General information for g4942.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TTS | g4942.t2 | 6121511 | 6121511 |
| chr_2 | g4942 | g4942.t2 | isoform | g4942.t2 | 6121645 | 6122587 |
| chr_2 | g4942 | g4942.t2 | exon | g4942.t2.exon1 | 6121645 | 6121754 |
| chr_2 | g4942 | g4942.t2 | cds | g4942.t2.CDS1 | 6121645 | 6121754 |
| chr_2 | g4942 | g4942.t2 | exon | g4942.t2.exon2 | 6121815 | 6122030 |
| chr_2 | g4942 | g4942.t2 | cds | g4942.t2.CDS2 | 6121815 | 6122030 |
| chr_2 | g4942 | g4942.t2 | exon | g4942.t2.exon3 | 6122086 | 6122190 |
| chr_2 | g4942 | g4942.t2 | cds | g4942.t2.CDS3 | 6122086 | 6122190 |
| chr_2 | g4942 | g4942.t2 | exon | g4942.t2.exon4 | 6122267 | 6122587 |
| chr_2 | g4942 | g4942.t2 | cds | g4942.t2.CDS4 | 6122267 | 6122555 |
| chr_2 | g4942 | g4942.t2 | TSS | g4942.t2 | NA | NA |
Sequences
>g4942.t2 Gene=g4942 Length=752
CGCTTGCTGCAGATGGAGTTATTGATCCAAATATGACAATTTCGCATGTGGGTAAAGCAT
TGACACCGCTTCAAAAGCAAGTCAGCGACAGTGTAAGTCGTCAACAAGCACTCGTGCAGG
AAATTCAAGATGCACATAAAGCTTTTACAAACGAATGCGGATCTGGAACAAATCAACGTG
ATCAAGTCACTTCACAATTAGCTTCTGCTTACGACATATTTACTGAATTGCAACATAATC
TTCAAGAAGGAACAAAATTTTACTCTGACCTCACACAACTTTTGATTGTTTTTCAAAATA
AGGTGTCAGATTTTTGCTTTGCACGAAAGACCGAAAAAGAAGAACTATTAAAAGATTTGA
CGGCTGAGTCATCACGTGTGGCGTCTGGTTTTCAACAACCAACTATTCCGAGTCACCATG
GAAATGCTCCTCCTGCTCGTCCACCGCCACCACAAGTCCAAGAGAGCACATCAGCAGTTC
CAGCAGCTAATGCTCCTTATCCAGTGGCAATGCCAGGAATGCCTCATCCTATGATGGGTT
ACAACTACATGCCACCATTGCCAACTTCTTTCAATCCCTATGCAACTTTACCTCATGGTG
GTATTCCTTATCCAACTAACTTTTCTTTTCCACAAGCTGGTGGAGCACAATATTATGGTA
CATACCCAGGAGCATATGCACAGCAAATACAACAAGCTAACTACCCTCATGCTCCACAAC
AACAAGATCCAAATAAGCCTTATGGCTTTTAA
>g4942.t2 Gene=g4942 Length=239
MTISHVGKALTPLQKQVSDSVSRQQALVQEIQDAHKAFTNECGSGTNQRDQVTSQLASAY
DIFTELQHNLQEGTKFYSDLTQLLIVFQNKVSDFCFARKTEKEELLKDLTAESSRVASGF
QQPTIPSHHGNAPPARPPPPQVQESTSAVPAANAPYPVAMPGMPHPMMGYNYMPPLPTSF
NPYATLPHGGIPYPTNFSFPQAGGAQYYGTYPGAYAQQIQQANYPHAPQQQDPNKPYGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4942.t2 | Gene3D | G3DSA:1.20.140.50 | alix/aip1 like domains | 6 | 97 | 8.1E-18 |
| 4 | g4942.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 128 | 148 | - |
| 3 | g4942.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 130 | 144 | - |
| 2 | g4942.t2 | PANTHER | PTHR23030 | PCD6 INTERACTING PROTEIN-RELATED | 6 | 230 | 6.8E-18 |
| 1 | g4942.t2 | Pfam | PF13949 | ALIX V-shaped domain binding to HIV | 9 | 101 | 8.0E-29 |
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.
