General information for g4942.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Programmed cell death 6-interacting protein.
Parent gene
- The parent gene g4942 is located on chr_2: 6122931..6124508 (- strand)
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.t1 | TTS | g4942.t1 | 6121511 | 6121511 |
| chr_2 | g4942 | g4942.t1 | isoform | g4942.t1 | 6121645 | 6124508 |
| chr_2 | g4942 | g4942.t1 | exon | g4942.t1.exon1 | 6121645 | 6121754 |
| chr_2 | g4942 | g4942.t1 | cds | g4942.t1.CDS1 | 6121645 | 6121754 |
| chr_2 | g4942 | g4942.t1 | exon | g4942.t1.exon2 | 6121815 | 6122030 |
| chr_2 | g4942 | g4942.t1 | cds | g4942.t1.CDS2 | 6121815 | 6122030 |
| chr_2 | g4942 | g4942.t1 | exon | g4942.t1.exon3 | 6122086 | 6122190 |
| chr_2 | g4942 | g4942.t1 | cds | g4942.t1.CDS3 | 6122086 | 6122190 |
| chr_2 | g4942 | g4942.t1 | exon | g4942.t1.exon4 | 6122267 | 6124012 |
| chr_2 | g4942 | g4942.t1 | cds | g4942.t1.CDS4 | 6122267 | 6124012 |
| chr_2 | g4942 | g4942.t1 | exon | g4942.t1.exon5 | 6124070 | 6124188 |
| chr_2 | g4942 | g4942.t1 | cds | g4942.t1.CDS5 | 6124070 | 6124188 |
| chr_2 | g4942 | g4942.t1 | exon | g4942.t1.exon6 | 6124309 | 6124508 |
| chr_2 | g4942 | g4942.t1 | cds | g4942.t1.CDS6 | 6124309 | 6124508 |
| chr_2 | g4942 | g4942.t1 | TSS | g4942.t1 | 6124600 | 6124600 |
Sequences
>g4942.t1 Gene=g4942 Length=2496
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
CATGGAAATGCTCCTCCTGCTCGTCCACCGCCACCACAAGTCCAAGAGAGCACATCAGCA
GTTCCAGCAGCTAATGCTCCTTATCCAGTGGCAATGCCAGGAATGCCTCATCCTATGATG
GGTTACAACTACATGCCACCATTGCCAACTTCTTTCAATCCCTATGCAACTTTACCTCAT
GGTGGTATTCCTTATCCAACTAACTTTTCTTTTCCACAAGCTGGTGGAGCACAATATTAT
GGTACATACCCAGGAGCATATGCACAGCAAATACAACAAGCTAACTACCCTCATGCTCCA
CAACAACAAGATCCAAATAAGCCTTATGGCTTTTAA
>g4942.t1 Gene=g4942 Length=831
MDLITVPLKKPYEVDLVKPLKNIIQSTNVKQADNSQIEKINSFNKQRNHAVFKVFEKNEA
ALEAIYGYYDQLNALEVKIPVHEFQVPFKYKDAFDKGSLFGGRASLTLSSLAYEKVCVLF
NIAALQSAIAANQCFDSDDGLKTAAKLFQQAAGIFSHLKSAAPALGQEPTPDLSPDTLHV
LSILMLAQAQEVCLFKAIKDGMKDQVIAKLACQNDEMYADVLKSMQKDGLKTLWDKEWLQ
IVCGKQAGIHAITLLYQANVYHTAKKIGHQIAALQKSVDLFKTASTRAGKPVFEEYNKKA
QMKLVEAKKENDFIYNAMIPDSSTLESSGKFQLAKAIPITIPMSTNFKDLFSDLVPVALQ
SALQACDAQKSEIVNAEIIKLRDATQTLNAVLSSLNLPAAIEVAAPGSSIPPSILEKANE
VREKGGVQSIRTLIEELPESLTRNKEILDETERMLNEEKQSDEQLRAQFKEKWTRTPSDK
LTEMFRSSAAKYREIITNAITADKVVRQKFESNAEGMEILSKSADELHQAIPASSGSVSN
CPSVIKLRSLMEAVETMKAERDVIESELKSATVDMKDQFLNALAADGVIDPNMTISHVGK
ALTPLQKQVSDSVSRQQALVQEIQDAHKAFTNECGSGTNQRDQVTSQLASAYDIFTELQH
NLQEGTKFYSDLTQLLIVFQNKVSDFCFARKTEKEELLKDLTAESSRVASGFQQPTIPSH
HGNAPPARPPPPQVQESTSAVPAANAPYPVAMPGMPHPMMGYNYMPPLPTSFNPYATLPH
GGIPYPTNFSFPQAGGAQYYGTYPGAYAQQIQQANYPHAPQQQDPNKPYGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4942.t1 | CDD | cd09235 | V_Alix | 356 | 690 | 0.0 |
| 8 | g4942.t1 | Coils | Coil | Coil | 448 | 468 | - |
| 7 | g4942.t1 | Coils | Coil | Coil | 547 | 574 | - |
| 6 | g4942.t1 | Gene3D | G3DSA:1.25.40.280 | alix/aip1 like domains | 1 | 355 | 3.8E-106 |
| 5 | g4942.t1 | Gene3D | G3DSA:1.20.120.560 | alix/aip1 in complex with the ypdl late domain | 362 | 632 | 8.5E-93 |
| 4 | g4942.t1 | Gene3D | G3DSA:1.20.140.50 | alix/aip1 like domains | 405 | 690 | 8.5E-93 |
| 13 | g4942.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 720 | 740 | - |
| 11 | g4942.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 722 | 736 | - |
| 12 | g4942.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 812 | 831 | - |
| 3 | g4942.t1 | PANTHER | PTHR23030 | PCD6 INTERACTING PROTEIN-RELATED | 2 | 821 | 1.7E-144 |
| 1 | g4942.t1 | Pfam | PF03097 | BRO1-like domain | 3 | 374 | 2.9E-99 |
| 2 | g4942.t1 | Pfam | PF13949 | ALIX V-shaped domain binding to HIV | 409 | 693 | 3.0E-86 |
| 14 | g4942.t1 | ProSiteProfiles | PS51180 | BRO1 domain profile. | 2 | 392 | 51.078 |
| 10 | g4942.t1 | 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
- This transcript has been annotated with K12200 (programmed cell death 6-interacting protein)
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.
