Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative RNA-binding protein 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_3 g1625 g1625.t16 TTS g1625.t16 12205289 12205289
chr_3 g1625 g1625.t16 isoform g1625.t16 12206322 12208169
chr_3 g1625 g1625.t16 exon g1625.t16.exon1 12206322 12206327
chr_3 g1625 g1625.t16 cds g1625.t16.CDS1 12206324 12206327
chr_3 g1625 g1625.t16 exon g1625.t16.exon2 12207081 12207264
chr_3 g1625 g1625.t16 cds g1625.t16.CDS2 12207081 12207264
chr_3 g1625 g1625.t16 exon g1625.t16.exon3 12207409 12207549
chr_3 g1625 g1625.t16 cds g1625.t16.CDS3 12207409 12207549
chr_3 g1625 g1625.t16 exon g1625.t16.exon4 12207695 12208169
chr_3 g1625 g1625.t16 cds g1625.t16.CDS4 12207695 12207695
chr_3 g1625 g1625.t16 TSS g1625.t16 NA NA

Sequences

>g1625.t16 Gene=g1625 Length=806
ATGTGTAAAAATCGATGTCAGTTAGGAAATTAAATAAATTTTTCAAGAAAATTGTCTTTT
TCATTTTGTAAATTTTAAAATTGAATTTTAATTATTTCATTGAATAATTTACTACAGTTT
TAATAAATAAAAAAAAATCTAAATTAATTTTAAATCAATTCTTAATTTCTACATTCAATT
GAAAAGAGCTTTTTATTAAAAATTTAATTATTTTACAAACCTAACTTCAAATATCATTTC
AACCCTGAATCATGCACATTCTTTTCGATATTTAACTTTAAAAATCAACTTAACTTATTA
TATCATAACATAAAATTAAATTTAAGAAAATATTGAGATTAAAAAATTTATTAAATCGTG
CAGTCTTTGATTATAAATTGATATAAAAGTAAGTTAATTTCACAGCTCAAATTATATTCT
TATAAAATATTCAAAATTAAGTTAAAAATTTCATCAATTTAGTCCCTAAAAAGAATGCCT
CGATATCGCGAATGGGATTTAAAATGTAAAGTTTATGTCGGTAATTTAGATCAGAGAGCA
ACAAAGCATCAAATTGAAGATATATTTAGTAAATATGGCCCATTAAGAAATGTGTGGGTG
GCAAGAAATCCACCAGGCTTTGCTTTTGTTGAATTCGAGGACAACCGCGATGCAGAAGAT
GCGGTAAGAAATTTGGACGGAAGTCGCGCGTGTGGTAGTCGCATTCGTGTGGAAATGTCA
AGTGGCAGAACTAGACATAATCGAGGCAGTGGCGGTTCAAGCGATAGACGTCGCAATGAT
CGTGGCAGTGGAAGATACAGGAAACA

>g1625.t16 Gene=g1625 Length=110
MPRYREWDLKCKVYVGNLDQRATKHQIEDIFSKYGPLRNVWVARNPPGFAFVEFEDNRDA
EDAVRNLDGSRACGSRIRVEMSSGRTRHNRGSGGSSDRRRNDRGSGRYRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g1625.t16 CDD cd12373 RRM_SRSF3_like 12 84 1.55536E-42
5 g1625.t16 Gene3D G3DSA:3.30.70.330 - 4 110 1.3E-26
8 g1625.t16 MobiDBLite mobidb-lite consensus disorder prediction 75 110 -
9 g1625.t16 MobiDBLite mobidb-lite consensus disorder prediction 81 110 -
2 g1625.t16 PANTHER PTHR23147:SF186 RNA-BINDING PROTEIN 1-RELATED 2 109 1.8E-47
3 g1625.t16 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 2 109 1.8E-47
1 g1625.t16 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 13 77 8.5E-20
10 g1625.t16 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 11 84 18.035
7 g1625.t16 SMART SM00360 rrm1_1 12 80 7.5E-23
4 g1625.t16 SUPERFAMILY SSF54928 RNA-binding domain, RBD 11 109 9.94E-29

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed