Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable isocitrate dehydrogenase [NAD] subunit alpha, 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_3 g2739 g2739.t7 TSS g2739.t7 19939005 19939005
chr_3 g2739 g2739.t7 isoform g2739.t7 19939642 19940855
chr_3 g2739 g2739.t7 exon g2739.t7.exon1 19939642 19940855
chr_3 g2739 g2739.t7 cds g2739.t7.CDS1 19939730 19940104
chr_3 g2739 g2739.t7 TTS g2739.t7 19940861 19940861

Sequences

>g2739.t7 Gene=g2739 Length=1214
TCTTTTCTTACGTTGTTGTCGTGAGACTGCTGATAAATTTCCAGAAATTAAATTTGAGGA
AAGATACCTTGATACTGTCTGCTTAAATATGGTACAAGATCCACGTCAATATGATGTTCT
TGTTATGCCAAACTTGTATGGTGATATTTTGTCAGACATGTGTGCTGGCTTAGTTGGTGG
TCTCGGACTTACACCCTCTGGAAATATTGGTCTTGGTGGTGCACTTTTTGAAAGTGTTCA
TGGTACAGCTCCTGATATTGCTGGCAAGGATTTGGCAAATCCAACTGCTCTTCTTCTGTC
GGCTGTTATGATGCTTCGTCATATGGAAATGAACGATAAAGCTGATAAAATTCAGAAAGC
ATGCTTCGAGACCATAAAAGAAGGCAAATATCTCACTGGAGATTTAGGTGGAAAGGCAAA
GTGCTCTGAATTTACAAATGCTATTTGTGAAAAATTAGCTTAATTATTAGGTATTCAATT
CGGATTAGATATGAAGCTCTACGTTTCTTCAGCGATCTCCATTTTTTTTAAAAATTGATC
CTACTTAATTGCATGTCCTAAGTTTAGTTGTTATCATAGATAACAAATGAATCTTAATAT
CAAAGAAATTTTTTAGATTATCCAAAAAAAACGCTTTAAATAACCTAAGTTCTTTCAACG
AATATTAATAAGTTATAACATCTCCCAAAAGTGTTTGATAGTCAAATGATCCCACCTAAT
TTCGCATCCTTCCCTCAAAATTATTATAACCATGTCCTTATCATTGCGAAGGAGAAATGT
AGACATAATAAGTAACATCTTAACACAAAAAATACAATGTTTTTGCATTGTCAACTGTAT
GACTATTATTGAAAAACGGAAAAAGAAAGAGATGATTAAGTTGTAAATTGAAAAAAAAAA
TTAATTTATTTAATACAACACAATAATTATTGTTAAACAGGTTTAAATATTATACACATA
GCCTCTCAATAGATGCAAAAAAATATGCAATAATTTATAAATTATTTGATATTTAATCTC
AATTAGATAGATCCGTCATTATCCGTTATTAATGGTGACTGATTCGATAGAGCACAGAAT
TCGTATTTAGCGAAATCTCTTAAAGATATTTTTGATCGACGTATGAAGTTTTAGTTGTTT
CTTAGAAATAAAACAATGAAATTTCATTTGAATCTGAACAAAAAAGACAATAAATTCATT
GATTGGACATTATT

>g2739.t7 Gene=g2739 Length=124
MVQDPRQYDVLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLGGALFESVHGTAPDIAGK
DLANPTALLLSAVMMLRHMEMNDKADKIQKACFETIKEGKYLTGDLGGKAKCSEFTNAIC
EKLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2739.t7 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 1 124 7.5E-58
2 g2739.t7 PANTHER PTHR11835 DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE 1 121 9.3E-65
3 g2739.t7 PANTHER PTHR11835:SF34 ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL 1 121 9.3E-65
1 g2739.t7 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 1 119 8.2E-49
6 g2739.t7 ProSitePatterns PS00470 Isocitrate and isopropylmalate dehydrogenases signature. 15 34 -
5 g2739.t7 SMART SM01329 Iso_dh_2 1 119 1.1E-9
4 g2739.t7 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 1 123 5.22E-52

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0000287 magnesium ion binding MF
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0051287 NAD binding 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.

Raw TPM values