ko00190 | Oxidative phosphorylation | LOC_Os02g49986;LOC_Os06g08080;LOC_Os08g33150 | 3 | 162 | 249 | 9820 | 0.78 |
| ko00053 | Ascorbate and aldarate metabolism | LOC_Os06g50380 | 1 | 162 | 94 | 9820 | 0.79 |
| ko03018 | RNA degradation | LOC_Os03g40020;LOC_Os04g40600;LOC_Os12g29330 | 3 | 162 | 253 | 9820 | 0.79 |
| ko00592 | alpha-Linolenic acid metabolism | LOC_Os06g13560 | 1 | 162 | 95 | 9820 | 0.80 |
| ko00051 | Fructose and mannose metabolism | LOC_Os01g02880 | 1 | 162 | 99 | 9820 | 0.81 |
| ko00380 | Tryptophan metabolism | LOC_Os06g50380 | 1 | 162 | 105 | 9820 | 0.83 |
| ko00945 | Stilbenoid, diarylheptanoid and gingerol biosynthesis | LOC_Os08g43040 | 1 | 162 | 107 | 9820 | 0.83 |
| ko00940 | Phenylpropanoid biosynthesis | LOC_Os03g25300;LOC_Os04g09654;LOC_Os06g46799;LOC_Os08g43040 | 4 | 162 | 358 | 9820 | 0.85 |
| ko04712 | Circadian rhythm - plant | LOC_Os01g43230 | 1 | 162 | 137 | 9820 | 0.90 |
| ko04144 | Endocytosis | LOC_Os01g68750;LOC_Os02g29140;LOC_Os03g02750;LOC_Os09g25390 | 4 | 162 | 416 | 9820 | 0.92 |
| ko00520 | Amino sugar and nucleotide sugar metabolism | LOC_Os01g04580;LOC_Os03g14540;LOC_Os03g30000 | 3 | 162 | 346 | 9820 | 0.93 |
| ko00564 | Glycerophospholipid metabolism | LOC_Os09g25390 | 1 | 162 | 158 | 9820 | 0.93 |
| ko00062 | Fatty acid elongation | LOC_Os03g14170 | 1 | 162 | 178 | 9820 | 0.95 |
| ko01230 | Biosynthesis of amino acids | LOC_Os01g02880 | 1 | 162 | 306 | 9820 | 0.99 |
document location: summary/5_differential_expression/*VS*/2_KEGG_Enrichment/*VS*_KEGG_enrichment_Gene.xlsx
Scatterplot of enriched KEGG pathways:
Number of differentially expressed genes enriched in KEGG pathway, p value and rich factor are shown in scatterplot. Rich factor=(number of differentially expressed genes in KEGG pathway)/(total number of genes in KEGG pathway). The larger rich factor is, the higher enrichment is.
document location:
summary/5_differential_expression/*VS*/2_KEGG_Enrichment/*VS*_KEGG_enrichment_scatterplot.png
KEGG pathway maps:
Graphical map objects
The KEGG pathway map is a moleculalr interaction/reaction network diagram represented in terms of the KEGG Orthology (KO) groups, so that experimental evidence in specific organisms can be generalized to other organisms through genomic information. Each map is manually drawn with in-house software called KegSketch, which generates the KGML+ file. This file is an SVG file containing graphics objects that are associated with KEGG objects (see KEGG object identifiers). Basic graphics objects in the reference KEGG pathway maps are:
boxes - ortholog (KO) groups identified by K numbers and, in metabolic maps, reactions identified by R numbers as well
circles - other molecules, usually chemical compounds identified by C numbers, but including glycans identified by G numbers
lines - reactions identified by R numbers in metabolic maps; ortholog (KO) groups identified by K numbers in global metabolism maps
and in organism specific pathway maps that are computationally generated:
boxes - genes or gene products identified by the combination of the KEGG organism code and gene identifiers
These map objects can be searched in the search box at the top of the KEGG PATHWAY page, in the search box in each pathway map, and by the KEGG Mapper tools.
Convention of map number prefix
Each pathway map is identified by the combination of 2-4 letter code and 5 digit number (see KEGG Identifiers). The prefix has the following meaning:
map - Reference pathway
ko - Reference pathway (KO)
ec - Reference pathway (EC)
rn - Reference pathway (Reaction)
org - Organism-specific pathway map
Only the first reference pathway map is manually drawn; all other maps are computationally generated. For metabolic pathways, each box (or line) in the reference map is linked to the K number (KO identifeir), the EC number, and the R number (reaction identifier). The KO, EC, and reaction maps are linked to only one of them. For all metabolic and non-metabolic maps, K numbers are converted to gene identifiers in each organism to generate organism-specific pathways.
As shown above, "map" pathways are not colored, "ko/ec/rn" pathways are colored blue, and organism-specific pathways are colored green, where coloring indicates that map objects exist and are linked to corresponding entries. For global metabolism maps, "map" pathways are fully colored, so that "ko/ec/rn" pathways and organism-specific pathways are generated by reducing the coloring indicating the absence of corresponding entries.
