Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyadenylate-binding protein 2.

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_2 g7193 g7193.t11 TSS g7193.t11 22029455 22029455
chr_2 g7193 g7193.t11 isoform g7193.t11 22029483 22031157
chr_2 g7193 g7193.t11 exon g7193.t11.exon1 22029483 22029529
chr_2 g7193 g7193.t11 exon g7193.t11.exon2 22029729 22029817
chr_2 g7193 g7193.t11 cds g7193.t11.CDS1 22029737 22029817
chr_2 g7193 g7193.t11 exon g7193.t11.exon3 22029877 22029940
chr_2 g7193 g7193.t11 cds g7193.t11.CDS2 22029877 22029940
chr_2 g7193 g7193.t11 exon g7193.t11.exon4 22030001 22030415
chr_2 g7193 g7193.t11 cds g7193.t11.CDS3 22030001 22030415
chr_2 g7193 g7193.t11 exon g7193.t11.exon5 22030469 22030598
chr_2 g7193 g7193.t11 cds g7193.t11.CDS4 22030469 22030511
chr_2 g7193 g7193.t11 exon g7193.t11.exon6 22030882 22031157
chr_2 g7193 g7193.t11 TTS g7193.t11 22031156 22031156

Sequences

>g7193.t11 Gene=g7193 Length=1021
AGTAAGGAAGACATTTTAAATTTTGTGTTTTAAAACGAAATAGTAAGAGAATAAAATGGC
AGATGAAGATATTTCACTTAATGAAGATCAACTTCTTGATAATCTTGATGATGCAAATGG
TGATTTATTAACAGAAGAAGAGTCTGGAATGCAGATAGATCCAGAATTGGAGGCAATTAA
GGCAAGAGTTAAAGAAATGGGTAGTCCCACTTCGAGTACACCCGCTTTATCAGTTGAAGA
GAAAATGGAGATTGACAATCGTTCTATATATGTTGGAAATGTTGATTATGGGGCCACAGC
TGAAGAGCTAGAAGCCCATTTTCACGGTTGTGGTAGCATAAATCGCGTAACGATTTTATG
TAACAAAATAGATGGACATCCTAAGGGTTTTGCTTACATTGAATTTGCATCAAAGGACTT
TGTTGAGACAGCATTAGCAATGAATGAGACTCTGTTTAGAGGACGTCAAATAAAAGTCAT
GTCCAAGAGGACCAACAGACCAGGACTTTGCGTTACTAATAGAATTCCCAGAGGTATGAG
AGGAAGAGGATTATCAAGAGGACGAGCTTCTTGTTGTCACACTGGCCATCGAGGTGGACG
AGCTTCACGTGCTATGGGATACCGAGGACGTGGGATGAATTACTACTCACCTTATTAGAA
AGAAAACAAAATTCATCAGTCAATGCAAACGTTTTCTTAGTCTTATAAGCATTTTTTACC
ATCATAATTTTCCTTTAATTACTAGATAAAAAAAATAAAAGAAAAAATGATTTATTCAAA
AAACATTATTTTGCTGCTCCGACGATTTTGAAAAAAAAAGGAAGTTTCAAATCAAAAAAA
AAATATATATGTGGATTGAAGCGTTAAAAGAAAGACATTCATTATGATTTGTTTTACTCA
CTACAAATAATGTTTTTTGACATTACACAAAATTTACACAATAGCATAAAACAATCTATC
AATCCAATCAAGATGAAAAAAGGACAAAAGATTTCAACAGAAGAAGAAAATTCCAAATCC
A

>g7193.t11 Gene=g7193 Length=200
MADEDISLNEDQLLDNLDDANGDLLTEEESGMQIDPELEAIKARVKEMGSPTSSTPALSV
EEKMEIDNRSIYVGNVDYGATAEELEAHFHGCGSINRVTILCNKIDGHPKGFAYIEFASK
DFVETALAMNETLFRGRQIKVMSKRTNRPGLCVTNRIPRGMRGRGLSRGRASCCHTGHRG
GRASRAMGYRGRGMNYYSPY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7193.t11 CDD cd12550 RRM_II_PABPN1 70 145 0.000
6 g7193.t11 Gene3D G3DSA:3.30.70.330 - 63 150 0.000
2 g7193.t11 PANTHER PTHR23236:SF16 POLYADENYLATE-BINDING PROTEIN 2 55 180 0.000
3 g7193.t11 PANTHER PTHR23236 EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H 55 180 0.000
1 g7193.t11 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 71 140 0.000
7 g7193.t11 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 69 146 15.596
5 g7193.t11 SMART SM00360 rrm1_1 70 142 0.000
4 g7193.t11 SUPERFAMILY SSF54928 RNA-binding domain, RBD 60 171 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:1904247 positive regulation of polynucleotide adenylyltransferase activity BP
GO:0003723 RNA binding MF
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