Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Isocitrate dehydrogenase [NADP], chloroplastic/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_1 g10682 g10682.t7 TSS g10682.t7 11292240 11292240
chr_1 g10682 g10682.t7 isoform g10682.t7 11292275 11294600
chr_1 g10682 g10682.t7 exon g10682.t7.exon1 11292275 11292303
chr_1 g10682 g10682.t7 exon g10682.t7.exon2 11292736 11292811
chr_1 g10682 g10682.t7 exon g10682.t7.exon3 11292879 11292969
chr_1 g10682 g10682.t7 exon g10682.t7.exon4 11293198 11293391
chr_1 g10682 g10682.t7 exon g10682.t7.exon5 11294093 11294600
chr_1 g10682 g10682.t7 cds g10682.t7.CDS1 11294236 11294598
chr_1 g10682 g10682.t7 TTS g10682.t7 11295205 11295205

Sequences

>g10682.t7 Gene=g10682 Length=898
ACTGGTCGAAACAGTTATTTCTGATTTCTATCGTCAAATAATCATTCCATTACTTGAAAA
CAGAATAAAAAGATGTCTCAAAAAATTAAAGTTGATAATCCAGTTGATGTCCTTGGTGAC
GAGATGACGCGGATTATTTGGGATAGCATCAAAGAAAAACTGATTCTTCCATTTCTCGAT
ATTGAACTCAAGGTTTGTATTTGACCTTGGAATTGAATACAGAGATCAAACAAACGATCA
AGTTACTATTGATTGTGCCAATGCAATTAAACAATATAATGTCGGTATTAAATGTGCAAC
AATCACTCCAGATGAAGCTCGTGTAAAAGAGTTTAATCTGAAACAAATGTGGAAATCACC
AAATGGCACTATAAGAAATATTTTAGGTGACTGGTTTTAGGGAAGCTATTATTTGTAATA
ATATTCCAAGACTTGTCCCAGGATGGATCAAGCCAATAATTATCGGTCGTCATGCTCATG
CAGATCAATATCGTGCTACAGATTTTGTCGTAAACTCTCCAGGAAAATTAGAAATGGTTT
TCACTCCAACTGATGGAAGTGCTCAACAACGATATACTGTCAATGAATATAAAGGACCAG
GCGTTGCACTTGGCATGTACAACACTCAAGAATCAATTAGAGATTTCGCTCACTCTTCAT
TCAAGTATGCTTTGGATCGAAAAATGCCACTTTATATGAGTACTAAGAATACAATTTTGA
AGAAATATGACGGCTACTTCAAGGACATTTTTCAAGAGCTCTATGATACACAATATAAGA
CCGATTTTGAAGCACAAGGATTATGGTATGAACACCGTCTTATTGATGACATGGTTGCTT
ATTGCTTGAAGAGTGAGGGAGGCTATGTTTGGGCTTGTAAAAACTACGACGGGGACGT

>g10682.t7 Gene=g10682 Length=121
MVFTPTDGSAQQRYTVNEYKGPGVALGMYNTQESIRDFAHSSFKYALDRKMPLYMSTKNT
ILKKYDGYFKDIFQELYDTQYKTDFEAQGLWYEHRLIDDMVAYCLKSEGGYVWACKNYDG
D

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g10682.t7 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 1 121 0
2 g10682.t7 PANTHER PTHR11822:SF15 ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC 1 121 0
3 g10682.t7 PANTHER PTHR11822 NADP-SPECIFIC ISOCITRATE DEHYDROGENASE 1 121 0
1 g10682.t7 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 20 121 0
4 g10682.t7 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 1 121 0

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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0006102 isocitrate metabolic process BP
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