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.t3 TTS g4942.t3 6121511 6121511
chr_2 g4942 g4942.t3 isoform g4942.t3 6122027 6124508
chr_2 g4942 g4942.t3 exon g4942.t3.exon1 6122027 6122030
chr_2 g4942 g4942.t3 cds g4942.t3.CDS1 6122029 6122030
chr_2 g4942 g4942.t3 exon g4942.t3.exon2 6122086 6122190
chr_2 g4942 g4942.t3 cds g4942.t3.CDS2 6122086 6122190
chr_2 g4942 g4942.t3 exon g4942.t3.exon3 6122267 6124012
chr_2 g4942 g4942.t3 cds g4942.t3.CDS3 6122267 6124012
chr_2 g4942 g4942.t3 exon g4942.t3.exon4 6124070 6124188
chr_2 g4942 g4942.t3 cds g4942.t3.CDS4 6124070 6124188
chr_2 g4942 g4942.t3 exon g4942.t3.exon5 6124309 6124508
chr_2 g4942 g4942.t3 cds g4942.t3.CDS5 6124309 6124508
chr_2 g4942 g4942.t3 TSS g4942.t3 6124600 6124600

Sequences

>g4942.t3 Gene=g4942 Length=2174
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
AACGCGCTTGCTGCAGATGGAGTTATTGATCCAAATATGACAATTTCGCATGTGGGTAAA
GCATTGACACCGCTTCAAAAGCAAGTCAGCGACAGTGTAAGTCGTCAACAAGCACTCGTG
CAGGAAATTCAAGATGCACATAAAGCTTTTACAAACGAATGCGGATCTGGAACAAATCAA
CGTGATCAAGTCACTTCACAATTAGCTTCTGCTTACGACATATTTACTGAATTGCAACAT
AATCTTCAAGAAGGAACAAAATTTTACTCTGACCTCACACAACTTTTGATTGTTTTTCAA
AATAAGGTGTCAGATTTTTGCTTTGCACGAAAGACCGAAAAAGAAGAACTATTAAAAGAT
TTGACGGCTGAGTCATCACGTGTGGCGTCTGGTTTTCAACAACCAACTATTCCGAGTCAC
CATGGAAATGCTCC

>g4942.t3 Gene=g4942 Length=724
MDLITVPLKKPYEVDLVKPLKNIIQSTNVKQADNSQIEKINSFNKQRNHAVFKVFEKNEA
ALEAIYGYYDQLNALEVKIPVHEFQVPFKYKDAFDKGSLFGGRASLTLSSLAYEKVCVLF
NIAALQSAIAANQCFDSDDGLKTAAKLFQQAAGIFSHLKSAAPALGQEPTPDLSPDTLHV
LSILMLAQAQEVCLFKAIKDGMKDQVIAKLACQNDEMYADVLKSMQKDGLKTLWDKEWLQ
IVCGKQAGIHAITLLYQANVYHTAKKIGHQIAALQKSVDLFKTASTRAGKPVFEEYNKKA
QMKLVEAKKENDFIYNAMIPDSSTLESSGKFQLAKAIPITIPMSTNFKDLFSDLVPVALQ
SALQACDAQKSEIVNAEIIKLRDATQTLNAVLSSLNLPAAIEVAAPGSSIPPSILEKANE
VREKGGVQSIRTLIEELPESLTRNKEILDETERMLNEEKQSDEQLRAQFKEKWTRTPSDK
LTEMFRSSAAKYREIITNAITADKVVRQKFESNAEGMEILSKSADELHQAIPASSGSVSN
CPSVIKLRSLMEAVETMKAERDVIESELKSATVDMKDQFLNALAADGVIDPNMTISHVGK
ALTPLQKQVSDSVSRQQALVQEIQDAHKAFTNECGSGTNQRDQVTSQLASAYDIFTELQH
NLQEGTKFYSDLTQLLIVFQNKVSDFCFARKTEKEELLKDLTAESSRVASGFQQPTIPSH
HGNA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4942.t3 CDD cd09235 V_Alix 356 690 0.0
9 g4942.t3 Coils Coil Coil 448 468 -
8 g4942.t3 Coils Coil Coil 547 574 -
7 g4942.t3 Gene3D G3DSA:1.25.40.280 alix/aip1 like domains 1 355 2.7E-106
6 g4942.t3 Gene3D G3DSA:1.20.120.560 alix/aip1 in complex with the ypdl late domain 362 632 6.2E-93
5 g4942.t3 Gene3D G3DSA:1.20.140.50 alix/aip1 like domains 405 690 6.2E-93
3 g4942.t3 PANTHER PTHR23030 PCD6 INTERACTING PROTEIN-RELATED 2 716 3.3E-138
1 g4942.t3 Pfam PF03097 BRO1-like domain 3 374 2.1E-99
2 g4942.t3 Pfam PF13949 ALIX V-shaped domain binding to HIV 409 693 2.2E-86
10 g4942.t3 ProSiteProfiles PS51180 BRO1 domain profile. 2 392 51.078
4 g4942.t3 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. There were no conditions that were differentially expressed