In this study, all KEGG pathway maps were deposited in summary/5_differential_expression/*VS*/3_KEGG_Pictures/.
| Sample | SNV | SNV(GeneRegion) | INDEL | INDEL(GeneRegion) |
| Lo7_1 | 51301 | 15315 | 5971 | 825 |
| Lo7_2 | 51834 | 15435 | 6710 | 950 |
| Lo7_3 | 51936 | 15260 | 6512 | 959 |
| Lo8_1 | 50456 | 15620 | 6079 | 925 |
| Lo8_2 | 51053 | 15812 | 6509 | 1045 |
| Lo8_3 | 54012 | 16232 | 6382 | 916 |
document location: summary/6_snp_and_Indel/1_SNV_INDEL_Statistics.xlsx
| Sample(SNV) | intergenic | intronic | exonic | UTR3 | UTR5 | upstream | downstream | splicing | Sample(INDEL) | intergenic | intronic | exonic | UTR3 | UTR5 | upstream | downstream | splicing | |
| Lo7_1 | 7606 | 13162 | 17162 | 4860 | 2462 | 2605 | 3174 | 270 | Lo7_1 | 631 | 1754 | 957 | 1014 | 834 | 351 | 422 | 8 | |
| Lo7_2 | 7862 | 12961 | 17311 | 4881 | 2440 | 2814 | 3270 | 295 | Lo7_2 | 702 | 2029 | 1104 | 1016 | 898 | 457 | 495 | 9 | |
| Lo7_3 | 7705 | 13339 | 17107 | 4932 | 2397 | 2841 | 3328 | 287 | Lo7_3 | 716 | 1913 | 1105 | 1032 | 842 | 415 | 472 | 17 | |
| Lo8_1 | 7458 | 11991 | 17473 | 4881 | 2502 | 2601 | 3262 | 288 | Lo8_1 | 651 | 1620 | 1055 | 984 | 913 | 390 | 456 | 10 | |
| Lo8_2 | 7689 | 11806 | 17720 | 4909 | 2585 | 2827 | 3252 | 265 | Lo8_2 | 706 | 1745 | 1181 | 1036 | 928 | 426 | 472 | 15 | |
| Lo8_3 | 8123 | 13431 | 18107 | 5026 | 2645 | 2932 | 3469 | 279 | Lo8_3 | 704 | 1775 | 1064 | 1025 | 909 | 412 | 479 | 14 |
document location: summary/6_snp_and_Indel/2_SNV_INEDL_Position_Type.xlsx
| SNP_type | Lo7_1 | Lo7_2 | Lo7_3 | Lo8_1 | Lo8_2 | Lo8_3 |
| Transition | 32134 | 33096 | 32750 | 31980 | 32258 | 34455 |
| A-G | 15823 | 16220 | 16163 | 15837 | 15990 | 17075 |
| C-T | 16311 | 16876 | 16587 | 16143 | 16268 | 17380 |
| Transversion | 18676 | 18203 | 18676 | 17988 | 18246 | 18986 |
| A-C | 5033 | 4868 | 4954 | 4816 | 4986 | 5161 |
| A-T | 4645 | 4635 | 4689 | 4379 | 4354 | 4625 |
| C-G | 4044 | 4023 | 4212 | 4046 | 4093 | 4234 |
| G-T | 4954 | 4677 | 4821 | 4747 | 4813 | 4966 |
| Total | 50810 | 51299 | 51426 | 49968 | 50504 | 53441 |
document location: summary/6_snp_and_Indel/3_SNP_Variation_Type.xlsx
| SNV(exonic) | Synonymous | NonSynonymous | StopGain | StopLoss | unknown | INDEL(exonic) | frameshift Insertion | frameshift Deletion | Nonframeshift Insertion | Nonframeshift Deletion | frameshift block substitution | nonframeshift block substitution | ||
| Lo7_1 | 15315 | 6935 | 7693 | 378 | 282 | 27 | Lo7_1 | 825 | 80 | 262 | 215 | 249 | 0 | 0 |
| Lo7_2 | 15435 | 6998 | 7771 | 353 | 287 | 26 | Lo7_2 | 950 | 86 | 376 | 220 | 244 | 0 | 0 |
| Lo7_3 | 15260 | 6849 | 7734 | 370 | 279 | 28 | Lo7_3 | 959 | 69 | 364 | 218 | 282 | 0 | 0 |
| Lo8_1 | 15620 | 6985 | 7953 | 391 | 264 | 27 | Lo8_1 | 925 | 72 | 311 | 241 | 277 | 0 | 0 |
| Lo8_2 | 15812 | 7084 | 8032 | 387 | 283 | 26 | Lo8_2 | 1045 | 99 | 394 | 244 | 281 | 0 | 0 |
| Lo8_3 | 16232 | 7327 | 8203 | 394 | 283 | 25 | Lo8_3 | 916 | 92 | 308 | 235 | 257 | 0 | 0 |
document location: summary/6_snp_and_Indel/4_SNV_INEDL_Annotation.xlsx
All SNPs/Indels were annotated by SnpEff in VCF format.
VCF format Description:
| Term | Description |
|---|---|
| CHROM | chromosome id |
| POS ID | chromosome position |
| REF | reference allele |
| ALT | alternative allele |
| QUAL | quality |
| FILTER | filter |
| INFO | information |
| AD | Allelic depths |
| DP | Approximate read depth |
| GQ | Genotype Quality |
| GT | genotype |
| PL | Phred-scaled likelihoods |
document location:
summary/6_snp_and_Indel/6_INDEL_All_Samples.xlsx
summary/6_snp_and_Indel/*/*.vcf
Alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. Consequently, the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions (see Figure). Notably, alternative splicing allows genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
Alternative splicing occurs as a normal phenomenon in eukaryotes, where it greatly increases the biodiversity of proteins that can be encoded by the genome; in humans, ~95% of multi-exonic genes are alternatively spliced.[2] There are numerous modes of alternative splicing observed, of which the most common is exon skipping. In this mode, a particular exon may be included in mRNAs under some conditions or in particular tissues, and omitted from the mRNA in others.
