Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyadenylate-binding protein.

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 g2932 g2932.t19 TSS g2932.t19 21295668 21295668
chr_3 g2932 g2932.t19 isoform g2932.t19 21296022 21297247
chr_3 g2932 g2932.t19 exon g2932.t19.exon1 21296022 21296195
chr_3 g2932 g2932.t19 cds g2932.t19.CDS1 21296030 21296195
chr_3 g2932 g2932.t19 exon g2932.t19.exon2 21296710 21296997
chr_3 g2932 g2932.t19 cds g2932.t19.CDS2 21296710 21296997
chr_3 g2932 g2932.t19 exon g2932.t19.exon3 21297056 21297247
chr_3 g2932 g2932.t19 cds g2932.t19.CDS3 21297056 21297246
chr_3 g2932 g2932.t19 TTS g2932.t19 NA NA

Sequences

>g2932.t19 Gene=g2932 Length=654
AGCAAAAAATGGCTTCATTATACGTAGGTGATTTACATGCTGACATTACGGAGGCGATGC
TTTTCGAAAAATTCTCTGCAGTTGGACCAGTGCTCTCGATTCGCGTTTGTCGAGATGTCA
TTTCTCGCCGCTCACTCGGATACGCCTATGTTAATTTCCAACAACCCGCTGATGCTGAAC
GTGTTCTTGATACAATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAATGTGGT
CACAACGCGATCCATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAAATTTGG
ACAAATCTATTGACAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATATTTTAA
GTTGCAAAGTCGCAACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTACATTATG
AAACTGAAGAAGCCGCTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTAAACGAAA
AGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAGGAGAAA
AGGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATGACGAGT
CATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGA

>g2932.t19 Gene=g2932 Length=215
MASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVISRRSLGYAYVNFQQPADAERVL
DTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCK
VATDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIPRKEREKELGEKAK
MYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2932.t19 CDD cd12378 RRM1_I_PABPs 3 82 0.0000000
17 g2932.t19 CDD cd12379 RRM2_I_PABPs 88 164 0.0000000
10 g2932.t19 Gene3D G3DSA:3.30.70.330 - 2 83 0.0000000
12 g2932.t19 Gene3D G3DSA:3.30.70.330 - 84 174 0.0000000
11 g2932.t19 Gene3D G3DSA:3.30.70.330 - 175 215 0.0000006
4 g2932.t19 PANTHER PTHR24012 RNA BINDING PROTEIN 1 215 0.0000000
5 g2932.t19 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 1 215 0.0000000
1 g2932.t19 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 4 74 0.0000000
2 g2932.t19 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 92 159 0.0000000
3 g2932.t19 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 185 215 0.0000220
15 g2932.t19 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 2 80 16.7390000
13 g2932.t19 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 90 167 16.3470000
14 g2932.t19 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 183 215 8.5180000
8 g2932.t19 SMART SM00360 rrm1_1 3 76 0.0000000
9 g2932.t19 SMART SM00360 rrm1_1 91 163 0.0000000
6 g2932.t19 SUPERFAMILY SSF54928 RNA-binding domain, RBD 3 171 0.0000000
7 g2932.t19 SUPERFAMILY SSF54928 RNA-binding domain, RBD 162 215 0.0000004

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.

Raw TPM values