General information for g2932.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Polyadenylate-binding protein 1A.
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.t1 | isoform | g2932.t1 | 21294877 | 21298479 |
| chr_3 | g2932 | g2932.t1 | exon | g2932.t1.exon1 | 21294877 | 21294916 |
| chr_3 | g2932 | g2932.t1 | cds | g2932.t1.CDS1 | 21294877 | 21294916 |
| chr_3 | g2932 | g2932.t1 | exon | g2932.t1.exon2 | 21295901 | 21295920 |
| chr_3 | g2932 | g2932.t1 | cds | g2932.t1.CDS2 | 21295901 | 21295920 |
| chr_3 | g2932 | g2932.t1 | exon | g2932.t1.exon3 | 21296024 | 21296195 |
| chr_3 | g2932 | g2932.t1 | cds | g2932.t1.CDS3 | 21296024 | 21296195 |
| chr_3 | g2932 | g2932.t1 | exon | g2932.t1.exon4 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t1 | cds | g2932.t1.CDS4 | 21296710 | 21296997 |
| chr_3 | g2932 | g2932.t1 | exon | g2932.t1.exon5 | 21297056 | 21298479 |
| chr_3 | g2932 | g2932.t1 | cds | g2932.t1.CDS5 | 21297056 | 21298479 |
| chr_3 | g2932 | g2932.t1 | TTS | g2932.t1 | 21298583 | 21298583 |
| chr_3 | g2932 | g2932.t1 | TSS | g2932.t1 | NA | NA |
Sequences
>g2932.t1 Gene=g2932 Length=1944
ATGGCTTGGCTTGAAGAGGAAAAAAGTTATATGGAAGAAAAAAAACGACAAAGAAAGAAA
CAAAAAATGGCTTCATTATACGTAGGTGATTTACATGCTGACATTACGGAGGCGATGCTT
TTCGAAAAATTCTCTGCAGTTGGACCAGTGCTCTCGATTCGCGTTTGTCGAGATGTCATT
TCTCGCCGCTCACTCGGATACGCCTATGTTAATTTCCAACAACCCGCTGATGCTGAACGT
GTTCTTGATACAATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATAATGTGGTCA
CAACGCGATCCATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAAAATTTGGAC
AAATCTATTGACAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAATATTTTAAGT
TGCAAAGTCGCAACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTACATTATGAA
ACTGAAGAAGCCGCTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTAAACGAAAAG
AAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTAGGAGAAAAG
GCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAATGACGAGTCA
TTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATGACTAAGGAT
GGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCTGAAGAAGCT
GTAAAGCAATTGAATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTTGGCCGTGCT
CAAAAGAAAAACGAACGTCAAATGGAATTGAAGCGTAAATTTGAGCAAATCAAGATTGAA
CGTATGTCACGCTATCAAGGAGTCAATCTTTACGTCAAAAATTTGGACGATTCAATTGAT
GATGAACGTTTACGAAAAGAGTTTGCTCCATTTGGAACAATTACTAGCGCCAAGGTAATG
ATGGAAGATGGACGTTCCAAAGGATTTGGATTCGTTTGTTTCTCTGCTGCTGAAGAAGCA
ACAAAGGCAGTCACAGAAATGAATGGTCGTATTGTTGGCTCAAAGCCATTGTATGTTGCA
TTGGCTCAAAAGAAGGAAGATCGTAAAGCTCATTTAGCATCTCAATACATGCAACGAATG
ACTAACATGCGCATGCAACAAATGGGTCAAATATTCCAACCAGGCGGTGCTGGAGGATAT
TTTGTTCCAACAATTCCGCAACCACAACGTTTCTATGGACCAGCAGTCACACAATTGCGT
ACTACACCAAGATGGGCAAGTCAACCACAAGTTCGTCAGCAACAAGGCGCTACTGCTTAT
CCAAATATGGCCGCAGTTAGTGCAACTCAATATCGTCAACCTGGTGCTGGCGGTGTTGCT
CGTCAACAAGTACAAAGTAACGCTCAAAATCCATCAGCAGCTGCTGCTGCTTTACGTAAT
CAAGCACGTCCAATCACTGGACAGCAAGCCGCTCAGATTCAACAAGGCCGTGGAATTAAT
GCACCAGTTGCACAACGTGGAGCTCCAGCTAATTATAAATACACTACAAATATGCGCAAT
GCTCCACAAGCTGTTCAAATGCCTGCTCAACCAACAGCACCACAGGCTGTCATCGTTAAA
GGCCAGGAGCCACTTACTGCTAGCATGTTAGCAGCTGCTCAGCCAGCAGAACAAAAACAA
ATGCTTGGTGAACGCTTATTCCCATTGATTGAGCAAATGTATCCAGCTTTGGCAGGAAAG
ATTACTGGCATGTTGCTTGAAATTGATAACTCTGAATTGTTGCACATGCTTGAGCACAAT
GAATCATTGAAATCTAAAGTTGAAGAAGCTGTTGCTGTATTACACGTTCATCAACAGAAG
CAGACTACCGCTAAAATCGAATAG
>g2932.t1 Gene=g2932 Length=647
MAWLEEEKSYMEEKKRQRKKQKMASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVI
