General information for g4942.t5
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.t5 | isoform | g4942.t5 | 6122931 | 6124508 |
| chr_2 | g4942 | g4942.t5 | exon | g4942.t5.exon1 | 6122931 | 6124012 |
| chr_2 | g4942 | g4942.t5 | cds | g4942.t5.CDS1 | 6122931 | 6123779 |
| chr_2 | g4942 | g4942.t5 | exon | g4942.t5.exon2 | 6124070 | 6124508 |
| chr_2 | g4942 | g4942.t5 | TSS | g4942.t5 | 6124600 | 6124600 |
| chr_2 | g4942 | g4942.t5 | TTS | g4942.t5 | NA | NA |
Sequences
>g4942.t5 Gene=g4942 Length=1521
ATGGATTTAATAACTGTGCCTTTGAAAAAACCGTATGAAGTTGATCTGGTGAAACCACTA
AAGAACATAATTCAAAGCACAAATGTAAAGCAAGCAGATAATTCGCAAATTGAAAAAATA
AATTCCTTCAATAAGCAACGAAATCATGCTGTATTCAAGGTGTTTGAGAAAAATGAAGCT
GCATTAGAAGCTATTTATGGGTAATTAGTACAAATTAAACAACTTTAGTTTAAATTTCAA
ATTTTATGTGATGACTCATTCGATTAATCATTCTATGTATTTTCTTTGTTGTTGCTCTTT
TCAACTTCTCTTTAATTTAGCTATTACGATCAGTTGAATGCTCTAGAAGTCAAAATTCCG
GTTCACGAATTTCAAGTTCCATTCAAATATAAAGATGCTTTCGATAAAGGATCACTATTT
GGTGGTCGTGCTAGCTTGACGCTTTCATCATTAGCGTATGAAAAAGTGTGTGTTCTTTTC
AATATTGCTGCTTTACAAAGTGCAATCGCTGCAAATCAATGCTTCGATAGTGATGATGGA
TTGAAGACAGCTGCAAAATTATTTCAGCAAGCAGCAGGTATTTTCTCCCATCTAAAAAGT
GCAGCACCAGCTTTAGGACAAGAACCGACGCCTGATTTATCACCAGATACACTTCATGTA
TTATCAATTTTAATGTTGGCGCAAGCTCAAGAAGTTTGCCTCTTTAAAGCTATTAAAGAT
GGAATGAAAGATCAAGTAATTGCAAAGTTGGCATGTCAAAATGATGAAATGTATGCTGAT
GTTTTAAAATCCATGCAAAAAGATGGTTTAAAAACGTTATGGGATAAAGAGTGGTTACAA
ATCGTTTGTGGCAAGCAAGCTGGAATTCATGCAATCACACTTTTATATCAAGCTAACGTC
TATCACACTGCAAAAAAAATTGGGCATCAAATTGCTGCTTTACAAAAATCAGTTGATTTA
TTTAAAACTGCTTCAACACGCGCTGGAAAGCCTGTTTTTGAAGAATATAATAAGAAAGCT
CAAATGAAACTTGTTGAAGCTAAAAAAGAAAATGATTTCATTTATAATGCAATGATACCA
GATTCATCAACTTTAGAGTCTTCTGGTAAATTTCAGCTAGCGAAAGCTATACCAATTACA
ATTCCAATGAGTACGAACTTTAAGGATCTTTTCAGTGATCTGGTACCAGTTGCATTGCAG
TCTGCATTGCAAGCATGCGACGCTCAAAAATCTGAAATCGTAAATGCTGAAATCATAAAA
CTTCGTGATGCTACTCAAACTTTGAATGCTGTCTTATCTAGCTTAAATCTTCCTGCAGCA
ATTGAAGTTGCAGCACCTGGTTCAAGCATTCCACCTTCAATTTTAGAAAAAGCAAATGAG
GTTCGTGAAAAAGGAGGAGTTCAAAGTATTCGTACATTAATTGAAGAATTACCAGAATCG
CTTACTCGTAATAAAGAGATTCTTGATGAGACCGAAAGAATGTTGAATGAAGAAAAACAA
TCTGATGAACAATTGCGTGCA
>g4942.t5 Gene=g4942 Length=283
MLAQAQEVCLFKAIKDGMKDQVIAKLACQNDEMYADVLKSMQKDGLKTLWDKEWLQIVCG
KQAGIHAITLLYQANVYHTAKKIGHQIAALQKSVDLFKTASTRAGKPVFEEYNKKAQMKL
VEAKKENDFIYNAMIPDSSTLESSGKFQLAKAIPITIPMSTNFKDLFSDLVPVALQSALQ
ACDAQKSEIVNAEIIKLRDATQTLNAVLSSLNLPAAIEVAAPGSSIPPSILEKANEVREK
GGVQSIRTLIEELPESLTRNKEILDETERMLNEEKQSDEQLRA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4942.t5 | Coils | Coil | Coil | 264 | 283 | - |
| 7 | g4942.t5 | Gene3D | G3DSA:1.25.40.280 | alix/aip1 like domains | 1 | 171 | 3.3E-44 |
| 6 | g4942.t5 | Gene3D | G3DSA:1.20.120.560 | alix/aip1 in complex with the ypdl late domain | 172 | 283 | 4.4E-20 |
| 5 | g4942.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 264 | 283 | - |
| 3 | g4942.t5 | PANTHER | PTHR23030 | PCD6 INTERACTING PROTEIN-RELATED | 1 | 283 | 7.9E-57 |
| 1 | g4942.t5 | Pfam | PF03097 | BRO1-like domain | 1 | 190 | 2.4E-45 |
| 2 | g4942.t5 | Pfam | PF13949 | ALIX V-shaped domain binding to HIV | 225 | 283 | 3.5E-16 |
| 9 | g4942.t5 | ProSiteProfiles | PS51180 | BRO1 domain profile. | 1 | 208 | 23.187 |
| 4 | g4942.t5 | SMART | SM01041 | BRO1_2 | 1 | 194 | 4.7E-4 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
