General information for g6560.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as L-2-hydroxyglutarate dehydrogenase, mitochondrial.
Parent gene
- The parent gene g6560 is located on chr_2: 17642663..17644667 (+ 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 | g6560 | g6560.t1 | TSS | g6560.t1 | 17641540 | 17641540 |
| chr_2 | g6560 | g6560.t1 | isoform | g6560.t1 | 17641592 | 17642663 |
| chr_2 | g6560 | g6560.t1 | exon | g6560.t1.exon1 | 17641592 | 17641632 |
| chr_2 | g6560 | g6560.t1 | cds | g6560.t1.CDS1 | 17641592 | 17641632 |
| chr_2 | g6560 | g6560.t1 | exon | g6560.t1.exon2 | 17641761 | 17641879 |
| chr_2 | g6560 | g6560.t1 | cds | g6560.t1.CDS2 | 17641761 | 17641879 |
| chr_2 | g6560 | g6560.t1 | exon | g6560.t1.exon3 | 17641944 | 17642198 |
| chr_2 | g6560 | g6560.t1 | cds | g6560.t1.CDS3 | 17641944 | 17642198 |
| chr_2 | g6560 | g6560.t1 | exon | g6560.t1.exon4 | 17642265 | 17642502 |
| chr_2 | g6560 | g6560.t1 | cds | g6560.t1.CDS4 | 17642265 | 17642502 |
| chr_2 | g6560 | g6560.t1 | exon | g6560.t1.exon5 | 17642561 | 17642663 |
| chr_2 | g6560 | g6560.t1 | cds | g6560.t1.CDS5 | 17642561 | 17642663 |
| chr_2 | g6560 | g6560.t1 | TTS | g6560.t1 | 17643099 | 17643099 |
Sequences
>g6560.t1 Gene=g6560 Length=756
ATGCTAAGGGAATTAGAGAAATTGAACCATATTGCAAAGGAAACAACAAATGATGCAGAC
TTCCCTGTAACAGTTACTTCTGCAAATGGTGAACAGATTAAGTCTAAATATATTTTAACA
TGTGGTGGCTTACAAGCTGATAAAATTGCTGCTTTAACTGGAAATAAAAATCCTCCAAAA
ATTGTGCCTTTTAGAGGCGAATATTTGCTGCTAAGTCCTGAAAAAGCCCATTATGTGAGA
GGAAATATTTACCCTGTTCCCGATCCAAGGTTTCCTTTTCTTGGAGTTCACTTCACTCCT
CGGATGGATGGAAGTGTTTGGCTTGGACCTAATGCAGTACTTGCTTTTAAAAGAGAAGGC
TATAAATGGACTGACATTAATTTACTAGAATTAATTGATGCATTAAAATATCCTGGTCTC
ATTCGAATGGCAACTAGGTATATGGGTGCGGGCATAAAGGAAATTACACAATCATTGATT
CCGGCTCTTCAAGTTCGTGAACTTCAAAAGTTTATACCAGAAATAACAAGAAAAGATGTA
CGAGCGGGACCGGCAGGAGTGCGTGCTCAAGCATTACGCAATGATGGCTCACTTGTTGAT
GACTTTATTTTTGAATATGGTGAAGGCGACATTGGAACAAGAATTTTGCACTGCTGTAAT
GCACCATCGCCAGGAGCGACATCAAGTTTATCAATTGCAAAAATGATTGCTGATAAAGTT
GAGAGTTCATTTAGATTCGTTAAGAAACATGATTAA
>g6560.t1 Gene=g6560 Length=251
MLRELEKLNHIAKETTNDADFPVTVTSANGEQIKSKYILTCGGLQADKIAALTGNKNPPK
IVPFRGEYLLLSPEKAHYVRGNIYPVPDPRFPFLGVHFTPRMDGSVWLGPNAVLAFKREG
YKWTDINLLELIDALKYPGLIRMATRYMGAGIKEITQSLIPALQVRELQKFIPEITRKDV
RAGPAGVRAQALRNDGSLVDDFIFEYGEGDIGTRILHCCNAPSPGATSSLSIAKMIADKV
ESSFRFVKKHD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g6560.t1 | Gene3D | G3DSA:3.30.9.10 | - | 3 | 192 | 0e+00 |
| 2 | g6560.t1 | PANTHER | PTHR43104 | L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL | 28 | 240 | 0e+00 |
| 1 | g6560.t1 | Pfam | PF01266 | FAD dependent oxidoreductase | 23 | 238 | 0e+00 |
| 3 | g6560.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 8 | 108 | 3e-06 |
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.
