General information for g2932.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Polyadenylate-binding protein.
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.t20 | isoform | g2932.t20 | 21296710 | 21297328 |
| chr_3 | g2932 | g2932.t20 | exon | g2932.t20.exon1 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t20 | cds | g2932.t20.CDS1 | 21296730 | 21296997 |
| chr_3 | g2932 | g2932.t20 | exon | g2932.t20.exon2 | 21297056 | 21297328 |
| chr_3 | g2932 | g2932.t20 | cds | g2932.t20.CDS2 | 21297056 | 21297327 |
| chr_3 | g2932 | g2932.t20 | TSS | g2932.t20 | NA | NA |
| chr_3 | g2932 | g2932.t20 | TTS | g2932.t20 | NA | NA |
Sequences
>g2932.t20 Gene=g2932 Length=561
CTGAACGTGTTCTTGATACAATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAA
TGTGGTCACAACGCGATCCATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAA
ATTTGGACAAATCTATTGACAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATA
TTTTAAGTTGCAAAGTCGCAACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTAC
ATTATGAAACTGAAGAAGCCGCTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTAA
ACGAAAAGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAG
GAGAAAAGGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATG
ACGAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGA
CTAAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCTG
AAGAAGCTGTAAAGCAATTGA
>g2932.t20 Gene=g2932 Length=180
MNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCKVA
TDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIPRKEREKELGEKAKMY
TNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFVAFESAEAAEEAVKQL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2932.t20 | CDD | cd12379 | RRM2_I_PABPs | 26 | 102 | 0.0000000 |
| 9 | g2932.t20 | Gene3D | G3DSA:3.30.70.330 | - | 17 | 109 | 0.0000000 |
| 10 | g2932.t20 | Gene3D | G3DSA:3.30.70.330 | - | 110 | 180 | 0.0000000 |
| 3 | g2932.t20 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 1 | 179 | 0.0000000 |
| 4 | g2932.t20 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 1 | 179 | 0.0000000 |
| 2 | g2932.t20 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 30 | 97 | 0.0000000 |
| 1 | g2932.t20 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 123 | 180 | 0.0000000 |
| 12 | g2932.t20 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 28 | 105 | 16.3470000 |
| 11 | g2932.t20 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 121 | 180 | 16.3640000 |
| 7 | g2932.t20 | SMART | SM00360 | rrm1_1 | 29 | 101 | 0.0000000 |
| 8 | g2932.t20 | SMART | SM00360 | rrm1_1 | 122 | 180 | 0.0000005 |
| 5 | g2932.t20 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 4 | 111 | 0.0000000 |
| 6 | g2932.t20 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 120 | 179 | 0.0000000 |
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. There were no conditions that were differentially expressed