Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyadenylate-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 g2932 g2932.t18 TSS g2932.t18 21295668 21295668
chr_3 g2932 g2932.t18 isoform g2932.t18 21295885 21297247
chr_3 g2932 g2932.t18 exon g2932.t18.exon1 21295885 21295920
chr_3 g2932 g2932.t18 exon g2932.t18.exon2 21296024 21296195
chr_3 g2932 g2932.t18 cds g2932.t18.CDS1 21296030 21296195
chr_3 g2932 g2932.t18 exon g2932.t18.exon3 21296710 21296988
chr_3 g2932 g2932.t18 cds g2932.t18.CDS2 21296710 21296988
chr_3 g2932 g2932.t18 exon g2932.t18.exon4 21297136 21297247
chr_3 g2932 g2932.t18 cds g2932.t18.CDS3 21297136 21297152
chr_3 g2932 g2932.t18 TTS g2932.t18 NA NA

Sequences

>g2932.t18 Gene=g2932 Length=599
GAAGTGAAGTGAAAAGAAAAACGACAAAGAAAGAAACAAAAAATGGCTTCATTATACGTA
GGTGATTTACATGCTGACATTACGGAGGCGATGCTTTTCGAAAAATTCTCTGCAGTTGGA
CCAGTGCTCTCGATTCGCGTTTGTCGAGATGTCATTTCTCGCCGCTCACTCGGATACGCC
TATGTTAATTTCCAACAACCCGCTGATGCTGAACGTGTTCTTGATACAATGAACTTTGAT
GTAATAAAAGGACGTCCAATTCGTATAATGTGGTCACAACGCGATCCATCACTTCGTAAA
TCAGGCGTTGGTAATGTTTTCATCAAAAATTTGGACAAATCTATTGACAACAAGGCTATG
TATGATACATTTGGAGCATTTGGAAATATTTTAAGTTGCAAAGTCGCAACTGACGAGAAT
GGCCAATCAAAAGGCTATGGATTCGTACATTATGAAACTGAAGAAGCCGCTACAATGTCG
ATTGAACGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATGA
CGAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGA

>g2932.t18 Gene=g2932 Length=153
MASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVISRRSLGYAYVNFQQPADAERVL
DTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCK
VATDENGQSKGYGFVHYETEEAATMSIERKNVY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g2932.t18 CDD cd12378 RRM1_I_PABPs 3 82 0.000
13 g2932.t18 CDD cd12379 RRM2_I_PABPs 88 151 0.000
8 g2932.t18 Gene3D G3DSA:3.30.70.330 - 2 83 0.000
9 g2932.t18 Gene3D G3DSA:3.30.70.330 - 84 143 0.000
3 g2932.t18 PANTHER PTHR24012 RNA BINDING PROTEIN 1 151 0.000
4 g2932.t18 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 1 151 0.000
1 g2932.t18 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 4 74 0.000
2 g2932.t18 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 92 151 0.000
11 g2932.t18 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 2 80 16.739
10 g2932.t18 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 90 153 14.505
6 g2932.t18 SMART SM00360 rrm1_1 3 76 0.000
7 g2932.t18 SMART SM00360 rrm1_1 91 153 0.000
5 g2932.t18 SUPERFAMILY SSF54928 RNA-binding domain, RBD 3 150 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: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