Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyadenylate-binding protein 1.

Parent gene

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.t12 TSS g2932.t12 21295668 21295668
chr_3 g2932 g2932.t12 isoform g2932.t12 21295766 21298479
chr_3 g2932 g2932.t12 exon g2932.t12.exon1 21295766 21295912
chr_3 g2932 g2932.t12 exon g2932.t12.exon2 21296024 21296195
chr_3 g2932 g2932.t12 cds g2932.t12.CDS1 21296030 21296195
chr_3 g2932 g2932.t12 exon g2932.t12.exon3 21296710 21296997
chr_3 g2932 g2932.t12 cds g2932.t12.CDS2 21296710 21296997
chr_3 g2932 g2932.t12 exon g2932.t12.exon4 21297056 21298479
chr_3 g2932 g2932.t12 cds g2932.t12.CDS3 21297056 21298479
chr_3 g2932 g2932.t12 TTS g2932.t12 21298583 21298583

Sequences

>g2932.t12 Gene=g2932 Length=2031
ACCCAAAAAAAACATAAAAAATTAATAAAAACCCTTAAAAAAATAATAAAACACGTGAAA
ACTCCAAAAATATAAGCAAATTTTGATTTTTTGTTTTCTCCAATCGTAAAAACGTGTCAG
AAGTGAAGTGAAAAGAAAAACGACAAACAAAAAATGGCTTCATTATACGTAGGTGATTTA
CATGCTGACATTACGGAGGCGATGCTTTTCGAAAAATTCTCTGCAGTTGGACCAGTGCTC
TCGATTCGCGTTTGTCGAGATGTCATTTCTCGCCGCTCACTCGGATACGCCTATGTTAAT
TTCCAACAACCCGCTGATGCTGAACGTGTTCTTGATACAATGAACTTTGATGTAATAAAA
GGACGTCCAATTCGTATAATGTGGTCACAACGCGATCCATCACTTCGTAAATCAGGCGTT
GGTAATGTTTTCATCAAAAATTTGGACAAATCTATTGACAACAAGGCTATGTATGATACA
TTTGGAGCATTTGGAAATATTTTAAGTTGCAAAGTCGCAACTGACGAGAATGGCCAATCA
AAAGGCTATGGATTCGTACATTATGAAACTGAAGAAGCCGCTACAATGTCGATTGAACGT
GTTAATGGAATGTTGTTAAACGAAAAGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAA
GAACGTGAGAAGGAATTAGGAGAAAAGGCAAAAATGTATACTAATGTATATGTTAAGAAC
TTTGGTGAAGAACTCAATGACGAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATT
ACATCGCATCGTGTTATGACTAAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTC
GAATCAGCAGAAGCAGCTGAAGAAGCTGTAAAGCAATTGAATGGAAAGAAACTCGGCGAT
GATAAAGTCCTTTATGTTGGCCGTGCTCAAAAGAAAAACGAACGTCAAATGGAATTGAAG
CGTAAATTTGAGCAAATCAAGATTGAACGTATGTCACGCTATCAAGGAGTCAATCTTTAC
GTCAAAAATTTGGACGATTCAATTGATGATGAACGTTTACGAAAAGAGTTTGCTCCATTT
GGAACAATTACTAGCGCCAAGGTAATGATGGAAGATGGACGTTCCAAAGGATTTGGATTC
GTTTGTTTCTCTGCTGCTGAAGAAGCAACAAAGGCAGTCACAGAAATGAATGGTCGTATT
GTTGGCTCAAAGCCATTGTATGTTGCATTGGCTCAAAAGAAGGAAGATCGTAAAGCTCAT
TTAGCATCTCAATACATGCAACGAATGACTAACATGCGCATGCAACAAATGGGTCAAATA
TTCCAACCAGGCGGTGCTGGAGGATATTTTGTTCCAACAATTCCGCAACCACAACGTTTC
TATGGACCAGCAGTCACACAATTGCGTACTACACCAAGATGGGCAAGTCAACCACAAGTT
CGTCAGCAACAAGGCGCTACTGCTTATCCAAATATGGCCGCAGTTAGTGCAACTCAATAT
CGTCAACCTGGTGCTGGCGGTGTTGCTCGTCAACAAGTACAAAGTAACGCTCAAAATCCA
TCAGCAGCTGCTGCTGCTTTACGTAATCAAGCACGTCCAATCACTGGACAGCAAGCCGCT
CAGATTCAACAAGGCCGTGGAATTAATGCACCAGTTGCACAACGTGGAGCTCCAGCTAAT
TATAAATACACTACAAATATGCGCAATGCTCCACAAGCTGTTCAAATGCCTGCTCAACCA
ACAGCACCACAGGCTGTCATCGTTAAAGGCCAGGAGCCACTTACTGCTAGCATGTTAGCA
GCTGCTCAGCCAGCAGAACAAAAACAAATGCTTGGTGAACGCTTATTCCCATTGATTGAG
CAAATGTATCCAGCTTTGGCAGGAAAGATTACTGGCATGTTGCTTGAAATTGATAACTCT
GAATTGTTGCACATGCTTGAGCACAATGAATCATTGAAATCTAAAGTTGAAGAAGCTGTT
GCTGTATTACACGTTCATCAACAGAAGCAGACTACCGCTAAAATCGAATAG

