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.t7 TSS g11728.t7 18096347 18096347
chr_1 g11728 g11728.t7 isoform g11728.t7 18096543 18097630
chr_1 g11728 g11728.t7 exon g11728.t7.exon1 18096543 18096628
chr_1 g11728 g11728.t7 cds g11728.t7.CDS1 18096543 18096628
chr_1 g11728 g11728.t7 exon g11728.t7.exon2 18096684 18096728
chr_1 g11728 g11728.t7 cds g11728.t7.CDS2 18096684 18096728
chr_1 g11728 g11728.t7 exon g11728.t7.exon3 18096790 18096942
chr_1 g11728 g11728.t7 cds g11728.t7.CDS3 18096790 18096942
chr_1 g11728 g11728.t7 exon g11728.t7.exon4 18097006 18097294
chr_1 g11728 g11728.t7 cds g11728.t7.CDS4 18097006 18097294
chr_1 g11728 g11728.t7 exon g11728.t7.exon5 18097348 18097442
chr_1 g11728 g11728.t7 cds g11728.t7.CDS5 18097348 18097442
chr_1 g11728 g11728.t7 exon g11728.t7.exon6 18097507 18097630
chr_1 g11728 g11728.t7 cds g11728.t7.CDS6 18097507 18097630
chr_1 g11728 g11728.t7 TTS g11728.t7 18097769 18097769

Sequences

>g11728.t7 Gene=g11728 Length=792
ATGGTGGTAGAAAAATCGCGTAGTGAAAAAGAAAAGGAAGAGAAATCATCTAAAAGAAGA
TCTCGTTCAACTAGTTCTAATGATAGTTCGGATAGTTCATCCAGCAGTAGTTCATCTTCT
AGTTCGTCTAGTTCATCTTCAACATCATCATCAAGTAGTGGTGGTGATCGTCGTAAACGC
AGAGAAAGAGGATCTCGATCCAAAAGTCGCAGTGTGCGAAAAGGTGGTGAATCAAAAGAT
AGAAAGGAGAAATCACGCGAGAGAGGACGTCAAAGTCCTGGAAGACGAACTCGTTCCCGA
TCAACTTCAGTTCGACGTAAACGTTATGAACGTTCACCAACACCAAAACCTACACGAATT
CATATAGGTCGTCTGACTCGTAATGTAACAAAGGATCATGTTCTTGAAATTTTCAGCAAC
TATGGAGAGATTAAATCTATTGATTTTCCAACTGATCGTTATCATCCACAAAATGGTAGA
GGCTTCTGTTATGTTGAATATTTAAATGCAGACGATGCTGAAAATGCTATGAAACACATG
GACGGAGGTCAAATTGATGGAACTGAAGTTGCTGTTGCACCAGTAAATAATCCAAAGCCA
ATGCAAATGATGCGTCGTTCTCCTATGCGAAGAGGAGGTATGCCTCCAAATCGTAATAAC
AATAGATGGAGAGGTGGTGGTAGAGATATGCAAAATCGACGCAGATCTCCGATAAGACGT
TCACCTCGACGCAGAGTTAGTCGAAGTCCAATAAGAAGACGCCACTCTAATTCATCAAGT
AGCTCGCGTTAG

>g11728.t7 Gene=g11728 Length=263
MVVEKSRSEKEKEEKSSKRRSRSTSSNDSSDSSSSSSSSSSSSSSSSTSSSSSGGDRRKR
RERGSRSKSRSVRKGGESKDRKEKSRERGRQSPGRRTRSRSTSVRRKRYERSPTPKPTRI
HIGRLTRNVTKDHVLEIFSNYGEIKSIDFPTDRYHPQNGRGFCYVEYLNADDAENAMKHM
DGGQIDGTEVAVAPVNNPKPMQMMRRSPMRRGGMPPNRNNNRWRGGGRDMQNRRRSPIRR
SPRRRVSRSPIRRRHSNSSSSSR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11728.t7 CDD cd12365 RRM_RNPS1 120 193 1.94583E-39
5 g11728.t7 Gene3D G3DSA:3.30.70.330 - 106 256 1.9E-22
12 g11728.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 25 -
13 g11728.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 117 -
11 g11728.t7 MobiDBLite mobidb-lite consensus disorder prediction 26 53 -
9 g11728.t7 MobiDBLite mobidb-lite consensus disorder prediction 69 94 -
10 g11728.t7 MobiDBLite mobidb-lite consensus disorder prediction 203 263 -
8 g11728.t7 MobiDBLite mobidb-lite consensus disorder prediction 237 252 -
2 g11728.t7 PANTHER PTHR15481 RIBONUCLEIC ACID BINDING PROTEIN S1 5 262 1.0E-55
3 g11728.t7 PANTHER PTHR15481:SF2 RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1 5 262 1.0E-55
1 g11728.t7 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 121 190 8.3E-17
14 g11728.t7 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 118 197 15.869
7 g11728.t7 SMART SM00360 rrm1_1 119 193 2.5E-20
4 g11728.t7 SUPERFAMILY SSF54928 RNA-binding domain, RBD 112 227 2.96E-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