Gene loci information

Transcript annotation

  • This transcript has been annotated as Partitioning defective protein 6.

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_1 g14008 g14008.t1 isoform g14008.t1 33973576 33974833
chr_1 g14008 g14008.t1 exon g14008.t1.exon1 33973576 33973848
chr_1 g14008 g14008.t1 cds g14008.t1.CDS1 33973576 33973848
chr_1 g14008 g14008.t1 exon g14008.t1.exon2 33973912 33974178
chr_1 g14008 g14008.t1 cds g14008.t1.CDS2 33973912 33974178
chr_1 g14008 g14008.t1 exon g14008.t1.exon3 33974326 33974688
chr_1 g14008 g14008.t1 cds g14008.t1.CDS3 33974326 33974688
chr_1 g14008 g14008.t1 exon g14008.t1.exon4 33974759 33974833
chr_1 g14008 g14008.t1 cds g14008.t1.CDS4 33974759 33974833
chr_1 g14008 g14008.t1 TSS g14008.t1 33975174 33975174
chr_1 g14008 g14008.t1 TTS g14008.t1 NA NA

Sequences

>g14008.t1 Gene=g14008 Length=978
ATGTCGAAAAATAAATTCAATGTTCAAAAGCAATCTACCGCAGCTGAGAGTACTCTAATT
GAGATAAAATCAAAGTTTGACGCAGAATTCCGAAGATGGTCCATAAAAAGAAATCCAGAA
AACAATCATACTTTTGACGAATTTTATTCCACAATTGAACGTTATCACAAGCTTTCGGGT
GTACCATTTCTAATTTCCTACATAGATCCTCGTGACAATGACCTATTGCCGATTAATAAT
GACGATAATTTTCACCGAGCATTAACTACAGCAAGACCTTTACTTCGAATTATTATTCAA
AAGAAAGGAGATAGTTTTGAAGATACAATGGGATATGGAACTATGAGACCGAAGAATCTT
ATTAGTACACTGCTAGGTGGTCAAACGCCTGTGAAATCAAAAGCTCTCGCTATTTCAAAT
CCACATGATTTTCGTCAGGTTTCACAAATCATTGATGTTGATATTGTTCCGGAAACCTGT
AGACGCGTGCGATTATTGAAGCATGGAAGTGATAAACCGCTTGGATTCTATATTCGCGAT
GGGACATCTGTAAAAGTCACCTCTAATGGAATTGAAAAGCAGCCCGGAATTTTCATCTCA
AGATTAGTGCCAGGTGGTTTAGCTGAATCAACAGGTCTTTTAGCAGTAAATGATGAGGTA
CTTGAAGTGAACGGCATTGAAGTTCATGGAAAAACTCTTGATCAGGTCACTGACATGATG
GTTGCAAATAGCTCAAATCTTATAATCACAGTAAAACCTGCAAACCAGAGAACATTAGCA
ACGCCACGACGTGGATCTTTCTCACGCAACAGTCAACTGTCGTCTGGTTCACATCAATCA
CATCACACAAACAATACAAACACTTCAGACGAAAATGACCACGACGATCAAGACGAAGTT
GTTGATTTGACGACGGGTATGGGGAATTTAGAAGAGAATAATTTGGTAGTGAATCAAAAT
GGGGTTTTACATTTGTAA

>g14008.t1 Gene=g14008 Length=325
MSKNKFNVQKQSTAAESTLIEIKSKFDAEFRRWSIKRNPENNHTFDEFYSTIERYHKLSG
VPFLISYIDPRDNDLLPINNDDNFHRALTTARPLLRIIIQKKGDSFEDTMGYGTMRPKNL
ISTLLGGQTPVKSKALAISNPHDFRQVSQIIDVDIVPETCRRVRLLKHGSDKPLGFYIRD
GTSVKVTSNGIEKQPGIFISRLVPGGLAESTGLLAVNDEVLEVNGIEVHGKTLDQVTDMM
VANSSNLIITVKPANQRTLATPRRGSFSRNSQLSSGSHQSHHTNNTNTSDENDHDDQDEV
VDLTTGMGNLEENNLVVNQNGVLHL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g14008.t1 CDD cd06403 PB1_Par6 20 102 1.21946E-39
9 g14008.t1 CDD cd00992 PDZ_signaling 161 252 1.2301E-18
7 g14008.t1 Gene3D G3DSA:3.10.20.90 - 14 102 2.9E-34
8 g14008.t1 Gene3D G3DSA:2.30.42.10 - 131 257 4.2E-38
13 g14008.t1 MobiDBLite mobidb-lite consensus disorder prediction 258 295 -
14 g14008.t1 MobiDBLite mobidb-lite consensus disorder prediction 258 286 -
3 g14008.t1 PANTHER PTHR14102 PAR-6-RELATED 10 301 2.4E-107
4 g14008.t1 PANTHER PTHR14102:SF4 PARTITIONING DEFECTIVE 6 HOMOLOG BETA 10 301 2.4E-107
2 g14008.t1 Pfam PF00564 PB1 domain 20 101 8.2E-13
1 g14008.t1 Pfam PF00595 PDZ domain 167 250 1.1E-11
15 g14008.t1 ProSiteProfiles PS51745 PB1 domain profile. 19 102 19.389
16 g14008.t1 ProSiteProfiles PS50106 PDZ domain profile. 162 255 16.325
12 g14008.t1 SMART SM00666 PB1_new 19 102 3.3E-14
11 g14008.t1 SMART SM00228 pdz_new 172 255 3.5E-13
6 g14008.t1 SUPERFAMILY SSF54277 CAD & PB1 domains 19 102 3.27E-30
5 g14008.t1 SUPERFAMILY SSF50156 PDZ domain-like 135 255 3.02E-23

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:0007043 cell-cell junction assembly BP
GO:0005515 protein binding MF
GO:0007163 establishment or maintenance of cell polarity BP

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