Gene loci information

Transcript annotation

  • This transcript has been annotated as RNA-binding protein 8A.

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 g1641 g1641.t1 TTS g1641.t1 12271065 12271065
chr_3 g1641 g1641.t1 isoform g1641.t1 12271182 12271799
chr_3 g1641 g1641.t1 exon g1641.t1.exon1 12271182 12271480
chr_3 g1641 g1641.t1 cds g1641.t1.CDS1 12271182 12271480
chr_3 g1641 g1641.t1 exon g1641.t1.exon2 12271539 12271679
chr_3 g1641 g1641.t1 cds g1641.t1.CDS2 12271539 12271679
chr_3 g1641 g1641.t1 exon g1641.t1.exon3 12271739 12271799
chr_3 g1641 g1641.t1 cds g1641.t1.CDS3 12271739 12271799
chr_3 g1641 g1641.t1 TSS g1641.t1 12271884 12271884

Sequences

>g1641.t1 Gene=g1641 Length=501
ATGGCTGACGTTTTAGATATTGATAATGCTGAAGATTTTGAGGTTGATGATGATGGTGAT
CAGGGAATTTTGCGATTAAAAGAAAAAGCAAAGAAGAAAAAAGGTCGTGGATTTGGAGCT
GATACAATCCATCGTGAAACAATTGATTATGAAAGTGTACGTGATGATACCAATGAAGAT
GTTGAACCAGGCCCACAAAGATCTGTAGAAGGCTGGATCTTGTTTATTACATCAATACAT
GAAGAGGCACATGAGGATGATATTCAAGAGAAATTCTGTGAATTTGGAGATATCAAAAAC
ATTCATCTTAATCTCGATCGAAGAACTGGCTTTCTTAAAGGATATGCTCTAGTCGAATAT
GAGACTTATAAGCAAGCACTTGCAGCTAAAGAAGCAATGGATGGTGCAGAAATTTTGGGA
CAAAAAATCAGTGTCGATTGGTGTTTCGTGAAAGGTCCGAAAAGATCGAGAAAAGGTGCT
GATCGCAAAAAGAAGCAGTAA

>g1641.t1 Gene=g1641 Length=166
MADVLDIDNAEDFEVDDDGDQGILRLKEKAKKKKGRGFGADTIHRETIDYESVRDDTNED
VEPGPQRSVEGWILFITSIHEEAHEDDIQEKFCEFGDIKNIHLNLDRRTGFLKGYALVEY
ETYKQALAAKEAMDGAEILGQKISVDWCFVKGPKRSRKGADRKKKQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1641.t1 CDD cd12324 RRM_RBM8 66 153 0.000
9 g1641.t1 Gene3D G3DSA:3.30.70.330 - 1 164 0.000
2 g1641.t1 PANTHER PTHR45894:SF1 RNA-BINDING PROTEIN 8A 2 162 0.000
3 g1641.t1 PANTHER PTHR45894 RNA-BINDING PROTEIN 8A 2 162 0.000
6 g1641.t1 PRINTS PR01738 RNA binding motif protein 8 family signature 27 39 0.000
4 g1641.t1 PRINTS PR01738 RNA binding motif protein 8 family signature 63 77 0.000
5 g1641.t1 PRINTS PR01738 RNA binding motif protein 8 family signature 119 135 0.000
7 g1641.t1 PRINTS PR01738 RNA binding motif protein 8 family signature 137 149 0.000
1 g1641.t1 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 74 143 0.000
12 g1641.t1 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 72 150 14.266
11 g1641.t1 SMART SM00360 rrm1_1 73 146 0.000
8 g1641.t1 SUPERFAMILY SSF54928 RNA-binding domain, RBD 57 159 0.000

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:0006396 RNA processing BP
GO:0005634 nucleus CC
GO:0003729 mRNA binding MF
GO:0003723 RNA binding MF
GO:0005737 cytoplasm CC
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