There are different kinds of alternative splicing including:
(A) Exon skipping (SKIP) and cassette exons (MSKIP)
(B) retention of single (IR) and multiple (MIR) introns
(C) alternative exon ends (AE)
(D) alternative transcription start site (TSS)
(E) alternative transcription termination site (TTS)
(F) Approximate SKIP (XSKIP)
(G) Approximate MSKIP (XMKIP)
(H) Approximate IR(XIR)
(I) Approximate MIR(XMIR)
(J) Approximate AE(XAE)
document location:
summary/7_AS_category_splicing/1_all_sample_AS_stat_histogram.png
summary/7_AS_category_splicing/1_AS_stat_all.xlsx
Alternative splicing in all samples
| chrom | event_type | event_start | event_end | event_pattern | strand | gene_id | txpt_id | Annotation | GO | KEGG | Lo7_1(fpkm) | Lo7_2(fpkm) | Lo7_3(fpkm) | Lo8_1(fpkm) | Lo8_2(fpkm) | Lo8_3(fpkm) |
| chr1 | AE | 10009054 | 10009149 | 10009054-10009149 | - | MSTRG.1019 | LOC_Os01g17396.1 | expressed protein | 3.12 | 1.59 | 2.06 | 1.67 | 1.36 | 1.32 | ||
| chr1 | AE | 10009054 | 10009164 | 10009054-10009164 | - | MSTRG.1019 | LOC_Os01g17396.2 | expressed protein | 3.35 | 1.45 | 1.79 | 1.22 | 0.29 | 0.49 | ||
| chr1 | AE | 10009054 | 10009164 | 10009054-10009164 | - | MSTRG.1019 | MSTRG.1019.1 | 1.58 | 1.58 | 3.73 | 0.40 | 0.96 | 0.08 | |||
| chr1 | AE | 10271683 | 10272168 | 10271683-10272168 | - | MSTRG.1041 | MSTRG.1041.1 | 9.12 | 5.49 | 8.53 | 5.46 | 5.44 | 3.16 | |||
| chr1 | AE | 10271683 | 10272183 | 10271683-10272183 | - | MSTRG.1041 | MSTRG.1041.3 | 2.03 | 1.48 | 1.53 | 1.59 | 0.69 | 1.76 | |||
| chr1 | AE | 10271683 | 10272183 | 10271683-10272183 | - | MSTRG.1041 | MSTRG.1041.4 | 0.23 | 0.90 | 0.31 | 0.48 | 0.38 | 0.37 | |||
| chr1 | AE | 10346898 | 10346929 | 10346898-10346929 | - | MSTRG.1050 | MSTRG.1050.8 | 0.50 | 1.45 | 0 | 0.15 | 0 | 0 | |||
| chr1 | AE | 10346898 | 10347107 | 10346898-10347107 | - | MSTRG.1050 | MSTRG.1050.6 | 0.82 | 1.22 | 0 | 0.41 | 0 | 0 | |||
| chr1 | AE | 10347398 | 10347488 | 10347398-10347488 | - | MSTRG.1050 | MSTRG.1050.3 | 0.26 | 0 | 2.98 | 1.70 | 0.88 | 0 | |||
| chr1 | AE | 10347398 | 10347488 | 10347398-10347488 | - | MSTRG.1050 | MSTRG.1050.5 | 0.03 | 0 | 1.28 | 1.05 | 0.14 | 0 | |||
| chr1 | AE | 10347398 | 10348219 | 10347398-10348219 | - | MSTRG.1050 | MSTRG.1050.1 | 2.91 | 0 | 0.67 | 0.86 | 1.11 | 0 | |||
| chr1 | AE | 10347398 | 10348219 | 10347398-10348219 | - | MSTRG.1050 | MSTRG.1050.4 | 0.31 | 0 | 0.57 | 0.13 | 1.12 | 0 | |||
| chr1 | AE | 10347398 | 10348219 | 10347398-10348219 | - | MSTRG.1050 | MSTRG.1050.7 | 0 | 0 | 0 | 0.22 | 0 | 0 | |||
| chr1 | AE | 10348427 | 10348614 | 10348427-10348614 | - | MSTRG.1050 | MSTRG.1050.2 | 1.03 | 0 | 0.30 | 0 | 0.45 | 0 | |||
| chr1 | AE | 10348427 | 10348614 | 10348427-10348614 | - | MSTRG.1050 | MSTRG.1050.6 | 0.82 | 0 | 2.43 | 0.41 | 1.18 | 0 | |||
| chr1 | AE | 10348427 | 10348614 | 10348427-10348614 | - | MSTRG.1050 | MSTRG.1050.8 | 0.50 | 0 | 0 | 0.15 | 0 | 0 | |||
| chr1 | AE | 10348455 | 10348614 | 10348455-10348614 | - | MSTRG.1050 | LOC_Os01g18410.1 | expressed protein | 0.04 | 0 | 0.41 | 0 | 0 | 0 | ||
| chr1 | AE | 10348455 | 10348614 | 10348455-10348614 | - | MSTRG.1050 | MSTRG.1050.3 | 0.26 | 0 | 2.98 | 1.70 | 0.88 | 0 | |||
| chr1 | AE | 10348455 | 10348614 | 10348455-10348614 | - | MSTRG.1050 | MSTRG.1050.5 | 0.03 | 0 | 1.28 | 1.05 | 0.14 | 0 | |||
| chr1 | AE | 10348455 | 10348965 | 10348455-10348965 | - | MSTRG.1050 | MSTRG.1050.1 | 2.91 | 0 | 0.67 | 0 | 0 | 0 | |||
| chr1 | AE | 10494698 | 10494972 | 10494698-10494972 | - | MSTRG.1053 | MSTRG.1053.12 | 1.84 | 0 | 0.30 | 0 | 0 | 0.02 | |||
| chr1 | AE | 10494698 | 10495041 | 10494698-10495041 | - | MSTRG.1053 | LOC_Os01g18630.1 | aspartic proteinase oryzasin-1 precursor, putative, expressed | GO:0004190(aspartic-type endopeptidase activity),GO:0006508(proteolysis),GO:0030163(protein catabolic process) | 0 | 0 | 0 | 0 | 0 | 5.88 | |