>g2932.t12 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.t12 CDD cd12378 RRM1_I_PABPs 3 82 2.16934E-55
19 g2932.t12 CDD cd12379 RRM2_I_PABPs 88 164 8.98362E-54
18 g2932.t12 CDD cd12381 RRM4_I_PABPs 285 362 1.84123E-53
16 g2932.t12 Coils Coil Coil 258 278 -
14 g2932.t12 Gene3D G3DSA:3.30.70.330 - 2 87 2.4E-22
11 g2932.t12 Gene3D G3DSA:3.30.70.330 - 90 179 6.1E-22
12 g2932.t12 Gene3D G3DSA:3.30.70.330 - 180 284 2.8E-24
13 g2932.t12 Gene3D G3DSA:3.30.70.330 - 285 387 3.8E-25
15 g2932.t12 Gene3D G3DSA:1.10.1900.10 - 538 625 1.2E-36
6 g2932.t12 PANTHER PTHR24012 RNA BINDING PROTEIN 1 616 5.8E-258
7 g2932.t12 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 1 616 5.8E-258
1 g2932.t12 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 4 74 6.0E-17
2 g2932.t12 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 92 159 1.2E-17
3 g2932.t12 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 185 251 7.8E-21
4 g2932.t12 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 288 355 1.1E-17
5 g2932.t12 Pfam PF00658 Poly-adenylate binding protein, unique domain 546 612 2.1E-28
33 g2932.t12 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 2 80 16.739
32 g2932.t12 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 90 167 16.347
31 g2932.t12 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 183 260 19.331
30 g2932.t12 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 286 362 18.751
29 g2932.t12 ProSiteProfiles PS51309 Poly(A)-binding protein C-terminal (PABC) domain profile. 540 617 21.3
24 g2932.t12 SMART SM00360 rrm1_1 3 76 1.8E-18
22 g2932.t12 SMART SM00361 rrm2_1 91 163 11.0
26 g2932.t12 SMART SM00360 rrm1_1 91 163 9.9E-21
20 g2932.t12 SMART SM00361 rrm2_1 184 255 0.5
27 g2932.t12 SMART SM00360 rrm1_1 184 256 1.3E-22
21 g2932.t12 SMART SM00361 rrm2_1 287 358 2.4
25 g2932.t12 SMART SM00360 rrm1_1 287 358 4.7E-24
23 g2932.t12 SMART SM00517 poly_2 552 615 5.0E-36
9 g2932.t12 SUPERFAMILY SSF54928 RNA-binding domain, RBD 3 171 7.51E-46
8 g2932.t12 SUPERFAMILY SSF54928 RNA-binding domain, RBD 183 366 8.88E-47
10 g2932.t12 SUPERFAMILY SSF63570 PABC (PABP) domain 499 622 5.36E-42
28 g2932.t12 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

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.

Raw TPM values