General information for g2932.t11
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.t11 | TSS | g2932.t11 | 21295668 | 21295668 |
| chr_3 | g2932 | g2932.t11 | isoform | g2932.t11 | 21295766 | 21298479 |
| chr_3 | g2932 | g2932.t11 | exon | g2932.t11.exon1 | 21295766 | 21295786 |
| chr_3 | g2932 | g2932.t11 | exon | g2932.t11.exon2 | 21296671 | 21296997 |
| chr_3 | g2932 | g2932.t11 | cds | g2932.t11.CDS1 | 21296685 | 21296997 |
| chr_3 | g2932 | g2932.t11 | exon | g2932.t11.exon3 | 21297056 | 21298479 |
| chr_3 | g2932 | g2932.t11 | cds | g2932.t11.CDS2 | 21297056 | 21298479 |
| chr_3 | g2932 | g2932.t11 | TTS | g2932.t11 | 21298583 | 21298583 |
Sequences
>g2932.t11 Gene=g2932 Length=1772
ACCCAAAAAAAACATAAAAAAAAATTTAAAGATTAATGATTTGGTTTATTCTACTTTTAG
CTGAACGTGTTCTTGATACAATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAA
TGTGGTCACAACGCGATCCATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAA
ATTTGGACAAATCTATTGACAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATA
TTTTAAGTTGCAAAGTCGCAACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTAC
ATTATGAAACTGAAGAAGCCGCTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTAA
ACGAAAAGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAG
GAGAAAAGGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATG
ACGAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGA
CTAAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCTG
AAGAAGCTGTAAAGCAATTGAATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTTG
GCCGTGCTCAAAAGAAAAACGAACGTCAAATGGAATTGAAGCGTAAATTTGAGCAAATCA
AGATTGAACGTATGTCACGCTATCAAGGAGTCAATCTTTACGTCAAAAATTTGGACGATT
CAATTGATGATGAACGTTTACGAAAAGAGTTTGCTCCATTTGGAACAATTACTAGCGCCA
AGGTAATGATGGAAGATGGACGTTCCAAAGGATTTGGATTCGTTTGTTTCTCTGCTGCTG
AAGAAGCAACAAAGGCAGTCACAGAAATGAATGGTCGTATTGTTGGCTCAAAGCCATTGT
ATGTTGCATTGGCTCAAAAGAAGGAAGATCGTAAAGCTCATTTAGCATCTCAATACATGC
AACGAATGACTAACATGCGCATGCAACAAATGGGTCAAATATTCCAACCAGGCGGTGCTG
GAGGATATTTTGTTCCAACAATTCCGCAACCACAACGTTTCTATGGACCAGCAGTCACAC
AATTGCGTACTACACCAAGATGGGCAAGTCAACCACAAGTTCGTCAGCAACAAGGCGCTA
CTGCTTATCCAAATATGGCCGCAGTTAGTGCAACTCAATATCGTCAACCTGGTGCTGGCG
GTGTTGCTCGTCAACAAGTACAAAGTAACGCTCAAAATCCATCAGCAGCTGCTGCTGCTT
TACGTAATCAAGCACGTCCAATCACTGGACAGCAAGCCGCTCAGATTCAACAAGGCCGTG
GAATTAATGCACCAGTTGCACAACGTGGAGCTCCAGCTAATTATAAATACACTACAAATA
TGCGCAATGCTCCACAAGCTGTTCAAATGCCTGCTCAACCAACAGCACCACAGGCTGTCA
TCGTTAAAGGCCAGGAGCCACTTACTGCTAGCATGTTAGCAGCTGCTCAGCCAGCAGAAC
AAAAACAAATGCTTGGTGAACGCTTATTCCCATTGATTGAGCAAATGTATCCAGCTTTGG
CAGGAAAGATTACTGGCATGTTGCTTGAAATTGATAACTCTGAATTGTTGCACATGCTTG
AGCACAATGAATCATTGAAATCTAAAGTTGAAGAAGCTGTTGCTGTATTACACGTTCATC
AACAGAAGCAGACTACCGCTAAAATCGAATAG
>g2932.t11 Gene=g2932 Length=578
MIWFILLLAERVLDTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMY
DTFGAFGNILSCKVATDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIP
RKEREKELGEKAKMYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFV
