General information for g2932.t21
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.t21 | isoform | g2932.t21 | 21297070 | 21298540 |
| chr_3 | g2932 | g2932.t21 | exon | g2932.t21.exon1 | 21297070 | 21298540 |
| chr_3 | g2932 | g2932.t21 | cds | g2932.t21.CDS1 | 21297142 | 21298479 |
| chr_3 | g2932 | g2932.t21 | TTS | g2932.t21 | 21298583 | 21298583 |
| chr_3 | g2932 | g2932.t21 | TSS | g2932.t21 | NA | NA |
Sequences
>g2932.t21 Gene=g2932 Length=1471
GAAAAGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAGGA
GAAAAGGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATGAC
GAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGACT
AAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCTGAA
GAAGCTGTAAAGCAATTGAATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTTGGC
CGTGCTCAAAAGAAAAACGAACGTCAAATGGAATTGAAGCGTAAATTTGAGCAAATCAAG
ATTGAACGTATGTCACGCTATCAAGGAGTCAATCTTTACGTCAAAAATTTGGACGATTCA
ATTGATGATGAACGTTTACGAAAAGAGTTTGCTCCATTTGGAACAATTACTAGCGCCAAG
GTAATGATGGAAGATGGACGTTCCAAAGGATTTGGATTCGTTTGTTTCTCTGCTGCTGAA
GAAGCAACAAAGGCAGTCACAGAAATGAATGGTCGTATTGTTGGCTCAAAGCCATTGTAT
GTTGCATTGGCTCAAAAGAAGGAAGATCGTAAAGCTCATTTAGCATCTCAATACATGCAA
CGAATGACTAACATGCGCATGCAACAAATGGGTCAAATATTCCAACCAGGCGGTGCTGGA
GGATATTTTGTTCCAACAATTCCGCAACCACAACGTTTCTATGGACCAGCAGTCACACAA
TTGCGTACTACACCAAGATGGGCAAGTCAACCACAAGTTCGTCAGCAACAAGGCGCTACT
GCTTATCCAAATATGGCCGCAGTTAGTGCAACTCAATATCGTCAACCTGGTGCTGGCGGT
GTTGCTCGTCAACAAGTACAAAGTAACGCTCAAAATCCATCAGCAGCTGCTGCTGCTTTA
CGTAATCAAGCACGTCCAATCACTGGACAGCAAGCCGCTCAGATTCAACAAGGCCGTGGA
ATTAATGCACCAGTTGCACAACGTGGAGCTCCAGCTAATTATAAATACACTACAAATATG
CGCAATGCTCCACAAGCTGTTCAAATGCCTGCTCAACCAACAGCACCACAGGCTGTCATC
GTTAAAGGCCAGGAGCCACTTACTGCTAGCATGTTAGCAGCTGCTCAGCCAGCAGAACAA
AAACAAATGCTTGGTGAACGCTTATTCCCATTGATTGAGCAAATGTATCCAGCTTTGGCA
GGAAAGATTACTGGCATGTTGCTTGAAATTGATAACTCTGAATTGTTGCACATGCTTGAG
CACAATGAATCATTGAAATCTAAAGTTGAAGAAGCTGTTGCTGTATTACACGTTCATCAA
CAGAAGCAGACTACCGCTAAAATCGAATAGAAGCTGTCATCGCCTGCGCCGTATAAAATC
TATTGCTACTGACTACTATCAGTGACGCAAG
>g2932.t21 Gene=g2932 Length=445
MYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFVAFESAEAAEEAVK
QLNGKKLGDDKVLYVGRAQKKNERQMELKRKFEQIKIERMSRYQGVNLYVKNLDDSIDDE
RLRKEFAPFGTITSAKVMMEDGRSKGFGFVCFSAAEEATKAVTEMNGRIVGSKPLYVALA
QKKEDRKAHLASQYMQRMTNMRMQQMGQIFQPGGAGGYFVPTIPQPQRFYGPAVTQLRTT
PRWASQPQVRQQQGATAYPNMAAVSATQYRQPGAGGVARQQVQSNAQNPSAAAAALRNQA
RPITGQQAAQIQQGRGINAPVAQRGAPANYKYTTNMRNAPQAVQMPAQPTAPQAVIVKGQ
EPLTASMLAAAQPAEQKQMLGERLFPLIEQMYPALAGKITGMLLEIDNSELLHMLEHNES
LKSKVEEAVAVLHVHQQKQTTAKIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2932.t21 | CDD | cd12381 | RRM4_I_PABPs | 105 | 182 | 1.22645E-55 |
| 11 | g2932.t21 | Coils | Coil | Coil | 78 | 98 | - |
| 8 | g2932.t21 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 103 | 3.5E-24 |
| 9 | g2932.t21 | Gene3D | G3DSA:3.30.70.330 | - | 104 | 207 | 2.2E-25 |
| 10 | g2932.t21 | Gene3D | G3DSA:1.10.1900.10 | - | 358 | 445 | 6.8E-37 |
| 4 | g2932.t21 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 2 | 437 | 9.2E-157 |
| 5 | g2932.t21 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 2 | 437 | 9.2E-157 |
| 1 | g2932.t21 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 5 | 71 | 4.8E-21 |
| 2 | g2932.t21 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 108 | 175 | 6.6E-18 |
| 3 | g2932.t21 | Pfam | PF00658 | Poly-adenylate binding protein, unique domain | 366 | 432 | 1.3E-28 |
| 19 | g2932.t21 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 3 | 80 | 19.331 |
| 20 | g2932.t21 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 106 | 182 | 18.751 |
| 18 | g2932.t21 | ProSiteProfiles | PS51309 | Poly(A)-binding protein C-terminal (PABC) domain profile. | 360 | 437 | 21.3 |
| 14 | g2932.t21 | SMART | SM00361 | rrm2_1 | 4 | 75 | 0.5 |
| 17 | g2932.t21 | SMART | SM00360 | rrm1_1 | 4 | 76 | 1.3E-22 |
| 13 | g2932.t21 | SMART | SM00361 | rrm2_1 | 107 | 178 | 2.4 |
| 16 | g2932.t21 | SMART | SM00360 | rrm1_1 | 107 | 178 | 4.7E-24 |
| 15 | g2932.t21 | SMART | SM00517 | poly_2 | 372 | 435 | 5.0E-36 |
| 6 | g2932.t21 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 3 | 186 | 5.05E-47 |
| 7 | g2932.t21 | SUPERFAMILY | SSF63570 | PABC (PABP) domain | 319 | 442 | 3.14E-42 |
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:0003723 | RNA binding | MF |
| 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.
