General information for g2932.t5
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.t5 | isoform | g2932.t5 | 21295326 | 21298479 |
| chr_3 | g2932 | g2932.t5 | exon | g2932.t5.exon1 | 21295326 | 21295552 |
| chr_3 | g2932 | g2932.t5 | exon | g2932.t5.exon2 | 21296024 | 21296195 |
| chr_3 | g2932 | g2932.t5 | cds | g2932.t5.CDS1 | 21296030 | 21296195 |
| chr_3 | g2932 | g2932.t5 | exon | g2932.t5.exon3 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t5 | cds | g2932.t5.CDS2 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t5 | exon | g2932.t5.exon4 | 21297056 | 21298479 |
| chr_3 | g2932 | g2932.t5 | cds | g2932.t5.CDS3 | 21297056 | 21298479 |
| chr_3 | g2932 | g2932.t5 | TTS | g2932.t5 | 21298583 | 21298583 |
| chr_3 | g2932 | g2932.t5 | TSS | g2932.t5 | NA | NA |
Sequences
>g2932.t5 Gene=g2932 Length=2111
ATGTTATTTTTAAAAAAAAGCAATAATAAGTTTGTAAATTCATAATTTAAAATGATTTTA
ATGTAACTGTCGAAAAAAATTAATTTCAAAATATAAGCTGAATTTGCAAAAAATTAACAG
CAACATTTCGTATTCGGCACATCAAATTATTTCTTTGATTTTCATTAGATAGTTGTCATT
AAAATAGATTTAAGAAACATTATTTAATCAGCGCATATCTTTAAAAGCAAAAAATGGCTT
CATTATACGTAGGTGATTTACATGCTGACATTACGGAGGCGATGCTTTTCGAAAAATTCT
CTGCAGTTGGACCAGTGCTCTCGATTCGCGTTTGTCGAGATGTCATTTCTCGCCGCTCAC
TCGGATACGCCTATGTTAATTTCCAACAACCCGCTGATGCTGAACGTGTTCTTGATACAA
TGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAATGTGGTCACAACGCGATCCAT
CACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAAATTTGGACAAATCTATTGACA
ACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATATTTTAAGTTGCAAAGTCGCAA
CTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTACATTATGAAACTGAAGAAGCCG
CTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTAAACGAAAAGAAAGTCTTCGTTG
GTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAGGAGAAAAGGCAAAAATGTATA
CTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATGACGAGTCATTGTATGAAATGT
TCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGACTAAGGATGGAAAATCACGTG
GATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCTGAAGAAGCTGTAAAGCAATTGA
ATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTTGGCCGTGCTCAAAAGAAAAACG
AACGTCAAATGGAATTGAAGCGTAAATTTGAGCAAATCAAGATTGAACGTATGTCACGCT
ATCAAGGAGTCAATCTTTACGTCAAAAATTTGGACGATTCAATTGATGATGAACGTTTAC
GAAAAGAGTTTGCTCCATTTGGAACAATTACTAGCGCCAAGGTAATGATGGAAGATGGAC
GTTCCAAAGGATTTGGATTCGTTTGTTTCTCTGCTGCTGAAGAAGCAACAAAGGCAGTCA
CAGAAATGAATGGTCGTATTGTTGGCTCAAAGCCATTGTATGTTGCATTGGCTCAAAAGA
AGGAAGATCGTAAAGCTCATTTAGCATCTCAATACATGCAACGAATGACTAACATGCGCA
TGCAACAAATGGGTCAAATATTCCAACCAGGCGGTGCTGGAGGATATTTTGTTCCAACAA
TTCCGCAACCACAACGTTTCTATGGACCAGCAGTCACACAATTGCGTACTACACCAAGAT
GGGCAAGTCAACCACAAGTTCGTCAGCAACAAGGCGCTACTGCTTATCCAAATATGGCCG
CAGTTAGTGCAACTCAATATCGTCAACCTGGTGCTGGCGGTGTTGCTCGTCAACAAGTAC
AAAGTAACGCTCAAAATCCATCAGCAGCTGCTGCTGCTTTACGTAATCAAGCACGTCCAA
TCACTGGACAGCAAGCCGCTCAGATTCAACAAGGCCGTGGAATTAATGCACCAGTTGCAC
AACGTGGAGCTCCAGCTAATTATAAATACACTACAAATATGCGCAATGCTCCACAAGCTG
TTCAAATGCCTGCTCAACCAACAGCACCACAGGCTGTCATCGTTAAAGGCCAGGAGCCAC
TTACTGCTAGCATGTTAGCAGCTGCTCAGCCAGCAGAACAAAAACAAATGCTTGGTGAAC
GCTTATTCCCATTGATTGAGCAAATGTATCCAGCTTTGGCAGGAAAGATTACTGGCATGT
TGCTTGAAATTGATAACTCTGAATTGTTGCACATGCTTGAGCACAATGAATCATTGAAAT
CTAAAGTTGAAGAAGCTGTTGCTGTATTACACGTTCATCAACAGAAGCAGACTACCGCTA
AAATCGAATAG
>g2932.t5 Gene=g2932 Length=625
MASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVISRRSLGYAYVNFQQPADAERVL
DTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCK
VATDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIPRKEREKELGEKAK
MYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFVAFESAEAAEEAVK
QLNGKKLGDDKVLYVGRAQKKNERQMELKRKFEQIKIERMSRYQGVNLYVKNLDDSIDDE
RLRKEFAPFGTITSAKVMMEDGRSKGFGFVCFSAAEEATKAVTEMNGRIVGSKPLYVALA
QKKEDRKAHLASQYMQRMTNMRMQQMGQIFQPGGAGGYFVPTIPQPQRFYGPAVTQLRTT
PRWASQPQVRQQQGATAYPNMAAVSATQYRQPGAGGVARQQVQSNAQNPSAAAAALRNQA
RPITGQQAAQIQQGRGINAPVAQRGAPANYKYTTNMRNAPQAVQMPAQPTAPQAVIVKGQ
EPLTASMLAAAQPAEQKQMLGERLFPLIEQMYPALAGKITGMLLEIDNSELLHMLEHNES
LKSKVEEAVAVLHVHQQKQTTAKIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g2932.t5 | CDD | cd12378 | RRM1_I_PABPs | 3 | 82 | 2.16934E-55 |
| 19 | g2932.t5 | CDD | cd12379 | RRM2_I_PABPs | 88 | 164 | 8.98362E-54 |
| 18 | g2932.t5 | CDD | cd12381 | RRM4_I_PABPs | 285 | 362 | 1.84123E-53 |
| 16 | g2932.t5 | Coils | Coil | Coil | 258 | 278 | - |
| 14 | g2932.t5 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 87 | 2.4E-22 |
| 11 | g2932.t5 | Gene3D | G3DSA:3.30.70.330 | - | 90 | 179 | 6.1E-22 |
| 12 | g2932.t5 | Gene3D | G3DSA:3.30.70.330 | - | 180 | 284 | 2.8E-24 |
| 13 | g2932.t5 | Gene3D | G3DSA:3.30.70.330 | - | 285 | 387 | 3.8E-25 |
| 15 | g2932.t5 | Gene3D | G3DSA:1.10.1900.10 | - | 538 | 625 | 1.2E-36 |
| 6 | g2932.t5 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 1 | 616 | 5.8E-258 |
| 7 | g2932.t5 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 1 | 616 | 5.8E-258 |
| 1 | g2932.t5 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 4 | 74 | 6.0E-17 |
| 2 | g2932.t5 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 92 | 159 | 1.2E-17 |
| 3 | g2932.t5 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 185 | 251 | 7.8E-21 |
| 4 | g2932.t5 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 288 | 355 | 1.1E-17 |
| 5 | g2932.t5 | Pfam | PF00658 | Poly-adenylate binding protein, unique domain | 546 | 612 | 2.1E-28 |
| 33 | g2932.t5 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 2 | 80 | 16.739 |
| 32 | g2932.t5 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 90 | 167 | 16.347 |
| 31 | g2932.t5 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 183 | 260 | 19.331 |
| 30 | g2932.t5 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 286 | 362 | 18.751 |
| 29 | g2932.t5 | ProSiteProfiles | PS51309 | Poly(A)-binding protein C-terminal (PABC) domain profile. | 540 | 617 | 21.3 |
| 24 | g2932.t5 | SMART | SM00360 | rrm1_1 | 3 | 76 | 1.8E-18 |
| 22 | g2932.t5 | SMART | SM00361 | rrm2_1 | 91 | 163 | 11.0 |
| 26 | g2932.t5 | SMART | SM00360 | rrm1_1 | 91 | 163 | 9.9E-21 |
| 20 | g2932.t5 | SMART | SM00361 | rrm2_1 | 184 | 255 | 0.5 |
| 27 | g2932.t5 | SMART | SM00360 | rrm1_1 | 184 | 256 | 1.3E-22 |
| 21 | g2932.t5 | SMART | SM00361 | rrm2_1 | 287 | 358 | 2.4 |
| 25 | g2932.t5 | SMART | SM00360 | rrm1_1 | 287 | 358 | 4.7E-24 |
| 23 | g2932.t5 | SMART | SM00517 | poly_2 | 552 | 615 | 5.0E-36 |
| 9 | g2932.t5 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 3 | 171 | 7.51E-46 |
| 8 | g2932.t5 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 183 | 366 | 8.88E-47 |
| 10 | g2932.t5 | SUPERFAMILY | SSF63570 | PABC (PABP) domain | 499 | 622 | 5.36E-42 |
| 28 | g2932.t5 | TIGRFAM | TIGR01628 | PABP-1234: polyadenylate binding protein, human types 1, 2, 3, 4 family | 2 | 612 | 2.8E-237 |
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 transcript has been annotated with K13126 (polyadenylate-binding protein)
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.