AFESAEAAEEAVKQLNGKKLGDDKVLYVGRAQKKNERQMELKRKFEQIKIERMSRYQGVN
LYVKNLDDSIDDERLRKEFAPFGTITSAKVMMEDGRSKGFGFVCFSAAEEATKAVTEMNG
RIVGSKPLYVALAQKKEDRKAHLASQYMQRMTNMRMQQMGQIFQPGGAGGYFVPTIPQPQ
RFYGPAVTQLRTTPRWASQPQVRQQQGATAYPNMAAVSATQYRQPGAGGVARQQVQSNAQ
NPSAAAAALRNQARPITGQQAAQIQQGRGINAPVAQRGAPANYKYTTNMRNAPQAVQMPA
QPTAPQAVIVKGQEPLTASMLAAAQPAEQKQMLGERLFPLIEQMYPALAGKITGMLLEID
NSELLHMLEHNESLKSKVEEAVAVLHVHQQKQTTAKIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g2932.t11 | CDD | cd12379 | RRM2_I_PABPs | 41 | 117 | 3.82669E-54 |
| 16 | g2932.t11 | CDD | cd12381 | RRM4_I_PABPs | 238 | 315 | 7.56604E-54 |
| 15 | g2932.t11 | Coils | Coil | Coil | 211 | 231 | - |
| 13 | g2932.t11 | Gene3D | G3DSA:3.30.70.330 | - | 32 | 127 | 1.6E-21 |
| 12 | g2932.t11 | Gene3D | G3DSA:3.30.70.330 | - | 128 | 236 | 2.6E-24 |
| 11 | g2932.t11 | Gene3D | G3DSA:3.30.70.330 | - | 237 | 340 | 3.3E-25 |
| 14 | g2932.t11 | Gene3D | G3DSA:1.10.1900.10 | - | 491 | 578 | 1.0E-36 |
| 5 | g2932.t11 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 6 | 570 | 5.5E-228 |
| 6 | g2932.t11 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 6 | 570 | 5.5E-228 |
| 2 | g2932.t11 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 45 | 112 | 1.1E-17 |
| 1 | g2932.t11 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 138 | 204 | 7.0E-21 |
| 3 | g2932.t11 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 241 | 308 | 9.7E-18 |
| 4 | g2932.t11 | Pfam | PF00658 | Poly-adenylate binding protein, unique domain | 499 | 565 | 1.9E-28 |
| 27 | g2932.t11 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 43 | 120 | 16.347 |
| 29 | g2932.t11 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 136 | 213 | 19.331 |
| 28 | g2932.t11 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 239 | 315 | 18.751 |
| 26 | g2932.t11 | ProSiteProfiles | PS51309 | Poly(A)-binding protein C-terminal (PABC) domain profile. | 493 | 570 | 21.3 |
| 18 | g2932.t11 | SMART | SM00361 | rrm2_1 | 44 | 116 | 11.0 |
| 22 | g2932.t11 | SMART | SM00360 | rrm1_1 | 44 | 116 | 9.9E-21 |
| 20 | g2932.t11 | SMART | SM00361 | rrm2_1 | 137 | 208 | 0.5 |
| 24 | g2932.t11 | SMART | SM00360 | rrm1_1 | 137 | 209 | 1.3E-22 |
| 19 | g2932.t11 | SMART | SM00361 | rrm2_1 | 240 | 311 | 2.4 |
| 23 | g2932.t11 | SMART | SM00360 | rrm1_1 | 240 | 311 | 4.7E-24 |
| 21 | g2932.t11 | SMART | SM00517 | poly_2 | 505 | 568 | 5.0E-36 |
| 8 | g2932.t11 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 13 | 125 | 2.0E-26 |
| 7 | g2932.t11 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 136 | 319 | 7.51E-47 |
| 9 | g2932.t11 | SUPERFAMILY | SSF63570 | PABC (PABP) domain | 452 | 575 | 4.97E-42 |
| 10 | g2932.t11 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 15 | - |
| 25 | g2932.t11 | TIGRFAM | TIGR01628 | PABP-1234: polyadenylate binding protein, human types 1, 2, 3, 4 family | 9 | 565 | 2.2E-201 |
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.