| chr1 | AE | 10494698 | 10495041 | 10494698-10495041 | - | MSTRG.1053 | LOC_Os01g18630.2 | aspartic proteinase oryzasin-1 precursor, putative, expressed | GO:0004190(aspartic-type endopeptidase activity),GO:0006508(proteolysis),GO:0030163(protein catabolic process) | 0.19 | 0 | 0.21 | 0 | 0 | 4.39 | |
| chr1 | AE | 10494698 | 10495041 | 10494698-10495041 | - | MSTRG.1053 | MSTRG.1053.3 | 20.40 | 0 | 16.82 | 0 | 0 | 0 | |||
| chr1 | AE | 10494698 | 10495041 | 10494698-10495041 | - | MSTRG.1053 | MSTRG.1053.4 | 20.20 | 0 | 18.15 | 0 | 0 | 0 | |||
| chr1 | AE | 10494698 | 10495041 | 10494698-10495041 | - | MSTRG.1053 | MSTRG.1053.6 | 0 | 0 | 0.00 | 0 | 0 | 0 | |||
| chr1 | AE | 10495393 | 10495686 | 10495393-10495686 | - | MSTRG.1053 | MSTRG.1053.13 | 2.87 | 0.20 | 0 | 0.06 | 0.18 | 0 | |||
| chr1 | AE | 10495393 | 10495798 | 10495393-10495798 | - | MSTRG.1053 | MSTRG.1053.9 | 0 | 1.52 | 0.12 | 0 | 0 | 0 | |||
| chr1 | AE | 10495533 | 10495686 | 10495533-10495686 | - | MSTRG.1053 | MSTRG.1053.12 | 0 | 0 | 0.30 | 0 | 0 | 0 | |||
| chr1 | AE | 10495533 | 10495686 | 10495533-10495686 | - | MSTRG.1053 | MSTRG.1053.3 | 20.40 | 3.09 | 16.82 | 14.78 | 18.15 | 0 | |||
| chr1 | AE | 10495533 | 10495686 | 10495533-10495686 | - | MSTRG.1053 | MSTRG.1053.4 | 20.20 | 2.28 | 18.15 | 14.16 | 16.70 | 0 | |||
| chr1 | AE | 10495533 | 10495686 | 10495533-10495686 | - | MSTRG.1053 | MSTRG.1053.5 | 0 | 0 | 0 | 0 | 3.57 | 0 | |||
| chr1 | AE | 10495533 | 10495798 | 10495533-10495798 | - | MSTRG.1053 | MSTRG.1053.8 | 0 | 10.17 | 0 | 0 | 0 | 0 | |||
| chr1 | AE | 10495533 | 10495803 | 10495533-10495803 | - | MSTRG.1053 | MSTRG.1053.6 | 0 | 11.15 | 0.00 | 2.71 | 0 | 0 | |||
| chr1 | AE | 10495533 | 10495803 | 10495533-10495803 | - | MSTRG.1053 | MSTRG.1053.7 | 0 | 14.15 | 0 | 0 | 2.44 | 0 | |||
| chr1 | AE | 1050498 | 1050624 | 1050498-1050624 | + | MSTRG.134 | MSTRG.134.2 | 5.76 | 10.13 | 9.17 | 6.29 | 6.66 | 11.53 | |||
| chr1 | AE | 1050498 | 1050624 | 1050498-1050624 | + | MSTRG.134 | MSTRG.134.3 | 1.86 | 0.72 | 0.92 | 2.44 | 1.65 | 1.00 | |||
| chr1 | AE | 1050498 | 1050624 | 1050498-1050624 | + | MSTRG.134 | MSTRG.134.4 | 1.22 | 0.68 | 2.09 | 0.62 | 0.47 | 0.57 | |||
| chr1 | AE | 1050498 | 1050624 | 1050498-1050624 | + | MSTRG.134 | MSTRG.134.7 | 2.95 | 2.21 | 1.52 | 1.07 | 1.44 | 2.20 | |||
| chr1 | AE | 1050508 | 1050624 | 1050508-1050624 | + | MSTRG.134 | MSTRG.134.1 | 8.12 | 6.96 | 6.61 | 6.11 | 10.12 | 10.80 | |||
| chr1 | AE | 1050508 | 1050624 | 1050508-1050624 | + | MSTRG.134 | MSTRG.134.6 | 2.81 | 2.89 | 2.18 | 1.99 | 0.85 | 2.95 | |||
| chr1 | AE | 1050511 | 1050624 | 1050511-1050624 | + | MSTRG.134 | LOC_Os01g02890.1 | phosphatidylserine synthase, putative, expressed | GO:0008654(phospholipid biosynthetic process),GO:0016021(integral component of membrane) | 00564(Glycerophospholipid metabolism) | 0.83 | 1.18 | 0.79 | 0.32 | 0.40 | 1.06 |
| chr1 | AE | 1051947 | 1052033 | 1051947-1052033 | + | MSTRG.134 | MSTRG.134.3 | 1.86 | 0.72 | 0.92 | 2.44 | 1.65 | 1.00 | |||
| chr1 | AE | 1051947 | 1052033 | 1051947-1052033 | + | MSTRG.134 | MSTRG.134.7 | 2.95 | 2.21 | 1.52 | 1.07 | 1.44 | 2.20 | |||
| chr1 | AE | 1051947 | 1052200 | 1051947-1052200 | + | MSTRG.134 | LOC_Os01g02890.1 | phosphatidylserine synthase, putative, expressed | GO:0008654(phospholipid biosynthetic process),GO:0016021(integral component of membrane) | 00564(Glycerophospholipid metabolism) | 0.83 | 1.18 | 0.79 | 0.32 | 0.40 | 1.06 |
| chr1 | AE | 1051947 | 1052200 | 1051947-1052200 | + | MSTRG.134 | MSTRG.134.1 | 8.12 | 6.96 | 6.61 | 6.11 | 10.12 | 10.80 | |||
