Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Isocitrate dehydrogenase [NAD] subunit gamma 1, 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.t5 TSS g5582.t5 10396252 10396252
chr_2 g5582 g5582.t5 isoform g5582.t5 10396340 10397317
chr_2 g5582 g5582.t5 exon g5582.t5.exon1 10396340 10396721
chr_2 g5582 g5582.t5 exon g5582.t5.exon2 10396780 10396843
chr_2 g5582 g5582.t5 cds g5582.t5.CDS1 10396804 10396843
chr_2 g5582 g5582.t5 exon g5582.t5.exon3 10396901 10397317
chr_2 g5582 g5582.t5 cds g5582.t5.CDS2 10396901 10397316
chr_2 g5582 g5582.t5 TTS g5582.t5 NA NA

Sequences

>g5582.t5 Gene=g5582 Length=863
ATGGCGCTTGCTGTTCGATTTGCAAAGCAATCAACTGAGAAGTTGTCACCGCTCTTGAGA
AGAGTAAGTGTTGATTTAATGAAAAAAATTGTTAGATAACTATTTTTCTCGAGTCCTTCA
AGTTTTTGCGATTTATTTATATTCTTATTTTTCCTGTAATTTGCTGTTACTCGTAAATGT
CACGGGTTTGAATGAAGATATAAAATGTATAAATTTTTCAATGACATTGATTAATAATTA
TTATTAATTACATTATATGATTCTGTGAAAATAATGGAATATCTTAAATGAAAAATTGTT
TTTCTAGAACTTCTGCTCTGCATACGAATTGCAACACAAAAATCCTATTCAAAAACGAAT
TGCTGCAATCCCAAAAGCTCAATATGGAGGTAGACACACGGTCACAATGCTCCCTGGTGG
TGGAATCGGATTAGAGCTCTCAAACTATGTTCGAGAAATTTTCCGCTATGCAGGTGTTCC
TGTTGATTTTGAAGTTATTGATATAGATCCAAATAGCGAAACCAATGATGATTTAGATTA
TGCAATTACATCAATTAAACGTAATGGTGTTGCAATTAAGGGAAATATTGAGACAAAAAG
TGAAGCAACTGGAATTATCTCAAGAAATGTTGCATTGCGAAATGAATTAGATTTGTTTGT
CAATGTATTGCATTGCAAATCATATCCTGGTGTGAGATCTCACCATAAAGACATTGATTT
AATTGTTGTACGTCAAAATACAGAAGGTGAGTATGCGATGTTGGAACACGAGTCAGTGCG
AGGTGTTGTTGAGTCATTGAAAATTATAACTGTGGAAGCTAGTGAGAGATTAAGTCGATT
TGCATTCGAATATGCTCGCAAAA

>g5582.t5 Gene=g5582 Length=152
MLPGGGIGLELSNYVREIFRYAGVPVDFEVIDIDPNSETNDDLDYAITSIKRNGVAIKGN
IETKSEATGIISRNVALRNELDLFVNVLHCKSYPGVRSHHKDIDLIVVRQNTEGEYAMLE
HESVRGVVESLKIITVEASERLSRFAFEYARK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5582.t5 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 1 152 0.0e+00
2 g5582.t5 PANTHER PTHR11835 DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE 1 152 0.0e+00
3 g5582.t5 PANTHER PTHR11835:SF60 ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL 1 152 0.0e+00
1 g5582.t5 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 2 152 0.0e+00
5 g5582.t5 SMART SM01329 Iso_dh_2 1 152 1.3e-06
4 g5582.t5 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 1 152 0.0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5582/g5582.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5582.t5.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