General information for g6558.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative L-2-hydroxyglutarate dehydrogenase, mitochondrial.
Parent gene
- The parent gene g6558 is located on chr_2: 17638114..17638803 (+ 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 | g6558 | g6558.t1 | TSS | g6558.t1 | 17637959 | 17637959 |
| chr_2 | g6558 | g6558.t1 | isoform | g6558.t1 | 17638114 | 17638803 |
| chr_2 | g6558 | g6558.t1 | exon | g6558.t1.exon1 | 17638114 | 17638322 |
| chr_2 | g6558 | g6558.t1 | cds | g6558.t1.CDS1 | 17638114 | 17638322 |
| chr_2 | g6558 | g6558.t1 | TTS | g6558.t1 | 17638537 | 17638537 |
| chr_2 | g6558 | g6558.t1 | exon | g6558.t1.exon2 | 17638590 | 17638803 |
| chr_2 | g6558 | g6558.t1 | cds | g6558.t1.CDS2 | 17638590 | 17638803 |
Sequences
>g6558.t1 Gene=g6558 Length=423
ATGTTACGTACACTTAATTCAAGTGGTTTAATTTTACGAAGATCCTTGAGTAGTGCTAAT
AATAATGCTGGTTATGATTTAAGCGTTATTGGCGGAGGAATTGTCGGAGTAGCATCAGCT
CGTGAAATCTTAATTCGGCATCCACATTTAAAAATTGCAATTGTAGAGAAAGAGAAAACT
TTAGCGTTCCATCAATCAGGACACAATAGTGGGGTCATCCATGCGGGAATCTATTATAAA
CCAGGATCATTAAAAGCAAAATTGTGTGTAGAAGGATTACATTTGACATACAAATATTGT
GATGAAAGAAATATACCGTACAAAAAAGTTGGTAAATTGATCGTAGCTACTAATAAGGTT
GAGGAGGAGAGATTAAAGGTCAGTAAATATGTTATGTTTGTTATCAATGTCGCTCTCACT
TGA
>g6558.t1 Gene=g6558 Length=140
MLRTLNSSGLILRRSLSSANNNAGYDLSVIGGGIVGVASAREILIRHPHLKIAIVEKEKT
LAFHQSGHNSGVIHAGIYYKPGSLKAKLCVEGLHLTYKYCDERNIPYKKVGKLIVATNKV
EEERLKVSKYVMFVINVALT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g6558.t1 | Gene3D | G3DSA:3.50.50.60 | - | 23 | 139 | 0 |
| 2 | g6558.t1 | PANTHER | PTHR43104 | L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL | 19 | 126 | 0 |
| 1 | g6558.t1 | Pfam | PF01266 | FAD dependent oxidoreductase | 27 | 125 | 0 |
| 3 | g6558.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 25 | 125 | 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:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00109 (2-hydroxyglutarate dehydrogenase)
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.
