Gene loci information

Transcript annotation

  • This transcript has been annotated as Polyadenylate-binding protein 4.

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.t8 isoform g2932.t8 21295552 21297706
chr_3 g2932 g2932.t8 exon g2932.t8.exon1 21295552 21295920
chr_3 g2932 g2932.t8 exon g2932.t8.exon2 21296024 21296195
chr_3 g2932 g2932.t8 cds g2932.t8.CDS1 21296030 21296195
chr_3 g2932 g2932.t8 exon g2932.t8.exon3 21296710 21296997
chr_3 g2932 g2932.t8 cds g2932.t8.CDS2 21296710 21296997
chr_3 g2932 g2932.t8 exon g2932.t8.exon4 21297056 21297706
chr_3 g2932 g2932.t8 cds g2932.t8.CDS3 21297056 21297705
chr_3 g2932 g2932.t8 TTS g2932.t8 21298583 21298583
chr_3 g2932 g2932.t8 TSS g2932.t8 NA NA

Sequences

>g2932.t8 Gene=g2932 Length=1480
GGTAAAATATATTTAAAAATTAGTGATTCATGCATAAAATTTAAGAAACTTTCAATAAGA
CAAAAATATTTTGTTTTGATCAGAGTGCTGAATTCAGTTTTTCTTCCATTTTTCTTCAGT
CGCGTTTAAAATTTCAAAGAGACTAGAAAGGAGAAACTTTTCTCCCGCAGAAAAGCACAC
TTTTAATTTCATTCGTGCAAAAAAAAATTAAAAAACCCAAAAAAAACATAAAAAATTAAT
AAAAACCCTTAAAAAAATAATAAAACACGTGAAAACTCCAAAAATATAAGCAAATTTTGA
TTTTTTGTTTTCTCCAATCGTAAAAACGTGTCAGAAGTGAAGTGAAAAGAAAAACGACAA
AGAAAGAAACAAAAAATGGCTTCATTATACGTAGGTGATTTACATGCTGACATTACGGAG
GCGATGCTTTTCGAAAAATTCTCTGCAGTTGGACCAGTGCTCTCGATTCGCGTTTGTCGA
GATGTCATTTCTCGCCGCTCACTCGGATACGCCTATGTTAATTTCCAACAACCCGCTGAT
GCTGAACGTGTTCTTGATACAATGAACTTTGATGTAATAAAAGGACGTCCAATTCGTATA
ATGTGGTCACAACGCGATCCATCACTTCGTAAATCAGGCGTTGGTAATGTTTTCATCAAA
AATTTGGACAAATCTATTGACAACAAGGCTATGTATGATACATTTGGAGCATTTGGAAAT
ATTTTAAGTTGCAAAGTCGCAACTGACGAGAATGGCCAATCAAAAGGCTATGGATTCGTA
CATTATGAAACTGAAGAAGCCGCTACAATGTCGATTGAACGTGTTAATGGAATGTTGTTA
AACGAAAAGAAAGTCTTCGTTGGTCGCTTTATTCCACGCAAAGAACGTGAGAAGGAATTA
GGAGAAAAGGCAAAAATGTATACTAATGTATATGTTAAGAACTTTGGTGAAGAACTCAAT
GACGAGTCATTGTATGAAATGTTCAAGCCATTCGGTGAAATTACATCGCATCGTGTTATG
ACTAAGGATGGAAAATCACGTGGATTTGGATTCGTCGCATTCGAATCAGCAGAAGCAGCT
GAAGAAGCTGTAAAGCAATTGAATGGAAAGAAACTCGGCGATGATAAAGTCCTTTATGTT
GGCCGTGCTCAAAAGAAAAACGAACGTCAAATGGAATTGAAGCGTAAATTTGAGCAAATC
AAGATTGAACGTATGTCACGCTATCAAGGAGTCAATCTTTACGTCAAAAATTTGGACGAT
TCAATTGATGATGAACGTTTACGAAAAGAGTTTGCTCCATTTGGAACAATTACTAGCGCC
AAGGTAATGATGGAAGATGGACGTTCCAAAGGATTTGGATTCGTTTGTTTCTCTGCTGCT
GAAGAAGCAACAAAGGCAGTCACAGAAATGAATGGTCGTATTGTTGGCTCAAAGCCATTG
TATGTTGCATTGGCTCAAAAGAAGGAAGATCGTAAAGCTC

>g2932.t8 Gene=g2932 Length=368
MASLYVGDLHADITEAMLFEKFSAVGPVLSIRVCRDVISRRSLGYAYVNFQQPADAERVL
DTMNFDVIKGRPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKAMYDTFGAFGNILSCK
VATDENGQSKGYGFVHYETEEAATMSIERVNGMLLNEKKVFVGRFIPRKEREKELGEKAK
MYTNVYVKNFGEELNDESLYEMFKPFGEITSHRVMTKDGKSRGFGFVAFESAEAAEEAVK
QLNGKKLGDDKVLYVGRAQKKNERQMELKRKFEQIKIERMSRYQGVNLYVKNLDDSIDDE
RLRKEFAPFGTITSAKVMMEDGRSKGFGFVCFSAAEEATKAVTEMNGRIVGSKPLYVALA
QKKEDRKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g2932.t8 CDD cd12378 RRM1_I_PABPs 3 82 7.72921E-56
17 g2932.t8 CDD cd12379 RRM2_I_PABPs 88 164 5.10323E-52
16 g2932.t8 CDD cd12381 RRM4_I_PABPs 285 362 3.58072E-53
14 g2932.t8 Coils Coil Coil 258 278 -
13 g2932.t8 Coils Coil Coil 360 368 -
9 g2932.t8 Gene3D G3DSA:3.30.70.330 - 2 87 1.0E-22
10 g2932.t8 Gene3D G3DSA:3.30.70.330 - 90 180 2.6E-22
12 g2932.t8 Gene3D G3DSA:3.30.70.330 - 181 266 6.7E-24
11 g2932.t8 Gene3D G3DSA:3.30.70.330 - 267 368 1.0E-25
5 g2932.t8 PANTHER PTHR24012 RNA BINDING PROTEIN 1 368 1.3E-194
6 g2932.t8 PANTHER PTHR24012:SF805 POLYADENYLATE-BINDING PROTEIN 1 368 1.3E-194
1 g2932.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 4 74 2.7E-17
2 g2932.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 92 159 5.6E-18
3 g2932.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 185 251 3.6E-21
4 g2932.t8 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 288 355 4.9E-18
29 g2932.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 2 80 16.739
28 g2932.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 90 167 16.347
27 g2932.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 183 260 19.331
26 g2932.t8 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 286 362 18.751
21 g2932.t8 SMART SM00360 rrm1_1 3 76 1.8E-18
20 g2932.t8 SMART SM00361 rrm2_1 91 163 11.0
23 g2932.t8 SMART SM00360 rrm1_1 91 163 9.9E-21
18 g2932.t8 SMART SM00361 rrm2_1 184 255 0.5
24 g2932.t8 SMART SM00360 rrm1_1 184 256 1.3E-22
19 g2932.t8 SMART SM00361 rrm2_1 287 358 2.4
22 g2932.t8 SMART SM00360 rrm1_1 287 358 4.7E-24
8 g2932.t8 SUPERFAMILY SSF54928 RNA-binding domain, RBD 3 171 2.53E-46
7 g2932.t8 SUPERFAMILY SSF54928 RNA-binding domain, RBD 183 366 3.21E-47
25 g2932.t8 TIGRFAM TIGR01628 PABP-1234: polyadenylate binding protein, human types 1, 2, 3, 4 family 2 368 7.6E-189

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