Gene loci information

Transcript annotation

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

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.t15 TSS g2932.t15 21295668 21295668
chr_3 g2932 g2932.t15 isoform g2932.t15 21295784 21298479
chr_3 g2932 g2932.t15 exon g2932.t15.exon1 21295784 21295920
chr_3 g2932 g2932.t15 exon g2932.t15.exon2 21296024 21296195
chr_3 g2932 g2932.t15 cds g2932.t15.CDS1 21296030 21296195
chr_3 g2932 g2932.t15 exon g2932.t15.exon3 21296710 21296997
chr_3 g2932 g2932.t15 cds g2932.t15.CDS2 21296710 21296997
chr_3 g2932 g2932.t15 exon g2932.t15.exon4 21297056 21297853
chr_3 g2932 g2932.t15 cds g2932.t15.CDS3 21297056 21297853
chr_3 g2932 g2932.t15 exon g2932.t15.exon5 21298124 21298479
chr_3 g2932 g2932.t15 cds g2932.t15.CDS4 21298124 21298479
chr_3 g2932 g2932.t15 TTS g2932.t15 21298583 21298583

Sequences

>g2932.t15 Gene=g2932 Length=1751
AAATTAATAAAAACCCTTAAAAAAATAATAAAACACGTGAAAACTCCAAAAATATAAGCA
AATTTTGATTTTTTGTTTTCTCCAATCGTAAAAACGTGTCAGAAGTGAAGTGAAAAGAAA
AACGACAAAGAAAGAAACAAAAAATGGCTTCATTATACGTAGGTGATTTACATGCTGACA
TTACGGAGGCGATGCTTTTCGAAAAATTCTCTGCAGTTGGACCAGTGCTCTCGATTCGCG
TTTGTCGAGATGTCATTTCTCGCCGCTCACTCGGATACGCCTATGTTAATTTCCAACAAC
CCGCTGATGCTGAACGTGTTCTTGATACAATGAACTTTGATGTAATAAAAGGACGTCCAA
TTCGTATAATGTGGTCACAACGCGATCCATCACTTCGTAAATCAGGCGTTGGTAATGTTT
TCATCAAAAATTTGGACAAATCTATTGACAACAAGGCTATGTATGATACATTTGGAGCAT
TTGGAAATATTTTAAGTTGCAAAGTCGCAACTGACGAGAATGGCCAATCAAAAGGCTATG
GATTCGTACATTATGAAACTGAAGAAGCCGCTACAATGTCGATTGAACGTGTTAATGGAA
TGTTGTTAAACGAAAAGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGA
AGGAATTAGGAGAAAAGGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAG
AACTCAATGACGAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATC
GTGTTATGACTAAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAG
AAGCAGCTGAAGAAGCTGTAAAGCAATTGAATGGAAAGAAACTCGGCGATGATAAAGTCC
TTTATGTTGGCCGTGCTCAAAAGAAAAACGAACGTCAAATGGAATTGAAGCGTAAATTTG
AGCAAATCAAGATTGAACGTATGTCACGCTATCAAGGAGTCAATCTTTACGTCAAAAATT
TGGACGATTCAATTGATGATGAACGTTTACGAAAAGAGTTTGCTCCATTTGGAACAATTA
CTAGCGCCAAGGTAATGATGGAAGATGGACGTTCCAAAGGATTTGGATTCGTTTGTTTCT
CTGCTGCTGAAGAAGCAACAAAGGCAGTCACAGAAATGAATGGTCGTATTGTTGGCTCAA
AGCCATTGTATGTTGCATTGGCTCAAAAGAAGGAAGATCGTAAAGCTCATTTAGCATCTC
AATACATGCAACGAATGACTAACATGCGCATGCAACAAATGGGTCAAATATTCCAACCAG
GCGGTGCTGGAGGATATTTTGTTCCAACAATTCCGCAACCACAACGTTTCTATGGACCAG
CAGTCACACAATTGCCTAATTATAAATACACTACAAATATGCGCAATGCTCCACAAGCTG
TTCAAATGCCTGCTCAACCAACAGCACCACAGGCTGTCATCGTTAAAGGCCAGGAGCCAC
TTACTGCTAGCATGTTAGCAGCTGCTCAGCCAGCAGAACAAAAACAAATGCTTGGTGAAC
GCTTATTCCCATTGATTGAGCAAATGTATCCAGCTTTGGCAGGAAAGATTACTGGCATGT
TGCTTGAAATTGATAACTCTGAATTGTTGCACATGCTTGAGCACAATGAATCATTGAAAT
CTAAAGTTGAAGAAGCTGTTGCTGTATTACACGTTCATCAACAGAAGCAGACTACCGCTA
AAATCGAATAG

