General information for g6560.t4
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.t4 | TSS | g6560.t4 | 17641540 | 17641540 |
| chr_2 | g6560 | g6560.t4 | isoform | g6560.t4 | 17641592 | 17643088 |
| chr_2 | g6560 | g6560.t4 | exon | g6560.t4.exon1 | 17641592 | 17642198 |
| chr_2 | g6560 | g6560.t4 | cds | g6560.t4.CDS1 | 17642087 | 17642198 |
| chr_2 | g6560 | g6560.t4 | exon | g6560.t4.exon2 | 17642265 | 17642502 |
| chr_2 | g6560 | g6560.t4 | cds | g6560.t4.CDS2 | 17642265 | 17642502 |
| chr_2 | g6560 | g6560.t4 | exon | g6560.t4.exon3 | 17642561 | 17643088 |
| chr_2 | g6560 | g6560.t4 | cds | g6560.t4.CDS3 | 17642561 | 17642663 |
| chr_2 | g6560 | g6560.t4 | TTS | g6560.t4 | 17643099 | 17643099 |
Sequences
>g6560.t4 Gene=g6560 Length=1373
ATGCTAAGGGAATTAGAGAAATTGAACCATATTGCAAAGGAGTACGTGCTATTCATTCTC
CACATACGGGTATTGTTGACTGGGCGTTAGTCACTCAGTACTATGCAAAAGACTTTAAGA
ATGCGGGTGGAGAGATTTATCTCAATTTCGAAGTCAAAAAATTTGAAAGAACAACAAATG
ATGCAGACTTCCCTGTAACAGTTACTTCTGCAAATGGTGAACAGATTAAGTCTAAATATA
TTTTAACATGTGGTGGCTTACAAGCTGATAAAATTGCTGCTTTAACTGGTAGATTGACAT
GATTTTATACATCATAACTTGATAATAATTTAAACATGTTTTTCAATATTAGGAAATAAA
AATCCTCCAAAAATTGTGCCTTTTAGAGGCGAATATTTGCTGCTAAGTCCTGAAAAAGCC
CATTATGTGAGAGGAAATATTTACCCTGTTCCCGATCCAAGGTTTCCTTTTCTTGGAGTT
CACTTCACTCCTCGGATGGATGGAAGTGTTTGGCTTGGACCTAATGCAGTACTTGCTTTT
AAAAGAGAAGGCTATAAATGGACTGACATTAATTTACTAGAATTAATTGATGCATTAAAA
TATCCTGGTCTCATTCGAATGGCAACTAGGTATATGGGTGCGGGCATAAAGGAAATTACA
CAATCATTGATTCCGGCTCTTCAAGTTCGTGAACTTCAAAAGTTTATACCAGAAATAACA
AGAAAAGATGTACGAGCGGGACCGGCAGGAGTGCGTGCTCAAGCATTACGCAATGATGGC
TCACTTGTTGATGACTTTATTTTTGAATATGGTGAAGGCGACATTGGAACAAGAATTTTG
CACTGCTGTAATGCACCATCGCCAGGAGCGACATCAAGTTTATCAATTGCAAAAATGATT
GCTGATAAAGTTGAGAGTTCATTTAGATTCGTTAAGAAACATGATTAAAATCGAGGTGAA
GGGAATGAAGATGTAGAATGTACTAAATCATATGCCTAAAAATATGCAATATTAAACGAT
AACATAAATGATAAAAAAATATTTCTGAAACTTTTAGTTTTATGATAGAAAGATTGAGCA
ATTCCATATAAATTTTTGATTCATTTTTTATGATAATTTATTTTTTGTTGCTTCTAAGCG
TTTTTACTATTTTTGTTGATTTCTTCACCAATGCTTTTTATATACGAAAAAGATATTTTT
TGTTATTTCTCTTTAAATTATTGTACAAAAACAAAGTTATGAAATTTTTAACAATTTTAT
TTTAATGTTGAATTACCTATATTTGCCCTATATTTTTTCTCTTCTTTTGTTAATAAAGTT
TTTTATTTTATAAATAAATTTAGAGATAATAACAGTCCTCTTATGGCCGAAAG
>g6560.t4 Gene=g6560 Length=150
MDGSVWLGPNAVLAFKREGYKWTDINLLELIDALKYPGLIRMATRYMGAGIKEITQSLIP
ALQVRELQKFIPEITRKDVRAGPAGVRAQALRNDGSLVDDFIFEYGEGDIGTRILHCCNA
PSPGATSSLSIAKMIADKVESSFRFVKKHD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6560.t4 | Gene3D | G3DSA:3.30.9.10 | - | 1 | 91 | 0 |
| 1 | g6560.t4 | PANTHER | PTHR43104 | L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL | 1 | 139 | 0 |
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.
