General information for g6560.t5
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 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.t5 | TSS | g6560.t5 | 17641540 | 17641540 |
| chr_2 | g6560 | g6560.t5 | isoform | g6560.t5 | 17642267 | 17643088 |
| chr_2 | g6560 | g6560.t5 | exon | g6560.t5.exon1 | 17642267 | 17642502 |
| chr_2 | g6560 | g6560.t5 | cds | g6560.t5.CDS1 | 17642276 | 17642502 |
| chr_2 | g6560 | g6560.t5 | exon | g6560.t5.exon2 | 17642561 | 17643088 |
| chr_2 | g6560 | g6560.t5 | cds | g6560.t5.CDS2 | 17642561 | 17642663 |
| chr_2 | g6560 | g6560.t5 | TTS | g6560.t5 | 17643099 | 17643099 |
Sequences
>g6560.t5 Gene=g6560 Length=764
CTCATTCGAATGGCAACTAGGTATATGGGTGCGGGCATAAAGGAAATTACACAATCATTG
ATTCCGGCTCTTCAAGTTCGTGAACTTCAAAAGTTTATACCAGAAATAACAAGAAAAGAT
GTACGAGCGGGACCGGCAGGAGTGCGTGCTCAAGCATTACGCAATGATGGCTCACTTGTT
GATGACTTTATTTTTGAATATGGTGAAGGCGACATTGGAACAAGAATTTTGCACTGCTGT
AATGCACCATCGCCAGGAGCGACATCAAGTTTATCAATTGCAAAAATGATTGCTGATAAA
GTTGAGAGTTCATTTAGATTCGTTAAGAAACATGATTAAAATCGAGGTGAAGGGAATGAA
GATGTAGAATGTACTAAATCATATGCCTAAAAATATGCAATATTAAACGATAACATAAAT
GATAAAAAAATATTTCTGAAACTTTTAGTTTTATGATAGAAAGATTGAGCAATTCCATAT
AAATTTTTGATTCATTTTTTATGATAATTTATTTTTTGTTGCTTCTAAGCGTTTTTACTA
TTTTTGTTGATTTCTTCACCAATGCTTTTTATATACGAAAAAGATATTTTTTGTTATTTC
TCTTTAAATTATTGTACAAAAACAAAGTTATGAAATTTTTAACAATTTTATTTTAATGTT
GAATTACCTATATTTGCCCTATATTTTTTCTCTTCTTTTGTTAATAAAGTTTTTTATTTT
ATAAATAAATTTAGAGATAATAACAGTCCTCTTATGGCCGAAAG
>g6560.t5 Gene=g6560 Length=109
MATRYMGAGIKEITQSLIPALQVRELQKFIPEITRKDVRAGPAGVRAQALRNDGSLVDDF
IFEYGEGDIGTRILHCCNAPSPGATSSLSIAKMIADKVESSFRFVKKHD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g6560.t5 | Gene3D | G3DSA:3.30.9.10 | - | 23 | 53 | 1.4e-06 |
| 2 | g6560.t5 | Gene3D | G3DSA:3.50.50.60 | - | 54 | 92 | 1.4e-06 |
| 1 | g6560.t5 | PANTHER | PTHR43104 | L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL | 13 | 98 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
