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.t14 TTS g1625.t14 12204643 12204643
chr_3 g1625 g1625.t14 isoform g1625.t14 12204684 12208169
chr_3 g1625 g1625.t14 exon g1625.t14.exon1 12204684 12205135
chr_3 g1625 g1625.t14 cds g1625.t14.CDS1 12205015 12205135
chr_3 g1625 g1625.t14 exon g1625.t14.exon2 12207081 12207241
chr_3 g1625 g1625.t14 cds g1625.t14.CDS2 12207081 12207241
chr_3 g1625 g1625.t14 exon g1625.t14.exon3 12207428 12207549
chr_3 g1625 g1625.t14 cds g1625.t14.CDS3 12207428 12207549
chr_3 g1625 g1625.t14 exon g1625.t14.exon4 12207782 12208169
chr_3 g1625 g1625.t14 cds g1625.t14.CDS4 12207782 12207782
chr_3 g1625 g1625.t14 TSS g1625.t14 NA NA

Sequences

>g1625.t14 Gene=g1625 Length=1123
ATGTGTAAAAATCGATGTCAGTTAGGAAATTAAATAAATTTTTCAAGAAAATTGTCTTTT
TCATTTTGTAAATTTTAAAATTGAATTTTAATTATTTCATTGAATAATTTACTACAGTTT
TAATAAATAAAAAAAAATCTAAATTAATTTTAAATCAATTCTTAATTTCTACATTCAATT
GAAAAGAGCTTTTTATTAAAAATTTAATTATTTTACAAACCTAACTTCAAATATCATTTC
AACCCTGAATCATGCACATTCTTTTCGATATTTAACTTTAAAAATCAACTTAACTTATTA
TATCATAACATAAAATTAAATTTAAGAAAATATTGAGATTAAAAAATTTATTAAATCGTG
CAGTCTTTGATTATAAATTGATATAAAATGCCTCGATATCGCGAATGGGATTTAAAATGT
AAAGTTTATGTCGGTAATTTAGATCAGAGAGCAACAAAGCATCAAATTGAAGATATATTT
AGTAAATATGGCCCATTAAGAAATGTGTGGGACAACCGCGATGCAGAAGATGCGGTAAGA
AATTTGGACGGAAGTCGCGCGTGTGGTAGTCGCATTCGTGTGGAAATGTCAAGTGGCAGA
ACTAGACATAATCGAGGCAGTGGCGGTTCAAGCGATAGACGTCGCAATGATCGTGGCAGT
GGAAGATACAGATCACGTTCGAGAGATAGATCAAGAAGTCCACGCCGATCACCACGTCGT
TCAAGACGTTCACGATCACGCTCAAGAAGTGGCGAAAGAAGCGACCGTTCTGAATCGCGT
GATCGTCGTTAAAATTATTTAATTATTTTCTTTGTGTCTTTCAAATATTTTTGTTTAATT
TTTTTGATCAAACTTAAATGCATTTTATTAAAAAACACAATTTTTATGTTCTCGTTTGTG
AGAAAAATAATTTAAAAAACAGGACAAAAAAATTATGAATTTGAATGGTAAAAAATTTTA
TATGACGATAATTGAGTTACAATGAATTAATTAATAATTATGTTTTTTGAACTCTCTTTT
GCTACTTATTTGTCTTCTTTAAATGAGTTTCATAAACTCACAAATGAAATAATATTTCCT
ATAGAAATTTTATTAACAAAACATAAAAATAAAACACTACTAA

>g1625.t14 Gene=g1625 Length=134
MPRYREWDLKCKVYVGNLDQRATKHQIEDIFSKYGPLRNVWDNRDAEDAVRNLDGSRACG
SRIRVEMSSGRTRHNRGSGGSSDRRRNDRGSGRYRSRSRDRSRSPRRSPRRSRRSRSRSR
SGERSDRSESRDRR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1625.t14 Coils Coil Coil 131 134 -
10 g1625.t14 Gene3D G3DSA:3.30.70.330 - 4 80 4.5E-10
9 g1625.t14 MobiDBLite mobidb-lite consensus disorder prediction 61 134 -
8 g1625.t14 MobiDBLite mobidb-lite consensus disorder prediction 67 98 -
7 g1625.t14 MobiDBLite mobidb-lite consensus disorder prediction 99 118 -
6 g1625.t14 MobiDBLite mobidb-lite consensus disorder prediction 119 134 -
2 g1625.t14 PANTHER PTHR23147:SF186 RNA-BINDING PROTEIN 1-RELATED 2 123 3.3E-28
3 g1625.t14 PANTHER PTHR23147 SERINE/ARGININE RICH SPLICING FACTOR 2 123 3.3E-28
1 g1625.t14 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 13 40 8.9E-6
5 g1625.t14 SMART SM00360 rrm1_1 12 66 6.3E-6
4 g1625.t14 SUPERFAMILY SSF54928 RNA-binding domain, RBD 11 99 2.96E-18

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