General information for g2932.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Polyadenylate-binding protein 1.
Parent gene
- The parent gene g2932 is located on chr_3: 21297247..21299488 (+ strand)
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.t16 | TSS | g2932.t16 | 21295668 | 21295668 |
| chr_3 | g2932 | g2932.t16 | isoform | g2932.t16 | 21295784 | 21299174 |
| chr_3 | g2932 | g2932.t16 | exon | g2932.t16.exon1 | 21295784 | 21295892 |
| chr_3 | g2932 | g2932.t16 | exon | g2932.t16.exon2 | 21296024 | 21296195 |
| chr_3 | g2932 | g2932.t16 | cds | g2932.t16.CDS1 | 21296030 | 21296195 |
| chr_3 | g2932 | g2932.t16 | exon | g2932.t16.exon3 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t16 | cds | g2932.t16.CDS2 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t16 | exon | g2932.t16.exon4 | 21298433 | 21299174 |
| chr_3 | g2932 | g2932.t16 | cds | g2932.t16.CDS3 | 21298433 | 21298479 |
| chr_3 | g2932 | g2932.t16 | TTS | g2932.t16 | 21299483 | 21299483 |
Sequences
>g2932.t16 Gene=g2932 Length=1311
AAATTAATAAAAACCCTTAAAAAAATAATAAAACACGTGAAAACTCCAAAAATATAAGCA
AATTTTGATTTTTTGTTTTCTCCAATCGTAAAAACGTGTCAGAAGTGAACAAAAAATGGC
TTCATTATACGTAGGTGATTTACATGCTGACATTACGGAGGCGATGCTTTTCGAAAAATT
CTCTGCAGTTGGACCAGTGCTCTCGATTCGCGTTTGTCGAGATGTCATTTCTCGCCGCTC
ACTCGGATACGCCTATGTTAATTTCCAACAACCCGCTGATGCTGAACGTGTTCTTGATAC
AATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAATGTGGTCACAACGCGATCC
ATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAAATTTGGACAAATCTATTGA
CAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATATTTTAAGTTGCAAAGTCGC
AACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTACATTATGAAACTGAAGAAGC
CGCTACAATGTCGATTGAACGTGTTAATGTATTACACGTTCATCAACAGAAGCAGACTAC
CGCTAAAATCGAATAGAAGCTGTCATCGCCTGCGCCGTATAAAATCTATTGCTACTGACT
ACTATCAGTGACGCAAGAAATAATTTTTCATCAAGCATATAAAAAATATTTAAAAAATCC
AAAAAAAGAGTAAAATTTAAAAAATCACAAGTAAAAAAAATTTTAAAAATACTTTCAAAA
ATATAAACATAAAAACGAAGAATTGAAACACACGCGCGACTAAAGAAACTTTGTAGTAAA
AAATGAAGAAAAAAATAACTTTCAAAAAGAAAAATCAACAAAAAAATCGAAAAATATTAT
TGAGGAAAAAATCTCAAAAAATAGGAAACTTATTAACTTTTTTGTACTGCACGGAGTGAA
GAATTTTTTTCCTTCGATTTGATTGCGTATACCGTGCCTAACTTGTTTTCATTTCTCTTT
TATTGTTTAAAGGACATTGTTAAATATTCTCCTTTCTTAATCTTTCAAAATTTTATAATT
TTTACATGCCGCAAATTTTTTTTAAAGTTATTAACTTTATTTTGTTCTTACCTTAATGAT
ATATGTTGATTCAATAAAGCGGTTATGTATGCAGGCAAGTTTTAAAACAAAACCACACAA
CATTATCCCCAATTTCAATCGCATATTTTTATTGGAAAAATATCCAATTATAATTAAATA
AACACGTTTATATTATTATGAACTATATAAAATATTTCTTTTATATCCAAA
>g2932.t16 Gene=g2932 Length=166
MASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVISRRSLGYAYVNFQQPADAERVL
DTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCK
VATDENGQSKGYGFVHYETEEAATMSIERVNVLHVHQQKQTTAKIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2932.t16 | CDD | cd12378 | RRM1_I_PABPs | 3 | 82 | 0.000 |
| 13 | g2932.t16 | CDD | cd12379 | RRM2_I_PABPs | 88 | 151 | 0.000 |
| 8 | g2932.t16 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 83 | 0.000 |
| 9 | g2932.t16 | Gene3D | G3DSA:3.30.70.330 | - | 84 | 143 | 0.000 |
| 3 | g2932.t16 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 1 | 156 | 0.000 |
| 4 | g2932.t16 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 1 | 156 | 0.000 |
| 1 | g2932.t16 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 4 | 74 | 0.000 |
| 2 | g2932.t16 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 92 | 151 | 0.000 |
| 11 | g2932.t16 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 2 | 80 | 16.739 |
| 10 | g2932.t16 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 90 | 166 | 15.085 |
| 6 | g2932.t16 | SMART | SM00360 | rrm1_1 | 3 | 76 | 0.000 |
| 7 | g2932.t16 | SMART | SM00360 | rrm1_1 | 91 | 156 | 0.000 |
| 5 | g2932.t16 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 3 | 151 | 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.
