General information for g2932.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Polyadenylate-binding protein 4.
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.t23 | isoform | g2932.t23 | 21297247 | 21298479 |
| chr_3 | g2932 | g2932.t23 | exon | g2932.t23.exon1 | 21297247 | 21297958 |
| chr_3 | g2932 | g2932.t23 | cds | g2932.t23.CDS1 | 21297397 | 21297958 |
| chr_3 | g2932 | g2932.t23 | exon | g2932.t23.exon2 | 21298072 | 21298479 |
| chr_3 | g2932 | g2932.t23 | cds | g2932.t23.CDS2 | 21298072 | 21298094 |
| chr_3 | g2932 | g2932.t23 | TTS | g2932.t23 | 21298583 | 21298583 |
| chr_3 | g2932 | g2932.t23 | TSS | g2932.t23 | NA | NA |
Sequences
>g2932.t23 Gene=g2932 Length=1120
ACTAAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCT
GAAGAAGCTGTAAAGCAATTGAATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTT
GGCCGTGCTCAAAAGAAAAACGAACGTCAAATGGAATTGAAGCGTAAATTTGAGCAAATC
AAGATTGAACGTATGTCACGCTATCAAGGAGTCAATCTTTACGTCAAAAATTTGGACGAT
TCAATTGATGATGAACGTTTACGAAAAGAGTTTGCTCCATTTGGAACAATTACTAGCGCC
AAGGTAATGATGGAAGATGGACGTTCCAAAGGATTTGGATTCGTTTGTTTCTCTGCTGCT
GAAGAAGCAACAAAGGCAGTCACAGAAATGAATGGTCGTATTGTTGGCTCAAAGCCATTG
TATGTTGCATTGGCTCAAAAGAAGGAAGATCGTAAAGCTCATTTAGCATCTCAATACATG
CAACGAATGACTAACATGCGCATGCAACAAATGGGTCAAATATTCCAACCAGGCGGTGCT
GGAGGATATTTTGTTCCAACAATTCCGCAACCACAACGTTTCTATGGACCAGCAGTCACA
CAATTGCGTACTACACCAAGATGGGCAAGTCAACCACAAGTTCGTCAGCAACAAGGCGCT
ACTGCTTATCCAAATATGGCCGCAGTTAGTGCAACTCAATATCGTCAACCTGATTCAACA
AGGCCGTGGAATTAATGCACCAGTTGCACAACGTGGAGCTCCAGCTAATTATAAATACAC
TACAAATATGCGCAATGCTCCACAAGCTGTTCAAATGCCTGCTCAACCAACAGCACCACA
GGCTGTCATCGTTAAAGGCCAGGAGCCACTTACTGCTAGCATGTTAGCAGCTGCTCAGCC
AGCAGAACAAAAACAAATGCTTGGTGAACGCTTATTCCCATTGATTGAGCAAATGTATCC
AGCTTTGGCAGGAAAGATTACTGGCATGTTGCTTGAAATTGATAACTCTGAATTGTTGCA
CATGCTTGAGCACAATGAATCATTGAAATCTAAAGTTGAAGAAGCTGTTGCTGTATTACA
CGTTCATCAACAGAAGCAGACTACCGCTAAAATCGAATAG
>g2932.t23 Gene=g2932 Length=194
MELKRKFEQIKIERMSRYQGVNLYVKNLDDSIDDERLRKEFAPFGTITSAKVMMEDGRSK
GFGFVCFSAAEEATKAVTEMNGRIVGSKPLYVALAQKKEDRKAHLASQYMQRMTNMRMQQ
MGQIFQPGGAGGYFVPTIPQPQRFYGPAVTQLRTTPRWASQPQVRQQQGATAYPNMAAVS
ATQYRQPDSTRPWN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2932.t23 | CDD | cd12381 | RRM4_I_PABPs | 20 | 97 | 4.94543E-59 |
| 5 | g2932.t23 | Gene3D | G3DSA:3.30.70.330 | - | 5 | 112 | 2.6E-26 |
| 8 | g2932.t23 | MobiDBLite | mobidb-lite | consensus disorder prediction | 156 | 194 | - |
| 2 | g2932.t23 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 2 | 177 | 7.9E-82 |
| 3 | g2932.t23 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 2 | 177 | 7.9E-82 |
| 1 | g2932.t23 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 23 | 90 | 1.5E-18 |
| 9 | g2932.t23 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 21 | 97 | 18.751 |
| 7 | g2932.t23 | SMART | SM00360 | rrm1_1 | 22 | 93 | 4.7E-24 |
| 4 | g2932.t23 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 19 | 118 | 4.57E-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
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.
