Gene loci information

Transcript annotation

  • This transcript has been annotated as Isocitrate dehydrogenase [NADP] cytoplasmic.

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_1 g10682 g10682.t2 isoform g10682.t2 11290577 11295009
chr_1 g10682 g10682.t2 exon g10682.t2.exon1 11290577 11290620
chr_1 g10682 g10682.t2 exon g10682.t2.exon2 11294204 11295009
chr_1 g10682 g10682.t2 cds g10682.t2.CDS1 11294236 11295009
chr_1 g10682 g10682.t2 TTS g10682.t2 11295205 11295205
chr_1 g10682 g10682.t2 TSS g10682.t2 NA NA

Sequences

>g10682.t2 Gene=g10682 Length=850
TTACACTCTCTGATGATATTTTCTTCATAAATTCATCACTAGGTATTTTGTCGTAAACTC
TCCAGGAAAATTAGAAATGGTTTTCACTCCAACTGATGGAAGTGCTCAACAACGATATAC
TGTCAATGAATATAAAGGACCAGGCGTTGCACTTGGCATGTACAACACTCAAGAATCAAT
TAGAGATTTCGCTCACTCTTCATTCAAGTATGCTTTGGATCGAAAAATGCCACTTTATAT
GAGTACTAAGAATACAATTTTGAAGAAATATGACGGCTACTTCAAGGACATTTTTCAAGA
GCTCTATGATACACAATATAAGACCGATTTTGAAGCACAAGGATTATGGTATGAACACCG
TCTTATTGATGACATGGTTGCTTATTGCTTGAAGAGTGAGGGAGGCTATGTTTGGGCTTG
TAAAAACTACGACGGGGACGTGCAATCTGATACAGTTGCCCAGGGATACGGTAGTCTTGG
TTTAATGACAAGCGTTTTAATTGCACCTGACGGTAAAACTGTTGAAGCTGAAGCAGCTCA
TGGAACTGTTACTCGTCATTATCGTCAATATCAACAAGGAAAAGAAACAAGTACTAATCC
AATTGCCTCAATATTTGCATGGACTCGCGGTTTACTTCATCGTGCAGCTCTAGACAATAA
TGCAGAACTCAAGAAATTCTGTGAAACATTAGAGAAAGTTTGTATCGATACAATTGAGAG
TGGATTTATGACAAAAGATTTGGCAATTTGTGTTAAGGGATCTATGAGTGCAGTAAAACG
CGAAGATTATCTTGAAACATTTGAGTTTATGGAAAAACTTGCTGATAATTTGAAAAAAGC
CCTCGCATGA

>g10682.t2 Gene=g10682 Length=257
MVFTPTDGSAQQRYTVNEYKGPGVALGMYNTQESIRDFAHSSFKYALDRKMPLYMSTKNT
ILKKYDGYFKDIFQELYDTQYKTDFEAQGLWYEHRLIDDMVAYCLKSEGGYVWACKNYDG
DVQSDTVAQGYGSLGLMTSVLIAPDGKTVEAEAAHGTVTRHYRQYQQGKETSTNPIASIF
AWTRGLLHRAALDNNAELKKFCETLEKVCIDTIESGFMTKDLAICVKGSMSAVKREDYLE
TFEFMEKLADNLKKALA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10682.t2 Coils Coil Coil 235 255 -
5 g10682.t2 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 1 257 1.3E-134
2 g10682.t2 PANTHER PTHR11822:SF21 ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL 1 256 2.6E-131
3 g10682.t2 PANTHER PTHR11822 NADP-SPECIFIC ISOCITRATE DEHYDROGENASE 1 256 2.6E-131
1 g10682.t2 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 20 236 6.4E-50
7 g10682.t2 ProSitePatterns PS00470 Isocitrate and isopropylmalate dehydrogenases signature. 117 136 -
8 g10682.t2 SMART SM01329 Iso_dh_2 2 248 7.8E-27
4 g10682.t2 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 1 256 1.54E-97
9 g10682.t2 TIGRFAM TIGR00127 nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent 1 256 1.4E-134

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:0004450 isocitrate dehydrogenase (NADP+) activity MF
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:0006102 isocitrate metabolic process BP
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. There were no conditions that were differentially expressed