General information for g16960.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial.
Parent gene
- The parent gene g16960 is located on chr_4: 11879110..11880536 (+ 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_4 | g16960 | g16960.t4 | TSS | g16960.t4 | 11877931 | 11877931 |
| chr_4 | g16960 | g16960.t4 | isoform | g16960.t4 | 11878813 | 11880536 |
| chr_4 | g16960 | g16960.t4 | exon | g16960.t4.exon1 | 11878813 | 11878869 |
| chr_4 | g16960 | g16960.t4 | cds | g16960.t4.CDS1 | 11878814 | 11878869 |
| chr_4 | g16960 | g16960.t4 | exon | g16960.t4.exon2 | 11879016 | 11879121 |
| chr_4 | g16960 | g16960.t4 | cds | g16960.t4.CDS2 | 11879016 | 11879121 |
| chr_4 | g16960 | g16960.t4 | exon | g16960.t4.exon3 | 11879327 | 11879479 |
| chr_4 | g16960 | g16960.t4 | cds | g16960.t4.CDS3 | 11879327 | 11879479 |
| chr_4 | g16960 | g16960.t4 | exon | g16960.t4.exon4 | 11879833 | 11880536 |
| chr_4 | g16960 | g16960.t4 | cds | g16960.t4.CDS4 | 11879833 | 11879907 |
| chr_4 | g16960 | g16960.t4 | TTS | g16960.t4 | NA | NA |
Sequences
>g16960.t4 Gene=g16960 Length=1020
TGATATTTTAAGAGTTGGTGGTGATGTGACATTAATTGGATGGGGAACACAAGTCCATGT
TTTAAGAGAAACTGCCGAATATGCAAAAAGAAAACTCAATGTTAATTGTGAAGTTATTGA
TTTAGTTTCTATTTTGCCATGGGATGTTGAGACTGTTTGCAATTCAGTAAAGAAGACTGG
TCGTTGTATTATTGCACATGAGGCTCCAGTAACAAATGGCTTTGGTGCAGAAATTGCAGC
TACAGTTCAAGAAGAATGTTTCTTGCATTTAGAAGCACCGATTCAAAGAGTTTGCGGATG
GGATACTCCGTTTCCGCATGTTTTTGAACCATTTTATCTTCCTGATAAATATCGATGCTT
AGAAGCAATTAAAAAAGTAATTGACTATTAAAACTTTGGTGCAAGATAAAAATTAATTTG
AACCCAACGTACAAAAATAATTTTTAAAACACTTAAAATTCTTTGGTTTAAATTTTTTGT
ACATAATTTTACATTCAAACAGTGTCCGAAATTATTTTAAATTTATTTACAAGTAAATAA
AAATTAAGTCAATTTTTTCGAGTAAAAAAATAAATTTTACTTAATTTTTAGTAACTCTTA
AATAAAATTTAAAACGATTTCGGACTTTGCTTTCAAAAATGAAATTTTACAAAAAATTTT
GATGGAAGAATTTTAAGTTTTGCATTTATTGAAATTTACTGGGAAATTATGAAAAAATAA
ATTTTTGTGTAAAAAATTCATGAAATATAACTGAAATATTGAAACTTGTTGCATTTATTA
ATTTTAAAATGAGAAAATTATAAATTTTGAGAATTTTCAAAAGATTTGTTAAAAAAAATG
TTGATGTATTTTATTGTAACAATAAAAACCGTTTAAAAAAAGGAAAAAAAATCAAGAATT
TTTTTTATTTTTCAAGGAAATAAAAACAAAAAATTGAATTTTTGATAAAAAGACTAAATT
TTATTCAAATTTTACTTTTTTAATCATTTTTGGAACAAAAATATTTTAAAATCTGTATTT
>g16960.t4 Gene=g16960 Length=129
DILRVGGDVTLIGWGTQVHVLRETAEYAKRKLNVNCEVIDLVSILPWDVETVCNSVKKTG
RCIIAHEAPVTNGFGAEIAATVQEECFLHLEAPIQRVCGWDTPFPHVFEPFYLPDKYRCL
EAIKKVIDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g16960.t4 | Gene3D | G3DSA:3.40.50.920 | - | 1 | 125 | 0 |
| 2 | g16960.t4 | PANTHER | PTHR42980 | 2-OXOISOVALERATE DEHYDROGENASE SUBUNIT BETA-RELATED | 1 | 128 | 0 |
| 1 | g16960.t4 | Pfam | PF02780 | Transketolase, C-terminal domain | 2 | 116 | 0 |
| 3 | g16960.t4 | SUPERFAMILY | SSF52922 | TK C-terminal domain-like | 2 | 129 | 0 |
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:0003824 | catalytic activity | 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.