| chr1 | AE | 1051947 | 1052200 | 1051947-1052200 | + | MSTRG.134 | MSTRG.134.2 | 5.76 | 10.13 | 9.17 | 6.29 | 6.66 | 11.53 | |||
| chr1 | AE | 1051947 | 1052200 | 1051947-1052200 | + | MSTRG.134 | MSTRG.134.4 | 1.22 | 0.68 | 2.09 | 0.62 | 0.47 | 0.57 | |||
| chr1 | AE | 1059263 | 1059433 | 1059263-1059433 | - | MSTRG.133 | LOC_Os01g02900.1 | glycosyltransferase, putative, expressed | GO:0005576(extracellular region),GO:0016757(transferase activity, transferring glycosyl groups) | 00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis) | 0.26 | 0 | 0 | 0 | 0 | 0.48 |
| chr1 | AE | 1059263 | 1059462 | 1059263-1059462 | - | MSTRG.133 | LOC_Os01g02900.2 | glycosyltransferase, putative, expressed | GO:0005576(extracellular region),GO:0016757(transferase activity, transferring glycosyl groups) | 00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis) | 1.81 | 0 | 0 | 0 | 0 | 0.03 |
| chr1 | AE | 10651010 | 10651656 | 10651010-10651656 | + | MSTRG.1058 | LOC_Os01g18850.3 | OsSPL1 - SBP-box gene family member, expressed | GO:0003677(DNA binding),GO:0003700(transcription factor activity, sequence-specific DNA binding),GO:0005634(nucleus),GO:0006351(transcription, DNA-templated),GO:0006355(regulation of transcription, DNA-templated),GO:0046872(metal ion binding) | 04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction) | 3.93 | 7.08 | 5.61 | 12.02 | 9.25 | 6.72 |
| chr1 | AE | 10651010 | 10651656 | 10651010-10651656 | + | MSTRG.1058 | MSTRG.1058.1 | 1.48 | 0 | 0 | 0.17 | 0 | 4.81 | |||
| chr1 | AE | 10651010 | 10651656 | 10651010-10651656 | + | MSTRG.1058 | MSTRG.1058.4 | 1.31 | 1.02 | 0.08 | 0.07 | 0.01 | 0.00 | |||
| chr1 | AE | 10651095 | 10651656 | 10651095-10651656 | + | MSTRG.1058 | LOC_Os01g18850.1 | OsSPL1 - SBP-box gene family member, expressed | GO:0003677(DNA binding),GO:0003700(transcription factor activity, sequence-specific DNA binding),GO:0005634(nucleus),GO:0006351(transcription, DNA-templated),GO:0006355(regulation of transcription, DNA-templated),GO:0046872(metal ion binding) | 04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction) | 0.34 | 0.52 | 0.68 | 0.93 | 0.71 | 0.32 |
| chr1 | AE | 10654337 | 10654454 | 10654337-10654454 | + | MSTRG.1058 | LOC_Os01g18850.1 | OsSPL1 - SBP-box gene family member, expressed | GO:0003677(DNA binding),GO:0003700(transcription factor activity, sequence-specific DNA binding),GO:0005634(nucleus),GO:0006351(transcription, DNA-templated),GO:0006355(regulation of transcription, DNA-templated),GO:0046872(metal ion binding) | 04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction) | 0.34 | 0.52 | 0.68 | 0.93 | 0.71 | 0.32 |
| chr1 | AE | 10654337 | 10654454 | 10654337-10654454 | + | MSTRG.1058 | LOC_Os01g18850.2 | OsSPL1 - SBP-box gene family member, expressed | GO:0003677(DNA binding),GO:0003700(transcription factor activity, sequence-specific DNA binding),GO:0005634(nucleus),GO:0006351(transcription, DNA-templated),GO:0006355(regulation of transcription, DNA-templated),GO:0046872(metal ion binding) | 04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction) | 0.24 | 0.06 | 2.78 | 0.95 | 0.36 | 0.03 |
| chr1 | AE | 10654337 | 10654454 | 10654337-10654454 | + | MSTRG.1058 | LOC_Os01g18850.3 | OsSPL1 - SBP-box gene family member, expressed | GO:0003677(DNA binding),GO:0003700(transcription factor activity, sequence-specific DNA binding),GO:0005634(nucleus),GO:0006351(transcription, DNA-templated),GO:0006355(regulation of transcription, DNA-templated),GO:0046872(metal ion binding) | 04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction) | 3.93 | 7.08 | 5.61 | 12.02 | 9.25 | 6.72 |
