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.t8 TSS g10682.t8 11292240 11292240
chr_1 g10682 g10682.t8 isoform g10682.t8 11292275 11294600
chr_1 g10682 g10682.t8 exon g10682.t8.exon1 11292275 11292303
chr_1 g10682 g10682.t8 exon g10682.t8.exon2 11292736 11292814
chr_1 g10682 g10682.t8 exon g10682.t8.exon3 11292879 11292969
chr_1 g10682 g10682.t8 exon g10682.t8.exon4 11293198 11293391
chr_1 g10682 g10682.t8 cds g10682.t8.CDS1 11293348 11293391
chr_1 g10682 g10682.t8 exon g10682.t8.exon5 11294103 11294600
chr_1 g10682 g10682.t8 cds g10682.t8.CDS2 11294103 11294598
chr_1 g10682 g10682.t8 TTS g10682.t8 11295205 11295205

Sequences

>g10682.t8 Gene=g10682 Length=891
ACTGGTCGAAACAGTTATTTCTGATTTCTATCGTCAAATAATCATTCCATTACTTGAAAA
CAGAATAAAAAGATGTCTCAAAAAATTAAAGTTGATAATCCAGTTGTGGATGTCCTTGGT
GACGAGATGACGCGGATTATTTGGGATAGCATCAAAGAAAAACTGATTCTTCCATTTCTC
GATATTGAACTCAAGGTTTGTATTTGACCTTGGAATTGAATACAGAGATCAAACAAACGA
TCAAGTTACTATTGATTGTGCCAATGCAATTAAACAATATAATGTCGGTATTAAATGTGC
AACAATCACTCCAGATGAAGCTCGTGTAAAAGAGTTTAATCTGAAACAAATGTGGAAATC
ACCAAATGGCACTATAAGAAATATTTTAGGTGAGGAAGCTATTATTTGTAATAATATTCC
AAGACTTGTCCCAGGATGGATCAAGCCAATAATTATCGGTCGTCATGCTCATGCAGATCA
ATATCGTGCTACAGATTTTGTCGTAAACTCTCCAGGAAAATTAGAAATGGTTTTCACTCC
AACTGATGGAAGTGCTCAACAACGATATACTGTCAATGAATATAAAGGACCAGGCGTTGC
ACTTGGCATGTACAACACTCAAGAATCAATTAGAGATTTCGCTCACTCTTCATTCAAGTA
TGCTTTGGATCGAAAAATGCCACTTTATATGAGTACTAAGAATACAATTTTGAAGAAATA
TGACGGCTACTTCAAGGACATTTTTCAAGAGCTCTATGATACACAATATAAGACCGATTT
TGAAGCACAAGGATTATGGTATGAACACCGTCTTATTGATGACATGGTTGCTTATTGCTT
GAAGAGTGAGGGAGGCTATGTTTGGGCTTGTAAAAACTACGACGGGGACGT

>g10682.t8 Gene=g10682 Length=180
MWKSPNGTIRNILGEEAIICNNIPRLVPGWIKPIIIGRHAHADQYRATDFVVNSPGKLEM
VFTPTDGSAQQRYTVNEYKGPGVALGMYNTQESIRDFAHSSFKYALDRKMPLYMSTKNTI
LKKYDGYFKDIFQELYDTQYKTDFEAQGLWYEHRLIDDMVAYCLKSEGGYVWACKNYDGD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10682.t8 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 1 180 0.0e+00
2 g10682.t8 PANTHER PTHR11822:SF15 ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC 1 180 0.0e+00
3 g10682.t8 PANTHER PTHR11822 NADP-SPECIFIC ISOCITRATE DEHYDROGENASE 1 180 0.0e+00
1 g10682.t8 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 1 180 0.0e+00
5 g10682.t8 SMART SM01329 Iso_dh_2 1 180 4.1e-05
4 g10682.t8 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 1 180 0.0e+00

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