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.t14 TSS g2932.t14 21295668 21295668
chr_3 g2932 g2932.t14 isoform g2932.t14 21295784 21297383
chr_3 g2932 g2932.t14 exon g2932.t14.exon1 21295784 21295920
chr_3 g2932 g2932.t14 exon g2932.t14.exon2 21296024 21296170
chr_3 g2932 g2932.t14 exon g2932.t14.exon3 21296710 21296997
chr_3 g2932 g2932.t14 cds g2932.t14.CDS1 21296730 21296997
chr_3 g2932 g2932.t14 exon g2932.t14.exon4 21297056 21297383
chr_3 g2932 g2932.t14 cds g2932.t14.CDS2 21297056 21297381
chr_3 g2932 g2932.t14 TTS g2932.t14 NA NA

Sequences

>g2932.t14 Gene=g2932 Length=900
AAATTAATAAAAACCCTTAAAAAAATAATAAAACACGTGAAAACTCCAAAAATATAAGCA
AATTTTGATTTTTTGTTTTCTCCAATCGTAAAAACGTGTCAGAAGTGAAGTGAAAAGAAA
AACGACAAAGAAAGAAACAAAAAATGGCTTCATTATACGTAGGTGATTTACATGCTGACA
TTACGGAGGCGATGCTTTTCGAAAAATTCTCTGCAGTTGGACCAGTGCTCTCGATTCGCG
TTTGTCGAGATGTCATTTCTCGCCGCTCACTCGGATACGCCTATCTGAACGTGTTCTTGA
TACAATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAATGTGGTCACAACGCGA
TCCATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAAATTTGGACAAATCTAT
TGACAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATATTTTAAGTTGCAAAGT
CGCAACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTACATTATGAAACTGAAGA
AGCCGCTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTAAACGAAAAGAAAGTCTT
CGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAGGAGAAAAGGCAAAAAT
GTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATGACGAGTCATTGTATGA
AATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGACTAAGGATGGAAAATC
ACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCTGAAGAAGCTGTAAAGCA
ATTGAATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTTGGCCGTGCTCAAAAGAA

>g2932.t14 Gene=g2932 Length=198
MNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCKVA
TDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIPRKEREKELGEKAKMY
TNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFVAFESAEAAEEAVKQL
NGKKLGDDKVLYVGRAQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2932.t14 CDD cd12379 RRM2_I_PABPs 26 102 0.000
9 g2932.t14 Gene3D G3DSA:3.30.70.330 - 28 116 0.000
10 g2932.t14 Gene3D G3DSA:3.30.70.330 - 117 198 0.000
3 g2932.t14 PANTHER PTHR24012 RNA BINDING PROTEIN 1 198 0.000
4 g2932.t14 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 1 198 0.000
2 g2932.t14 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 30 97 0.000
1 g2932.t14 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 123 189 0.000
12 g2932.t14 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 28 105 16.347
11 g2932.t14 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 121 198 19.331
7 g2932.t14 SMART SM00360 rrm1_1 29 101 0.000
8 g2932.t14 SMART SM00360 rrm1_1 122 194 0.000
5 g2932.t14 SUPERFAMILY SSF54928 RNA-binding domain, RBD 4 111 0.000
6 g2932.t14 SUPERFAMILY SSF54928 RNA-binding domain, RBD 120 197 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.

Raw TPM values