General information for g6560.t3
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.t3 | TSS | g6560.t3 | 17641540 | 17641540 |
| chr_2 | g6560 | g6560.t3 | isoform | g6560.t3 | 17641592 | 17642663 |
| chr_2 | g6560 | g6560.t3 | exon | g6560.t3.exon1 | 17641592 | 17641879 |
| chr_2 | g6560 | g6560.t3 | exon | g6560.t3.exon2 | 17641944 | 17642198 |
| chr_2 | g6560 | g6560.t3 | cds | g6560.t3.CDS1 | 17642087 | 17642198 |
| chr_2 | g6560 | g6560.t3 | exon | g6560.t3.exon3 | 17642265 | 17642663 |
| chr_2 | g6560 | g6560.t3 | cds | g6560.t3.CDS2 | 17642265 | 17642560 |
| chr_2 | g6560 | g6560.t3 | TTS | g6560.t3 | 17643099 | 17643099 |
Sequences
>g6560.t3 Gene=g6560 Length=942
ATGCTAAGGGAATTAGAGAAATTGAACCATATTGCAAAGGAGTACGTGCTATTCATTCTC
CACATACGGGTATTGTTGACTGGGCGTTAGTCACTCAGTACTATGCAAAAGACTTTAAGA
ATGCGGGTGGAGAGATTTATCTCAATTTCGAAGTCAAAAAATTTGAAAGAACAACAAATG
ATGCAGACTTCCCTGTAACAGTTACTTCTGCAAATGGTGAACAGATTAAGTCTAAATATA
TTTTAACATGTGGTGGCTTACAAGCTGATAAAATTGCTGCTTTAACTGGAAATAAAAATC
CTCCAAAAATTGTGCCTTTTAGAGGCGAATATTTGCTGCTAAGTCCTGAAAAAGCCCATT
ATGTGAGAGGAAATATTTACCCTGTTCCCGATCCAAGGTTTCCTTTTCTTGGAGTTCACT
TCACTCCTCGGATGGATGGAAGTGTTTGGCTTGGACCTAATGCAGTACTTGCTTTTAAAA
GAGAAGGCTATAAATGGACTGACATTAATTTACTAGAATTAATTGATGCATTAAAATATC
CTGGTCTCATTCGAATGGCAACTAGGTATATGGGTGCGGGCATAAAGGAAATTACACAAT
CATTGATTCCGGCTCTTCAAGTTCGTGAACTTCAAAAGTTTATACCAGAAATAACAAGAA
AAGATGTACGAGCGGGACCGGCAGGAGTGCGTGCTCAAGCATTACGCAATGATGGCTCAC
TTGTTGATGACTTTATTTTTGAATATGGTGAAGGCGACATTGGAACAAGAATTTTGCACT
GGTATTTTTTACTCTTCTTTTTACGCATAACGGTATTAACATGTTTTTTTTTCTTTTAGC
TGTAATGCACCATCGCCAGGAGCGACATCAAGTTTATCAATTGCAAAAATGATTGCTGAT
AAAGTTGAGAGTTCATTTAGATTCGTTAAGAAACATGATTAA
>g6560.t3 Gene=g6560 Length=135
MDGSVWLGPNAVLAFKREGYKWTDINLLELIDALKYPGLIRMATRYMGAGIKEITQSLIP
ALQVRELQKFIPEITRKDVRAGPAGVRAQALRNDGSLVDDFIFEYGEGDIGTRILHWYFL
LFFLRITVLTCFFFF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g6560.t3 | Gene3D | G3DSA:3.30.9.10 | - | 1 | 91 | 8.5E-10 |
| 1 | g6560.t3 | PANTHER | PTHR43104 | L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL | 1 | 109 | 1.7E-18 |
| 5 | g6560.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 114 | - |
| 6 | g6560.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 134 | - |
| 4 | g6560.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 135 | 135 | - |
| 2 | g6560.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 134 | - |
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.