SRRSLGYAYVNFQQPADAERVLDTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLD
KSIDNKAMYDTFGAFGNILSCKVATDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEK
KVFVGRFIPRKEREKELGEKAKMYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKD
GKSRGFGFVAFESAEAAEEAVKQLNGKKLGDDKVLYVGRAQKKNERQMELKRKFEQIKIE
RMSRYQGVNLYVKNLDDSIDDERLRKEFAPFGTITSAKVMMEDGRSKGFGFVCFSAAEEA
TKAVTEMNGRIVGSKPLYVALAQKKEDRKAHLASQYMQRMTNMRMQQMGQIFQPGGAGGY
FVPTIPQPQRFYGPAVTQLRTTPRWASQPQVRQQQGATAYPNMAAVSATQYRQPGAGGVA
RQQVQSNAQNPSAAAAALRNQARPITGQQAAQIQQGRGINAPVAQRGAPANYKYTTNMRN
APQAVQMPAQPTAPQAVIVKGQEPLTASMLAAAQPAEQKQMLGERLFPLIEQMYPALAGK
ITGMLLEIDNSELLHMLEHNESLKSKVEEAVAVLHVHQQKQTTAKIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g2932.t1 | CDD | cd12378 | RRM1_I_PABPs | 25 | 104 | 3.11548E-55 |
| 19 | g2932.t1 | CDD | cd12379 | RRM2_I_PABPs | 110 | 186 | 9.4165E-54 |
| 18 | g2932.t1 | CDD | cd12381 | RRM4_I_PABPs | 307 | 384 | 2.51806E-53 |
| 16 | g2932.t1 | Coils | Coil | Coil | 280 | 300 | - |
| 13 | g2932.t1 | Gene3D | G3DSA:3.30.70.330 | - | 4 | 110 | 8.2E-25 |
| 14 | g2932.t1 | Gene3D | G3DSA:3.30.70.330 | - | 112 | 201 | 6.4E-22 |
| 12 | g2932.t1 | Gene3D | G3DSA:3.30.70.330 | - | 202 | 305 | 2.9E-24 |
| 11 | g2932.t1 | Gene3D | G3DSA:3.30.70.330 | - | 306 | 409 | 3.9E-25 |
| 15 | g2932.t1 | Gene3D | G3DSA:1.10.1900.10 | - | 560 | 647 | 1.2E-36 |
| 6 | g2932.t1 | PANTHER | PTHR24012 | RNA BINDING PROTEIN | 19 | 638 | 3.5E-258 |
| 7 | g2932.t1 | PANTHER | PTHR24012:SF805 | POLYADENYLATE-BINDING PROTEIN | 19 | 638 | 3.5E-258 |
| 4 | g2932.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 26 | 96 | 6.3E-17 |
| 3 | g2932.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 114 | 181 | 1.3E-17 |
| 2 | g2932.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 207 | 273 | 8.2E-21 |
| 1 | g2932.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 310 | 377 | 1.1E-17 |
| 5 | g2932.t1 | Pfam | PF00658 | Poly-adenylate binding protein, unique domain | 568 | 634 | 2.2E-28 |
| 31 | g2932.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 24 | 102 | 16.739 |
| 32 | g2932.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 112 | 189 | 16.347 |
| 30 | g2932.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 205 | 282 | 19.331 |
| 33 | g2932.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 308 | 384 | 18.751 |
| 29 | g2932.t1 | ProSiteProfiles | PS51309 | Poly(A)-binding protein C-terminal (PABC) domain profile. | 562 | 639 | 21.3 |
| 25 | g2932.t1 | SMART | SM00360 | rrm1_1 | 25 | 98 | 1.8E-18 |
| 20 | g2932.t1 | SMART | SM00361 | rrm2_1 | 113 | 185 | 11.0 |
| 26 | g2932.t1 | SMART | SM00360 | rrm1_1 | 113 | 185 | 9.9E-21 |
| 21 | g2932.t1 | SMART | SM00361 | rrm2_1 | 206 | 277 | 0.5 |
| 24 | g2932.t1 | SMART | SM00360 | rrm1_1 | 206 | 278 | 1.3E-22 |
| 22 | g2932.t1 | SMART | SM00361 | rrm2_1 | 309 | 380 | 2.4 |
| 27 | g2932.t1 | SMART | SM00360 | rrm1_1 | 309 | 380 | 4.7E-24 |
| 23 | g2932.t1 | SMART | SM00517 | poly_2 | 574 | 637 | 5.0E-36 |
| 8 | g2932.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 24 | 193 | 5.87E-46 |
| 9 | g2932.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 205 | 388 | 9.56E-47 |
| 10 | g2932.t1 | SUPERFAMILY | SSF63570 | PABC (PABP) domain | 521 | 644 | 5.76E-42 |
| 28 | g2932.t1 | TIGRFAM | TIGR01628 | PABP-1234: polyadenylate binding protein, human types 1, 2, 3, 4 family | 24 | 634 | 3.2E-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.
