Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA-binding protein with serine-rich domain 1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11728 g11728.t6 TSS g11728.t6 18096347 18096347
chr_1 g11728 g11728.t6 isoform g11728.t6 18096543 18097630
chr_1 g11728 g11728.t6 exon g11728.t6.exon1 18096543 18096628
chr_1 g11728 g11728.t6 cds g11728.t6.CDS1 18096543 18096628
chr_1 g11728 g11728.t6 exon g11728.t6.exon2 18096693 18096728
chr_1 g11728 g11728.t6 cds g11728.t6.CDS2 18096693 18096728
chr_1 g11728 g11728.t6 exon g11728.t6.exon3 18096790 18096942
chr_1 g11728 g11728.t6 cds g11728.t6.CDS3 18096790 18096942
chr_1 g11728 g11728.t6 exon g11728.t6.exon4 18097006 18097294
chr_1 g11728 g11728.t6 cds g11728.t6.CDS4 18097006 18097294
chr_1 g11728 g11728.t6 exon g11728.t6.exon5 18097348 18097442
chr_1 g11728 g11728.t6 cds g11728.t6.CDS5 18097348 18097442
chr_1 g11728 g11728.t6 exon g11728.t6.exon6 18097507 18097630
chr_1 g11728 g11728.t6 cds g11728.t6.CDS6 18097507 18097630
chr_1 g11728 g11728.t6 TTS g11728.t6 18097769 18097769

Sequences

>g11728.t6 Gene=g11728 Length=783
ATGGTGGTAGAAAAATCGCGTAGTGAAAAAGAAAAGGAAGAGAAATCATCTAAAAGAAGA
TCTCGTTCAACTAGTTCTAATGATAGTTCATCCAGCAGTAGTTCATCTTCTAGTTCGTCT
AGTTCATCTTCAACATCATCATCAAGTAGTGGTGGTGATCGTCGTAAACGCAGAGAAAGA
GGATCTCGATCCAAAAGTCGCAGTGTGCGAAAAGGTGGTGAATCAAAAGATAGAAAGGAG
AAATCACGCGAGAGAGGACGTCAAAGTCCTGGAAGACGAACTCGTTCCCGATCAACTTCA
GTTCGACGTAAACGTTATGAACGTTCACCAACACCAAAACCTACACGAATTCATATAGGT
CGTCTGACTCGTAATGTAACAAAGGATCATGTTCTTGAAATTTTCAGCAACTATGGAGAG
ATTAAATCTATTGATTTTCCAACTGATCGTTATCATCCACAAAATGGTAGAGGCTTCTGT
TATGTTGAATATTTAAATGCAGACGATGCTGAAAATGCTATGAAACACATGGACGGAGGT
CAAATTGATGGAACTGAAGTTGCTGTTGCACCAGTAAATAATCCAAAGCCAATGCAAATG
ATGCGTCGTTCTCCTATGCGAAGAGGAGGTATGCCTCCAAATCGTAATAACAATAGATGG
AGAGGTGGTGGTAGAGATATGCAAAATCGACGCAGATCTCCGATAAGACGTTCACCTCGA
CGCAGAGTTAGTCGAAGTCCAATAAGAAGACGCCACTCTAATTCATCAAGTAGCTCGCGT
TAG

>g11728.t6 Gene=g11728 Length=260
MVVEKSRSEKEKEEKSSKRRSRSTSSNDSSSSSSSSSSSSSSSSTSSSSSGGDRRKRRER
GSRSKSRSVRKGGESKDRKEKSRERGRQSPGRRTRSRSTSVRRKRYERSPTPKPTRIHIG
RLTRNVTKDHVLEIFSNYGEIKSIDFPTDRYHPQNGRGFCYVEYLNADDAENAMKHMDGG
QIDGTEVAVAPVNNPKPMQMMRRSPMRRGGMPPNRNNNRWRGGGRDMQNRRRSPIRRSPR
RRVSRSPIRRRHSNSSSSSR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11728.t6 CDD cd12365 RRM_RNPS1 117 190 1.78763E-39
5 g11728.t6 Gene3D G3DSA:3.30.70.330 - 47 204 1.1E-25
10 g11728.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 113 -
12 g11728.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
8 g11728.t6 MobiDBLite mobidb-lite consensus disorder prediction 23 50 -
9 g11728.t6 MobiDBLite mobidb-lite consensus disorder prediction 66 91 -
11 g11728.t6 MobiDBLite mobidb-lite consensus disorder prediction 200 260 -
13 g11728.t6 MobiDBLite mobidb-lite consensus disorder prediction 234 249 -
2 g11728.t6 PANTHER PTHR15481 RIBONUCLEIC ACID BINDING PROTEIN S1 5 259 1.7E-55
3 g11728.t6 PANTHER PTHR15481:SF2 RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1 5 259 1.7E-55
1 g11728.t6 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 118 187 8.1E-17
14 g11728.t6 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 115 194 15.869
7 g11728.t6 SMART SM00360 rrm1_1 116 190 2.5E-20
4 g11728.t6 SUPERFAMILY SSF54928 RNA-binding domain, RBD 109 224 2.82E-27

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003676 nucleic acid binding MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values