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.t18 TSS g7193.t18 22029455 22029455
chr_2 g7193 g7193.t18 isoform g7193.t18 22029527 22031157
chr_2 g7193 g7193.t18 exon g7193.t18.exon1 22029527 22029529
chr_2 g7193 g7193.t18 exon g7193.t18.exon2 22029729 22029817
chr_2 g7193 g7193.t18 exon g7193.t18.exon3 22029881 22030415
chr_2 g7193 g7193.t18 cds g7193.t18.CDS1 22029889 22030415
chr_2 g7193 g7193.t18 exon g7193.t18.exon4 22030469 22030598
chr_2 g7193 g7193.t18 cds g7193.t18.CDS2 22030469 22030511
chr_2 g7193 g7193.t18 exon g7193.t18.exon5 22030882 22031157
chr_2 g7193 g7193.t18 TTS g7193.t18 22031156 22031156

Sequences

>g7193.t18 Gene=g7193 Length=1033
AAGAGAATAAAATGGCAGATGAAGATATTTCACTTAATGAAGATCAACTTCTTGATAATC
TTGATGATGCAAATGGTGATTTATTAACAGAAAGTCTGGAATGCAGATAGATCCAGAATT
GGAGGCAATTAAGGCAAGAGTTAAAGAAATGGAAGAAGAAGCAGAGAAACTTAAGCAGCT
ACAATCAGAAGTTAATAAGCAAATGACCTTAGGTAGTCCCACTTCGAGTACACCCGCTTT
ATCAGTTGAAGAGAAAATGGAGATTGACAATCGTTCTATATATGTTGGAAATGTTGATTA
TGGGGCCACAGCTGAAGAGCTAGAAGCCCATTTTCACGGTTGTGGTAGCATAAATCGCGT
AACGATTTTATGTAACAAAATAGATGGACATCCTAAGGGTTTTGCTTACATTGAATTTGC
ATCAAAGGACTTTGTTGAGACAGCATTAGCAATGAATGAGACTCTGTTTAGAGGACGTCA
AATAAAAGTCATGTCCAAGAGGACCAACAGACCAGGACTTTGCGTTACTAATAGAATTCC
CAGAGGTATGAGAGGAAGAGGATTATCAAGAGGACGAGCTTCTTGTTGTCACACTGGCCA
TCGAGGTGGACGAGCTTCACGTGCTATGGGATACCGAGGACGTGGGATGAATTACTACTC
ACCTTATTAGAAAGAAAACAAAATTCATCAGTCAATGCAAACGTTTTCTTAGTCTTATAA
GCATTTTTTACCATCATAATTTTCCTTTAATTACTAGATAAAAAAAATAAAAGAAAAAAT
GATTTATTCAAAAAACATTATTTTGCTGCTCCGACGATTTTGAAAAAAAAAGGAAGTTTC
AAATCAAAAAAAAAATATATATGTGGATTGAAGCGTTAAAAGAAAGACATTCATTATGAT
TTGTTTTACTCACTACAAATAATGTTTTTTGACATTACACAAAATTTACACAATAGCATA
AAACAATCTATCAATCCAATCAAGATGAAAAAAGGACAAAAGATTTCAACAGAAGAAGAA
AATTCCAAATCCA

>g7193.t18 Gene=g7193 Length=189
MQIDPELEAIKARVKEMEEEAEKLKQLQSEVNKQMTLGSPTSSTPALSVEEKMEIDNRSI
YVGNVDYGATAEELEAHFHGCGSINRVTILCNKIDGHPKGFAYIEFASKDFVETALAMNE
TLFRGRQIKVMSKRTNRPGLCVTNRIPRGMRGRGLSRGRASCCHTGHRGGRASRAMGYRG
RGMNYYSPY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g7193.t18 CDD cd12550 RRM_II_PABPN1 59 134 2.64046E-54
6 g7193.t18 Coils Coil Coil 7 37 -
5 g7193.t18 Gene3D G3DSA:3.30.70.330 - 52 139 3.4E-25
2 g7193.t18 PANTHER PTHR23236 EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H 4 177 3.9E-76
3 g7193.t18 PANTHER PTHR23236:SF21 PABPN1 PROTEIN-RELATED 4 177 3.9E-76
1 g7193.t18 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 60 129 4.4E-17
9 g7193.t18 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 58 135 15.596
8 g7193.t18 SMART SM00360 rrm1_1 59 131 1.8E-18
4 g7193.t18 SUPERFAMILY SSF54928 RNA-binding domain, RBD 44 160 7.66E-28

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. There were no conditions that were differentially expressed