Gene loci information

Transcript annotation

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

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.t5 TSS g11728.t5 18096347 18096347
chr_1 g11728 g11728.t5 isoform g11728.t5 18096543 18097630
chr_1 g11728 g11728.t5 exon g11728.t5.exon1 18096543 18096628
chr_1 g11728 g11728.t5 cds g11728.t5.CDS1 18096543 18096628
chr_1 g11728 g11728.t5 exon g11728.t5.exon2 18096678 18096728
chr_1 g11728 g11728.t5 cds g11728.t5.CDS2 18096678 18096728
chr_1 g11728 g11728.t5 exon g11728.t5.exon3 18096790 18096942
chr_1 g11728 g11728.t5 cds g11728.t5.CDS3 18096790 18096942
chr_1 g11728 g11728.t5 exon g11728.t5.exon4 18097006 18097630
chr_1 g11728 g11728.t5 cds g11728.t5.CDS4 18097006 18097303
chr_1 g11728 g11728.t5 TTS g11728.t5 18097769 18097769

Sequences

>g11728.t5 Gene=g11728 Length=915
ATGGTGGTAGAAAAATCGCGTAGTGAAAAAGAAAAGGAAGAGAAATCATCTAAAAGAAGA
TCTCGTTCAACTAGTTCTAATGATAGTTCTAGTTCGGATAGTTCATCCAGCAGTAGTTCA
TCTTCTAGTTCGTCTAGTTCATCTTCAACATCATCATCAAGTAGTGGTGGTGATCGTCGT
AAACGCAGAGAAAGAGGATCTCGATCCAAAAGTCGCAGTGTGCGAAAAGGTGGTGAATCA
AAAGATAGAAAGGAGAAATCACGCGAGAGAGGACGTCAAAGTCCTGGAAGACGAACTCGT
TCCCGATCAACTTCAGTTCGACGTAAACGTTATGAACGTTCACCAACACCAAAACCTACA
CGAATTCATATAGGTCGTCTGACTCGTAATGTAACAAAGGATCATGTTCTTGAAATTTTC
AGCAACTATGGAGAGATTAAATCTATTGATTTTCCAACTGATCGTTATCATCCACAAAAT
GGTAGAGGCTTCTGTTATGTTGAATATTTAAATGCAGACGATGCTGAAAATGCTATGAAA
CACATGGACGGAGGTCAAATTGATGGAACTGAAGTTGCTGTAAGTTAATTGGAATGAAAC
TTTTAAAATATTATTTTAAAAATTACTTTTAGGTTGCACCAGTAAATAATCCAAAGCCAA
TGCAAATGATGCGTCGTTCTCCTATGCGAAGAGGAGGTATGCCTCCAAATCGTAATAACA
ATAGATGGTAGGAATAATTTAAAAGTATTCAATATTGATGAAAATTTATTGGCCTTTTTA
AAAAATTTTAGGAGAGGTGGTGGTAGAGATATGCAAAATCGACGCAGATCTCCGATAAGA
CGTTCACCTCGACGCAGAGTTAGTCGAAGTCCAATAAGAAGACGCCACTCTAATTCATCA
AGTAGCTCGCGTTAG

>g11728.t5 Gene=g11728 Length=195
MVVEKSRSEKEKEEKSSKRRSRSTSSNDSSSSDSSSSSSSSSSSSSSSSTSSSSSGGDRR
KRRERGSRSKSRSVRKGGESKDRKEKSRERGRQSPGRRTRSRSTSVRRKRYERSPTPKPT
RIHIGRLTRNVTKDHVLEIFSNYGEIKSIDFPTDRYHPQNGRGFCYVEYLNADDAENAMK
HMDGGQIDGTEVAVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11728.t5 CDD cd12365 RRM_RNPS1 122 195 8.06747E-40
5 g11728.t5 Gene3D G3DSA:3.30.70.330 - 117 195 8.4E-22
9 g11728.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 118 -
10 g11728.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
8 g11728.t5 MobiDBLite mobidb-lite consensus disorder prediction 23 55 -
11 g11728.t5 MobiDBLite mobidb-lite consensus disorder prediction 71 96 -
2 g11728.t5 PANTHER PTHR15481 RIBONUCLEIC ACID BINDING PROTEIN S1 5 193 8.8E-47
3 g11728.t5 PANTHER PTHR15481:SF2 RNA-BINDING PROTEIN WITH SERINE-RICH DOMAIN 1 5 193 8.8E-47
1 g11728.t5 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 123 192 4.6E-17
12 g11728.t5 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 120 195 16.295
7 g11728.t5 SMART SM00360 rrm1_1 121 195 1.0E-20
4 g11728.t5 SUPERFAMILY SSF54928 RNA-binding domain, RBD 114 194 1.33E-22

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