| chr1 | AE | 10654337 | 10654454 | 10654337-10654454 | + | MSTRG.1058 | LOC_Os01g18850.4 | OsSPL1 - SBP-box gene family member, expressed | GO:0003677(DNA binding),GO:0003700(transcription factor activity, sequence-specific DNA binding),GO:0005634(nucleus),GO:0006351(transcription, DNA-templated),GO:0006355(regulation of transcription, DNA-templated),GO:0046872(metal ion binding) | 04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction),04075(Plant hormone signal transduction) | 0.22 | 0.24 | 0 | 0.85 | 1.63 | 0.10 |
| chr1 | AE | 10654337 | 10654454 | 10654337-10654454 | + | MSTRG.1058 | MSTRG.1058.1 | 1.48 | 0 | 0 | 0.17 | 0 | 4.81 | |||
| chr1 | AE | 10654337 | 10654454 | 10654337-10654454 | + | MSTRG.1058 | MSTRG.1058.5 | 1.27 | 0.11 | 2.81 | 0.31 | 0.56 | 0.03 | |||
| chr1 | AE | 10654407 | 10654454 | 10654407-10654454 | + | MSTRG.1058 | MSTRG.1058.4 | 1.31 | 1.02 | 0.08 | 0.07 | 0.01 | 0.00 | |||
| chr1 | AE | 10679445 | 10679661 | 10679445-10679661 | + | MSTRG.1060 | MSTRG.1060.5 | 0.59 | 0.35 | 0.69 | 0.24 | 0.74 | 0.09 | |||
| chr1 | AE | 10679574 | 10679661 | 10679574-10679661 | + | MSTRG.1060 | MSTRG.1060.3 | 1.07 | 0.29 | 0.70 | 3.00 | 1.49 | 0.06 | |||
| chr1 | AE | 10815789 | 10815893 | 10815789-10815893 | - | MSTRG.1063 | LOC_Os01g19140.1 | O-sialoglycoprotein endopeptidase, putative, expressed | GO:0000408(EKC/KEOPS complex),GO:0002949(tRNA threonylcarbamoyladenosine modification) | 0.97 | 0.26 | 0.80 | 0.65 | 0.38 | 0.55 | |
| chr1 | AE | 10815789 | 10815903 | 10815789-10815903 | - | MSTRG.1063 | MSTRG.1063.2 | 2.01 | 2.62 | 2.56 | 1.82 | 1.29 | 1.93 | |||
| chr1 | AE | 10826083 | 10826166 | 10826083-10826166 | + | MSTRG.1066 | LOC_Os01g19150.1 | CGMC_GSK.3 - CGMC includes CDA, MAPK, GSK3, and CLKC kinases, expressed | GO:0004672(protein kinase activity),GO:0004674(protein serine/threonine kinase activity),GO:0005524(ATP binding),GO:0005634(nucleus),GO:0005829(cytosol),GO:0006468(protein phosphorylation),GO:0009651(response to salt stress),GO:0009933(meristem structural organization),GO:0016310(phosphorylation),GO:0042538(hyperosmotic salinity response),GO:1901002(positive regulation of response to salt stress) | 04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance) | 26.31 | 11.73 | 20.86 | 18.29 | 17.76 | 23.82 |
| chr1 | AE | 10826083 | 10826166 | 10826083-10826166 | + | MSTRG.1066 | LOC_Os01g19150.3 | CGMC_GSK.3 - CGMC includes CDA, MAPK, GSK3, and CLKC kinases, expressed | GO:0004672(protein kinase activity),GO:0004674(protein serine/threonine kinase activity),GO:0005524(ATP binding),GO:0005634(nucleus),GO:0005829(cytosol),GO:0006468(protein phosphorylation),GO:0009651(response to salt stress),GO:0009933(meristem structural organization),GO:0016310(phosphorylation),GO:0042538(hyperosmotic salinity response),GO:1901002(positive regulation of response to salt stress) | 04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance) | 8.43 | 9.02 | 3.09 | 2.39 | 3.79 | 7.23 |
| chr1 | AE | 10826083 | 10826166 | 10826083-10826166 | + | MSTRG.1066 | LOC_Os01g19150.5 | CGMC_GSK.3 - CGMC includes CDA, MAPK, GSK3, and CLKC kinases, expressed | GO:0004672(protein kinase activity),GO:0004674(protein serine/threonine kinase activity),GO:0005524(ATP binding),GO:0005634(nucleus),GO:0005829(cytosol),GO:0006468(protein phosphorylation),GO:0009651(response to salt stress),GO:0009933(meristem structural organization),GO:0016310(phosphorylation),GO:0042538(hyperosmotic salinity response),GO:1901002(positive regulation of response to salt stress) | 04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance) | 0.95 | 0 | 1.23 | 0.86 | 0.42 | 4.77 |
