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.t16 TSS g7193.t16 22029455 22029455
chr_2 g7193 g7193.t16 isoform g7193.t16 22029527 22030940
chr_2 g7193 g7193.t16 exon g7193.t16.exon1 22029527 22029529
chr_2 g7193 g7193.t16 exon g7193.t16.exon2 22029729 22029817
chr_2 g7193 g7193.t16 cds g7193.t16.CDS1 22029737 22029817
chr_2 g7193 g7193.t16 exon g7193.t16.exon3 22029877 22030415
chr_2 g7193 g7193.t16 cds g7193.t16.CDS2 22029877 22030415
chr_2 g7193 g7193.t16 exon g7193.t16.exon4 22030469 22030598
chr_2 g7193 g7193.t16 cds g7193.t16.CDS3 22030469 22030511
chr_2 g7193 g7193.t16 exon g7193.t16.exon5 22030882 22030940
chr_2 g7193 g7193.t16 TTS g7193.t16 22031156 22031156

Sequences

>g7193.t16 Gene=g7193 Length=820
AAGAGAATAAAATGGCAGATGAAGATATTTCACTTAATGAAGATCAACTTCTTGATAATC
TTGATGATGCAAATGGTGATTTATTAACAGAAGAAGAGTCTGGAATGCAGATAGATCCAG
AATTGGAGGCAATTAAGGCAAGAGTTAAAGAAATGGAAGAAGAAGCAGAGAAACTTAAGC
AGCTACAATCAGAAGTTAATAAGCAAATGACCTTAGGTAGTCCCACTTCGAGTACACCCG
CTTTATCAGTTGAAGAGAAAATGGAGATTGACAATCGTTCTATATATGTTGGAAATGTTG
ATTATGGGGCCACAGCTGAAGAGCTAGAAGCCCATTTTCACGGTTGTGGTAGCATAAATC
GCGTAACGATTTTATGTAACAAAATAGATGGACATCCTAAGGGTTTTGCTTACATTGAAT
TTGCATCAAAGGACTTTGTTGAGACAGCATTAGCAATGAATGAGACTCTGTTTAGAGGAC
GTCAAATAAAAGTCATGTCCAAGAGGACCAACAGACCAGGACTTTGCGTTACTAATAGAA
TTCCCAGAGGTATGAGAGGAAGAGGATTATCAAGAGGACGAGCTTCTTGTTGTCACACTG
GCCATCGAGGTGGACGAGCTTCACGTGCTATGGGATACCGAGGACGTGGGATGAATTACT
ACTCACCTTATTAGAAAGAAAACAAAATTCATCAGTCAATGCAAACGTTTTCTTAGTCTT
ATAAGCATTTTTTACCATCATAATTTTCCTTTAATTACTAGATAAAAAAAATAAAAGAAA
AAATGATTTATTCAAAAAACATTATTTTGCTGCTCCGACG

>g7193.t16 Gene=g7193 Length=220
MADEDISLNEDQLLDNLDDANGDLLTEEESGMQIDPELEAIKARVKEMEEEAEKLKQLQS
EVNKQMTLGSPTSSTPALSVEEKMEIDNRSIYVGNVDYGATAEELEAHFHGCGSINRVTI
LCNKIDGHPKGFAYIEFASKDFVETALAMNETLFRGRQIKVMSKRTNRPGLCVTNRIPRG
MRGRGLSRGRASCCHTGHRGGRASRAMGYRGRGMNYYSPY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7193.t16 CDD cd12550 RRM_II_PABPN1 90 165 3.60068E-54
6 g7193.t16 Coils Coil Coil 38 68 -
5 g7193.t16 Gene3D G3DSA:3.30.70.330 - 83 170 4.8E-25
2 g7193.t16 PANTHER PTHR23236 EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H 23 207 4.9E-77
3 g7193.t16 PANTHER PTHR23236:SF21 PABPN1 PROTEIN-RELATED 23 207 4.9E-77
1 g7193.t16 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 91 160 6.0E-17
9 g7193.t16 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 89 166 15.596
8 g7193.t16 SMART SM00360 rrm1_1 90 162 1.8E-18
4 g7193.t16 SUPERFAMILY SSF54928 RNA-binding domain, RBD 76 191 1.25E-27

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

Pathway

  • This transcript belongs to the following pathways

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