Gene loci information

Transcript annotation

  • This transcript has been annotated as Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial.

Parent gene

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.t21 TSS g5582.t21 10396252 10396252
chr_2 g5582 g5582.t21 isoform g5582.t21 10396964 10398003
chr_2 g5582 g5582.t21 exon g5582.t21.exon1 10396964 10397560
chr_2 g5582 g5582.t21 cds g5582.t21.CDS1 10397212 10397560
chr_2 g5582 g5582.t21 exon g5582.t21.exon2 10397612 10397779
chr_2 g5582 g5582.t21 cds g5582.t21.CDS2 10397612 10397779
chr_2 g5582 g5582.t21 exon g5582.t21.exon3 10397836 10398003
chr_2 g5582 g5582.t21 cds g5582.t21.CDS3 10397836 10397915
chr_2 g5582 g5582.t21 TTS g5582.t21 10398686 10398686

Sequences

>g5582.t21 Gene=g5582 Length=933
CAAATAGCGAAACCAATGATGATTTAGATTATGCAATTACATCAATTAAACGTAATGGTG
TTGCAATTAAGGGAAATATTGAGACAAAAAGTGAAGCAACTGGAATTATCTCAAGAAATG
TTGCATTGCGAAATGAATTAGATTTGTTTGTCAATGTATTGCATTGCAAATCATATCCTG
GTGTGAGATCTCACCATAAAGACATTGATTTAATTGTTGTACGTCAAAATACAGAAGGTG
AGTATGCGATGTTGGAACACGAGTCAGTGCGAGGTGTTGTTGAGTCATTGAAAATTATAA
CTGTGGAAGCTAGTGAGAGATTAAGTCGATTTGCATTCGAATATGCTCGCAAAAATGGTC
GCAAGAAGGTGACAACTATTCATAAAGCTAACATCATGAAGCTCTCCGATGGATGCTTCC
TAGAAACTTCAAAGCGTATTGCCAAAGAATATCCAGATATCGAGCACAATAATATGATTA
TTGACAATACATGCATGCAATTGGTGGCAAAGCCTCAACAATTTGATGTTCTTTTAACAA
CTAATTTGTATGGATCAATTTGCACAAATGTAATTTGTGGATTAGTTGGAGGAGCTGGCA
CACGTAACACAGGAAGCTCAATTGCTGGAAAGAATATTTGCAATCCTTTTGCAATGCTTA
ATGCAAGTGTTGACATGTTGAATCATCTTGGTCATACTCAACATGCAAATGCCATCTCTA
CAGCCATATACGAGACAATTGTCAAAGATAAAATTCATACAGCCGACCTTGGTGGAACTG
CATCTTCAACCGATTGTATTCAAAATGTGTTGAAGCATCTTGCAGCTGGACAAGTTTCTT
GGTAAGATTTATGTTTTGTTTTTAAAGGTTGAGAGTTTTTATTAACATTAACAATAAACG
TTTGTTCTGTACAGGCATGGTTTAGCTAATTAA

>g5582.t21 Gene=g5582 Length=198
MLEHESVRGVVESLKIITVEASERLSRFAFEYARKNGRKKVTTIHKANIMKLSDGCFLET
SKRIAKEYPDIEHNNMIIDNTCMQLVAKPQQFDVLLTTNLYGSICTNVICGLVGGAGTRN
TGSSIAGKNICNPFAMLNASVDMLNHLGHTQHANAISTAIYETIVKDKIHTADLGGTASS
TDCIQNVLKHLAAGQVSW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5582.t21 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 1 197 0
2 g5582.t21 PANTHER PTHR11835 DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE 1 193 0
3 g5582.t21 PANTHER PTHR11835:SF60 ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL 1 193 0
1 g5582.t21 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 10 179 0
5 g5582.t21 SMART SM01329 Iso_dh_2 2 187 0
4 g5582.t21 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 5 191 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5582/g5582.t21; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5582.t21.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. There were no conditions that were differentially expressed