General information for g5582.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial.
Parent gene
- The parent gene g5582 is located on chr_2: 10397560..10398678 (+ 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 | g5582 | g5582.t20 | TSS | g5582.t20 | 10396252 | 10396252 |
| chr_2 | g5582 | g5582.t20 | isoform | g5582.t20 | 10396863 | 10398678 |
| chr_2 | g5582 | g5582.t20 | exon | g5582.t20.exon1 | 10396863 | 10397779 |
| chr_2 | g5582 | g5582.t20 | cds | g5582.t20.CDS1 | 10397212 | 10397779 |
| chr_2 | g5582 | g5582.t20 | exon | g5582.t20.exon2 | 10397836 | 10397911 |
| chr_2 | g5582 | g5582.t20 | cds | g5582.t20.CDS2 | 10397836 | 10397911 |
| chr_2 | g5582 | g5582.t20 | exon | g5582.t20.exon3 | 10398603 | 10398678 |
| chr_2 | g5582 | g5582.t20 | cds | g5582.t20.CDS3 | 10398603 | 10398603 |
| chr_2 | g5582 | g5582.t20 | TTS | g5582.t20 | 10398686 | 10398686 |
Sequences
>g5582.t20 Gene=g5582 Length=1069
TTTCTTTACTGTTTTAATAAAAACTTAATTTATTTTAGATGTTCGAGAAATTTTCCGCTA
TGCAGGTGTTCCTGTTGATTTTGAAGTTATTGATATAGATCCAAATAGCGAAACCAATGA
TGATTTAGATTATGCAATTACATCAATTAAACGTAATGGTGTTGCAATTAAGGGAAATAT
TGAGACAAAAAGTGAAGCAACTGGAATTATCTCAAGAAATGTTGCATTGCGAAATGAATT
AGATTTGTTTGTCAATGTATTGCATTGCAAATCATATCCTGGTGTGAGATCTCACCATAA
AGACATTGATTTAATTGTTGTACGTCAAAATACAGAAGGTGAGTATGCGATGTTGGAACA
CGAGTCAGTGCGAGGTGTTGTTGAGTCATTGAAAATTATAACTGTGGAAGCTAGTGAGAG
ATTAAGTCGATTTGCATTCGAATATGCTCGCAAAAATGGTCGCAAGAAGGTGACAACTAT
TCATAAAGCTAACATCATGAAGCTCTCCGATGGATGCTTCCTAGAAACTTCAAAGCGTAT
TGCCAAAGAATATCCAGATATCGAGCACAATAATATGATTATTGACAATACATGCATGCA
ATTGGTGGCAAAGCCTCAACAATTTGATGTTCTTTTAACAACTAATTTGTATGGATCAAT
TTGCACAAATGTAATTTGTGGATTAGTTGGAGGAGCTGGTTTATATAGCGGACGTAACTA
TGGTGATCATTATGCTGTCTTTGAGCCAGGCACACGTAACACAGGAAGCTCAATTGCTGG
AAAGAATATTTGCAATCCTTTTGCAATGCTTAATGCAAGTGTTGACATGTTGAATCATCT
TGGTCATACTCAACATGCAAATGCCATCTCTACAGCCATATACGAGACAATTGTCAAAGA
TAAAATTCATACAGCCGACCTTGGTGGAACTGCATCTTCAACCGATTGTATTCAAAATGT
GTTGAAGCATCTTGCAGCTGGACAAGTTTCTTGATTTAAAATACTGAAAAACTAATAATT
TATTATTTATTGTTAAAAACATGAAATAAAGAAGAAAGAAAAAAGACAC
>g5582.t20 Gene=g5582 Length=214
MLEHESVRGVVESLKIITVEASERLSRFAFEYARKNGRKKVTTIHKANIMKLSDGCFLET
SKRIAKEYPDIEHNNMIIDNTCMQLVAKPQQFDVLLTTNLYGSICTNVICGLVGGAGLYS
GRNYGDHYAVFEPGTRNTGSSIAGKNICNPFAMLNASVDMLNHLGHTQHANAISTAIYET
IVKDKIHTADLGGTASSTDCIQNVLKHLAAGQVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5582.t20 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 1 | 213 | 0 |
| 2 | g5582.t20 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 1 | 209 | 0 |
| 3 | g5582.t20 | PANTHER | PTHR11835:SF60 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL | 1 | 209 | 0 |
| 1 | g5582.t20 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 10 | 196 | 0 |
| 5 | g5582.t20 | SMART | SM01329 | Iso_dh_2 | 2 | 204 | 0 |
| 4 | g5582.t20 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 5 | 208 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5582/g5582.t20; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5582.t20.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | MF |
| GO:0055114 | NA | NA |
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.
