Gene loci information

Transcript annotation

  • This transcript has been annotated as Programmed cell death 6-interacting 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_2 g4942 g4942.t4 TTS g4942.t4 6121647 6121647
chr_2 g4942 g4942.t4 isoform g4942.t4 6122587 6124508
chr_2 g4942 g4942.t4 exon g4942.t4.exon1 6122587 6124012
chr_2 g4942 g4942.t4 cds g4942.t4.CDS1 6122589 6124012
chr_2 g4942 g4942.t4 exon g4942.t4.exon2 6124070 6124188
chr_2 g4942 g4942.t4 cds g4942.t4.CDS2 6124070 6124188
chr_2 g4942 g4942.t4 exon g4942.t4.exon3 6124309 6124508
chr_2 g4942 g4942.t4 cds g4942.t4.CDS3 6124309 6124508
chr_2 g4942 g4942.t4 TSS g4942.t4 6124600 6124600

Sequences

>g4942.t4 Gene=g4942 Length=1745
ATGGATTTAATAACTGTGCCTTTGAAAAAACCGTATGAAGTTGATCTGGTGAAACCACTA
AAGAACATAATTCAAAGCACAAATGTAAAGCAAGCAGATAATTCGCAAATTGAAAAAATA
AATTCCTTCAATAAGCAACGAAATCATGCTGTATTCAAGGTGTTTGAGAAAAATGAAGCT
GCATTAGAAGCTATTTATGGCTATTACGATCAGTTGAATGCTCTAGAAGTCAAAATTCCG
GTTCACGAATTTCAAGTTCCATTCAAATATAAAGATGCTTTCGATAAAGGATCACTATTT
GGTGGTCGTGCTAGCTTGACGCTTTCATCATTAGCGTATGAAAAAGTGTGTGTTCTTTTC
AATATTGCTGCTTTACAAAGTGCAATCGCTGCAAATCAATGCTTCGATAGTGATGATGGA
TTGAAGACAGCTGCAAAATTATTTCAGCAAGCAGCAGGTATTTTCTCCCATCTAAAAAGT
GCAGCACCAGCTTTAGGACAAGAACCGACGCCTGATTTATCACCAGATACACTTCATGTA
TTATCAATTTTAATGTTGGCGCAAGCTCAAGAAGTTTGCCTCTTTAAAGCTATTAAAGAT
GGAATGAAAGATCAAGTAATTGCAAAGTTGGCATGTCAAAATGATGAAATGTATGCTGAT
GTTTTAAAATCCATGCAAAAAGATGGTTTAAAAACGTTATGGGATAAAGAGTGGTTACAA
ATCGTTTGTGGCAAGCAAGCTGGAATTCATGCAATCACACTTTTATATCAAGCTAACGTC
TATCACACTGCAAAAAAAATTGGGCATCAAATTGCTGCTTTACAAAAATCAGTTGATTTA
TTTAAAACTGCTTCAACACGCGCTGGAAAGCCTGTTTTTGAAGAATATAATAAGAAAGCT
CAAATGAAACTTGTTGAAGCTAAAAAAGAAAATGATTTCATTTATAATGCAATGATACCA
GATTCATCAACTTTAGAGTCTTCTGGTAAATTTCAGCTAGCGAAAGCTATACCAATTACA
ATTCCAATGAGTACGAACTTTAAGGATCTTTTCAGTGATCTGGTACCAGTTGCATTGCAG
TCTGCATTGCAAGCATGCGACGCTCAAAAATCTGAAATCGTAAATGCTGAAATCATAAAA
CTTCGTGATGCTACTCAAACTTTGAATGCTGTCTTATCTAGCTTAAATCTTCCTGCAGCA
ATTGAAGTTGCAGCACCTGGTTCAAGCATTCCACCTTCAATTTTAGAAAAAGCAAATGAG
GTTCGTGAAAAAGGAGGAGTTCAAAGTATTCGTACATTAATTGAAGAATTACCAGAATCG
CTTACTCGTAATAAAGAGATTCTTGATGAGACCGAAAGAATGTTGAATGAAGAAAAACAA
TCTGATGAACAATTGCGTGCACAATTCAAAGAAAAATGGACTCGAACACCCTCTGATAAA
TTAACAGAGATGTTTAGATCTAGTGCAGCAAAATATCGTGAAATAATCACAAATGCAATT
ACAGCTGATAAGGTTGTTCGACAAAAGTTTGAGAGCAATGCTGAAGGAATGGAAATTTTA
TCTAAATCTGCAGATGAATTGCATCAAGCAATTCCAGCATCGAGCGGAAGTGTGTCAAAT
TGTCCATCAGTAATTAAATTGCGTAGTCTTATGGAGGCCGTTGAAACAATGAAGGCCGAA
CGAGATGTTATTGAATCTGAATTAAAGTCTGCAACAGTAGATATGAAAGATCAATTTTTG
AACGC

>g4942.t4 Gene=g4942 Length=581
MDLITVPLKKPYEVDLVKPLKNIIQSTNVKQADNSQIEKINSFNKQRNHAVFKVFEKNEA
ALEAIYGYYDQLNALEVKIPVHEFQVPFKYKDAFDKGSLFGGRASLTLSSLAYEKVCVLF
NIAALQSAIAANQCFDSDDGLKTAAKLFQQAAGIFSHLKSAAPALGQEPTPDLSPDTLHV
LSILMLAQAQEVCLFKAIKDGMKDQVIAKLACQNDEMYADVLKSMQKDGLKTLWDKEWLQ
IVCGKQAGIHAITLLYQANVYHTAKKIGHQIAALQKSVDLFKTASTRAGKPVFEEYNKKA
QMKLVEAKKENDFIYNAMIPDSSTLESSGKFQLAKAIPITIPMSTNFKDLFSDLVPVALQ
SALQACDAQKSEIVNAEIIKLRDATQTLNAVLSSLNLPAAIEVAAPGSSIPPSILEKANE
VREKGGVQSIRTLIEELPESLTRNKEILDETERMLNEEKQSDEQLRAQFKEKWTRTPSDK
LTEMFRSSAAKYREIITNAITADKVVRQKFESNAEGMEILSKSADELHQAIPASSGSVSN
CPSVIKLRSLMEAVETMKAERDVIESELKSATVDMKDQFLN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4942.t4 Coils Coil Coil 448 468 -
7 g4942.t4 Coils Coil Coil 547 574 -
6 g4942.t4 Gene3D G3DSA:1.25.40.280 alix/aip1 like domains 1 355 1.5E-106
5 g4942.t4 Gene3D G3DSA:1.20.140.50 alix/aip1 like domains 406 572 8.2E-44
3 g4942.t4 PANTHER PTHR23030 PCD6 INTERACTING PROTEIN-RELATED 2 570 4.7E-118
1 g4942.t4 Pfam PF03097 BRO1-like domain 3 374 1.1E-99
2 g4942.t4 Pfam PF13949 ALIX V-shaped domain binding to HIV 409 581 7.8E-51
9 g4942.t4 ProSiteProfiles PS51180 BRO1 domain profile. 2 392 51.078
4 g4942.t4 SMART SM01041 BRO1_2 2 378 1.7E-124

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:0005515 protein 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