| chr1 | AE | 10826117 | 10826166 | 10826117-10826166 | + | MSTRG.1066 | LOC_Os01g19150.4 | CGMC_GSK.3 - CGMC includes CDA, MAPK, GSK3, and CLKC kinases, expressed | GO:0004672(protein kinase activity),GO:0004674(protein serine/threonine kinase activity),GO:0005524(ATP binding),GO:0005634(nucleus),GO:0005829(cytosol),GO:0006468(protein phosphorylation),GO:0009651(response to salt stress),GO:0009933(meristem structural organization),GO:0016310(phosphorylation),GO:0042538(hyperosmotic salinity response),GO:1901002(positive regulation of response to salt stress) | 04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance),04931(Insulin resistance) | 1.27 | 7.60 | 0.53 | 0.30 | 0.33 | 0.10 |
| chr1 | AE | 1093100 | 1093315 | 1093100-1093315 | - | MSTRG.138 | LOC_Os01g02940.1 | glycosyltransferase protein, putative, expressed | GO:0005576(extracellular region),GO:0016757(transferase activity, transferring glycosyl groups) | 00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis) | 3.04 | 0.22 | 0.98 | 0 | 0.29 | 0.06 |
| chr1 | AE | 1093100 | 1093315 | 1093100-1093315 | - | MSTRG.138 | MSTRG.138.6 | 0.17 | 0.61 | 7.56 | 0.23 | 0.08 | 0.51 | |||
| chr1 | AE | 1093100 | 1093342 | 1093100-1093342 | - | MSTRG.138 | LOC_Os01g02940.2 | glycosyltransferase protein, putative, expressed | GO:0005576(extracellular region),GO:0016757(transferase activity, transferring glycosyl groups) | 00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis) | 1.30 | 2.11 | 0.62 | 0.17 | 1.31 | 2.38 |
| chr1 | AE | 1093100 | 1093355 | 1093100-1093355 | - | MSTRG.138 | LOC_Os01g02940.3 | glycosyltransferase protein, putative, expressed | GO:0005576(extracellular region),GO:0016757(transferase activity, transferring glycosyl groups) | 00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis),00514(Other types of O-glycan biosynthesis) | 1.72 | 1.32 | 0.83 | 1.71 | 0.69 | 1.27 |
| chr1 | AE | 10961242 | 10961300 | 10961242-10961300 | - | MSTRG.1080 | MSTRG.1080.2 | 1.35 | 0.05 | 0.11 | 0.13 | 0.50 | 0.01 | |||
| chr1 | AE | 10961242 | 10961315 | 10961242-10961315 | - | MSTRG.1080 | MSTRG.1080.1 | 0.27 | 0.45 | 1.48 | 1.87 | 0.82 | 1.91 | |||
| chr1 | AE | 10981176 | 10981320 | 10981176-10981320 | - | MSTRG.1086 | LOC_Os01g19410.3 | expressed protein | GO:0003674(molecular_function),GO:0005634(nucleus),GO:0008150(biological_process),GO:0016021(integral component of membrane) | 17.75 | 0.12 | 7.30 | 7.45 | 3.25 | 12.97 | |
| chr1 | AE | 10981176 | 10981320 | 10981176-10981320 | - | MSTRG.1086 | MSTRG.1086.1 | 0 | 32.16 | 17.84 | 11.76 | 16.34 | 0 | |||
| chr1 | AE | 10981176 | 10981423 | 10981176-10981423 | - | MSTRG.1086 | MSTRG.1086.3 | 6.02 | 3.52 | 4.09 | 2.77 | 2.50 | 5.55 | |||
| chr1 | AE | 10981400 | 10981423 | 10981400-10981423 | - | MSTRG.1086 | LOC_Os01g19410.2 | expressed protein | GO:0003674(molecular_function),GO:0005634(nucleus),GO:0008150(biological_process),GO:0016021(integral component of membrane) | 7.26 | 0.14 | 4.57 | 4.21 | 1.88 | 2.40 | |
| chr1 | AE | 10981400 | 10981423 | 10981400-10981423 | - | MSTRG.1086 | MSTRG.1086.2 | 17.04 | 15.64 | 13.54 | 8.57 | 10.85 | 14.74 | |||
| chr1 | AE | 10981400 | 10981581 | 10981400-10981581 | - | MSTRG.1086 | LOC_Os01g19410.1 | expressed protein | GO:0003674(molecular_function),GO:0005634(nucleus),GO:0008150(biological_process),GO:0016021(integral component of membrane) | 7.97 | 2.24 | 6.17 | 4.68 | 4.49 | 7.28 | |
| chr1 | AE | 11003173 | 11003307 | 11003173-11003307 | - | MSTRG.1090 | LOC_Os01g19450.1 | ATP-citrate synthase subunit 1, putative, expressed | GO:0003878(ATP citrate synthase activity),GO:0005524(ATP binding),GO:0005737(cytoplasm),GO:0005829(cytosol),GO:0005886(plasma membrane),GO:0006085(acetyl-CoA biosynthetic process),GO:0006629(lipid metabolic process),GO:0009346(citrate lyase complex),GO:0046872(metal ion binding) | 00020(Citrate cycle (TCA cycle)),00020(Citrate cycle (TCA cycle)) | 42.55 | 44.49 | 30.65 | 57.90 | 48.34 | 54.32 |