>g2932.t15 Gene=g2932 Length=535
MASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVISRRSLGYAYVNFQQPADAERVL
DTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCK
VATDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIPRKEREKELGEKAK
MYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFVAFESAEAAEEAVK
QLNGKKLGDDKVLYVGRAQKKNERQMELKRKFEQIKIERMSRYQGVNLYVKNLDDSIDDE
RLRKEFAPFGTITSAKVMMEDGRSKGFGFVCFSAAEEATKAVTEMNGRIVGSKPLYVALA
QKKEDRKAHLASQYMQRMTNMRMQQMGQIFQPGGAGGYFVPTIPQPQRFYGPAVTQLPNY
KYTTNMRNAPQAVQMPAQPTAPQAVIVKGQEPLTASMLAAAQPAEQKQMLGERLFPLIEQ
MYPALAGKITGMLLEIDNSELLHMLEHNESLKSKVEEAVAVLHVHQQKQTTAKIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g2932.t15 CDD cd12378 RRM1_I_PABPs 3 82 1.46444E-55
21 g2932.t15 CDD cd12379 RRM2_I_PABPs 88 164 3.24468E-53
20 g2932.t15 CDD cd12381 RRM4_I_PABPs 285 362 2.4199E-53
18 g2932.t15 Coils Coil Coil 258 278 -
14 g2932.t15 Gene3D G3DSA:3.30.70.330 - 2 83 1.8E-22
13 g2932.t15 Gene3D G3DSA:3.30.70.330 - 84 171 1.4E-21
16 g2932.t15 Gene3D G3DSA:3.30.70.330 - 172 272 4.0E-24
15 g2932.t15 Gene3D G3DSA:3.30.70.330 - 273 375 1.9E-25
17 g2932.t15 Gene3D G3DSA:1.10.1900.10 - 448 535 9.1E-37
6 g2932.t15 PANTHER PTHR24012 RNA BINDING PROTEIN 1 443 1.1E-245
8 g2932.t15 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 1 443 1.1E-245
7 g2932.t15 PANTHER PTHR24012 RNA BINDING PROTEIN 413 527 1.1E-245
9 g2932.t15 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 413 527 1.1E-245
1 g2932.t15 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 4 74 4.8E-17
2 g2932.t15 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 92 159 9.8E-18
3 g2932.t15 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 185 251 6.3E-21
4 g2932.t15 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 288 355 8.7E-18
5 g2932.t15 Pfam PF00658 Poly-adenylate binding protein, unique domain 456 522 1.7E-28
35 g2932.t15 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 2 80 16.739
34 g2932.t15 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 90 167 16.347
33 g2932.t15 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 183 260 19.331
32 g2932.t15 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 286 362 18.751
31 g2932.t15 ProSiteProfiles PS51309 Poly(A)-binding protein C-terminal (PABC) domain profile. 450 527 21.3
26 g2932.t15 SMART SM00360 rrm1_1 3 76 1.8E-18
24 g2932.t15 SMART SM00361 rrm2_1 91 163 11.0
28 g2932.t15 SMART SM00360 rrm1_1 91 163 9.9E-21
22 g2932.t15 SMART SM00361 rrm2_1 184 255 0.5
29 g2932.t15 SMART SM00360 rrm1_1 184 256 1.3E-22
23 g2932.t15 SMART SM00361 rrm2_1 287 358 2.4
27 g2932.t15 SMART SM00360 rrm1_1 287 358 4.7E-24
25 g2932.t15 SMART SM00517 poly_2 462 525 5.0E-36
11 g2932.t15 SUPERFAMILY SSF54928 RNA-binding domain, RBD 3 171 5.67E-46
10 g2932.t15 SUPERFAMILY SSF54928 RNA-binding domain, RBD 183 366 6.49E-47
12 g2932.t15 SUPERFAMILY SSF63570 PABC (PABP) domain 406 532 2.09E-40
30 g2932.t15 TIGRFAM TIGR01628 PABP-1234: polyadenylate binding protein, human types 1, 2, 3, 4 family 2 392 3.7E-195

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