| chr1 | AE | 11003173 | 11003307 | 11003173-11003307 | - | MSTRG.1090 | LOC_Os01g19450.2 | ATP-citrate synthase subunit 1, putative, expressed | GO:0003878(ATP citrate synthase activity),GO:0005524(ATP binding),GO:0005737(cytoplasm),GO:0005829(cytosol),GO:0005886(plasma membrane),GO:0006085(acetyl-CoA biosynthetic process),GO:0006629(lipid metabolic process),GO:0009346(citrate lyase complex),GO:0046872(metal ion binding) | 00020(Citrate cycle (TCA cycle)),00020(Citrate cycle (TCA cycle)) | 1.15 | 0.37 | 0 | 2.50 | 0 | 1.76 |
| chr1 | AE | 11003173 | 11003410 | 11003173-11003410 | - | MSTRG.1090 | MSTRG.1090.3 | 0.00 | 0.08 | 12.00 | 0.19 | 0.08 | 0.06 | |||
| chr1 | AE | 11003566 | 11003666 | 11003566-11003666 | - | MSTRG.1090 | LOC_Os01g19450.2 | ATP-citrate synthase subunit 1, putative, expressed | GO:0003878(ATP citrate synthase activity),GO:0005524(ATP binding),GO:0005737(cytoplasm),GO:0005829(cytosol),GO:0005886(plasma membrane),GO:0006085(acetyl-CoA biosynthetic process),GO:0006629(lipid metabolic process),GO:0009346(citrate lyase complex),GO:0046872(metal ion binding) | 00020(Citrate cycle (TCA cycle)),00020(Citrate cycle (TCA cycle)) | 1.15 | 0.37 | 0 | 2.50 | 0 | 1.76 |
| chr1 | AE | 11003566 | 11003689 | 11003566-11003689 | - | MSTRG.1090 | LOC_Os01g19450.1 | ATP-citrate synthase subunit 1, putative, expressed | GO:0003878(ATP citrate synthase activity),GO:0005524(ATP binding),GO:0005737(cytoplasm),GO:0005829(cytosol),GO:0005886(plasma membrane),GO:0006085(acetyl-CoA biosynthetic process),GO:0006629(lipid metabolic process),GO:0009346(citrate lyase complex),GO:0046872(metal ion binding) | 00020(Citrate cycle (TCA cycle)),00020(Citrate cycle (TCA cycle)) | 42.55 | 44.49 | 0 | 57.90 | 0 | 54.32 |
| chr1 | AE | 11003566 | 11003689 | 11003566-11003689 | - | MSTRG.1090 | MSTRG.1090.3 | 0.00 | 0.08 | 0 | 0.19 | 0 | 0.06 | |||
| chr1 | AE | 11036825 | 11036991 | 11036825-11036991 | - | MSTRG.1092 | LOC_Os01g19470.1 | nodal modulator 1 precursor, putative, expressed | GO:0005576(extracellular region),GO:0005774(vacuolar membrane),GO:0005783(endoplasmic reticulum),GO:0005794(Golgi apparatus),GO:0009505(plant-type cell wall),GO:0016021(integral component of membrane) | 0 | 0 | 11.10 | 0 | 0 | 0 | |
| chr1 | AE | 11036887 | 11036991 | 11036887-11036991 | - | MSTRG.1092 | MSTRG.1092.1 | 0 | 0 | 5.28 | 0 | 0 | 0 | |||
| chr1 | AE | 11131178 | 11131235 | 11131178-11131235 | + | MSTRG.1099 | LOC_Os01g19630.1 | expressed protein | 0 | 0.08 | 0.35 | 0 | 0 | 0 | ||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | LOC_Os01g19630.2 | expressed protein | 0 | 3.08 | 3.85 | 0 | 0 | 0 | ||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | LOC_Os01g19630.3 | expressed protein | 0 | 2.51 | 1.35 | 0 | 0 | 0 | ||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | LOC_Os01g19630.4 | expressed protein | 0 | 1.29 | 0.64 | 0 | 0 | 0 | ||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | MSTRG.1099.1 | 0 | 2.33 | 1.72 | 0 | 0 | 0 | |||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | MSTRG.1099.2 | 0 | 2.61 | 3.15 | 0 | 0 | 0 | |||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | MSTRG.1099.3 | 0 | 0.85 | 0 | 0 | 0 | 0 | |||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | MSTRG.1099.4 | 0 | 0.36 | 0 | 0 | 0 | 0 | |||
| chr1 | AE | 11131178 | 11131265 | 11131178-11131265 | + | MSTRG.1099 | MSTRG.1099.5 | 0 | 1.33 | 1.57 | 0 | 0 | 0 | |||
| chr1 | AE | 11255901 | 11256301 | 11255901-11256301 | - | MSTRG.1110 | MSTRG.1110.1 | 1.30 | 0 | 0.02 | 0 | 0 | 1.31 |
document location:summary/7_AS_category_splicing/2_AS_All_sample.xlsx
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