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.t4 isoform g10682.t4 11292164 11295009
chr_1 g10682 g10682.t4 exon g10682.t4.exon1 11292164 11292303
chr_1 g10682 g10682.t4 TSS g10682.t4 11292240 11292240
chr_1 g10682 g10682.t4 exon g10682.t4.exon2 11292736 11292814
chr_1 g10682 g10682.t4 cds g10682.t4.CDS1 11292779 11292814
chr_1 g10682 g10682.t4 exon g10682.t4.exon3 11292879 11292965
chr_1 g10682 g10682.t4 cds g10682.t4.CDS2 11292879 11292965
chr_1 g10682 g10682.t4 exon g10682.t4.exon4 11293198 11293285
chr_1 g10682 g10682.t4 cds g10682.t4.CDS3 11293198 11293285
chr_1 g10682 g10682.t4 exon g10682.t4.exon5 11294225 11295009
chr_1 g10682 g10682.t4 cds g10682.t4.CDS4 11294225 11295009
chr_1 g10682 g10682.t4 TTS g10682.t4 11295205 11295205

Sequences

>g10682.t4 Gene=g10682 Length=1179
ATTTGAAAAATGAAAACAATGAATTGTTACGTAATACATATAACCGGCCTTCGAATTTTA
TCATCATCATCATCATTCTCATTCTCATTACTTGTGTTCACTTCGTAGACGACTGGTCGA
AACAGTTATTTCTGATTTCTATCGTCAAATAATCATTCCATTACTTGAAAACAGAATAAA
AAGATGTCTCAAAAAATTAAAGTTGATAATCCAGTTGTGGATGTCCTTGGTGACGAGATG
ACGCGGATTATTTGGGATAGCATCAAAGAAAAACTGATTCTTCCATTTCTCGATATTGAA
CTCAAGGTATTTGACCTTGGAATTGAATACAGAGATCAAACAAACGATCAAGTTACTATT
GATTGTGCCAATGCAATTAAACAATATAATGTCGGAAAATTAGAAATGGTTTTCACTCCA
ACTGATGGAAGTGCTCAACAACGATATACTGTCAATGAATATAAAGGACCAGGCGTTGCA
CTTGGCATGTACAACACTCAAGAATCAATTAGAGATTTCGCTCACTCTTCATTCAAGTAT
GCTTTGGATCGAAAAATGCCACTTTATATGAGTACTAAGAATACAATTTTGAAGAAATAT
GACGGCTACTTCAAGGACATTTTTCAAGAGCTCTATGATACACAATATAAGACCGATTTT
GAAGCACAAGGATTATGGTATGAACACCGTCTTATTGATGACATGGTTGCTTATTGCTTG
AAGAGTGAGGGAGGCTATGTTTGGGCTTGTAAAAACTACGACGGGGACGTGCAATCTGAT
ACAGTTGCCCAGGGATACGGTAGTCTTGGTTTAATGACAAGCGTTTTAATTGCACCTGAC
GGTAAAACTGTTGAAGCTGAAGCAGCTCATGGAACTGTTACTCGTCATTATCGTCAATAT
CAACAAGGAAAAGAAACAAGTACTAATCCAATTGCCTCAATATTTGCATGGACTCGCGGT
TTACTTCATCGTGCAGCTCTAGACAATAATGCAGAACTCAAGAAATTCTGTGAAACATTA
GAGAAAGTTTGTATCGATACAATTGAGAGTGGATTTATGACAAAAGATTTGGCAATTTGT
GTTAAGGGATCTATGAGTGCAGTAAAACGCGAAGATTATCTTGAAACATTTGAGTTTATG
GAAAAACTTGCTGATAATTTGAAAAAAGCCCTCGCATGA

>g10682.t4 Gene=g10682 Length=331
MSQKIKVDNPVVDVLGDEMTRIIWDSIKEKLILPFLDIELKVFDLGIEYRDQTNDQVTID
CANAIKQYNVGKLEMVFTPTDGSAQQRYTVNEYKGPGVALGMYNTQESIRDFAHSSFKYA
LDRKMPLYMSTKNTILKKYDGYFKDIFQELYDTQYKTDFEAQGLWYEHRLIDDMVAYCLK
SEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLIAPDGKTVEAEAAHGTVTRHYRQYQ
QGKETSTNPIASIFAWTRGLLHRAALDNNAELKKFCETLEKVCIDTIESGFMTKDLAICV
KGSMSAVKREDYLETFEFMEKLADNLKKALA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10682.t4 Coils Coil Coil 309 329 -
9 g10682.t4 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 2 70 7.6E-30
8 g10682.t4 Gene3D G3DSA:3.40.718.10 Isopropylmalate Dehydrogenase 71 331 1.2E-136
3 g10682.t4 PANTHER PTHR11822:SF21 ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL 3 71 1.3E-161
5 g10682.t4 PANTHER PTHR11822 NADP-SPECIFIC ISOCITRATE DEHYDROGENASE 3 71 1.3E-161
4 g10682.t4 PANTHER PTHR11822:SF21 ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL 71 330 1.3E-161
6 g10682.t4 PANTHER PTHR11822 NADP-SPECIFIC ISOCITRATE DEHYDROGENASE 71 330 1.3E-161
12 g10682.t4 PIRSF PIRSF000108 IDH_NADP 1 72 7.5E-33
11 g10682.t4 PIRSF PIRSF000108 IDH_NADP 69 331 3.0E-138
2 g10682.t4 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 7 83 3.8E-7
1 g10682.t4 Pfam PF00180 Isocitrate/isopropylmalate dehydrogenase 95 310 1.8E-49
13 g10682.t4 ProSitePatterns PS00470 Isocitrate and isopropylmalate dehydrogenases signature. 191 210 -
14 g10682.t4 SMART SM01329 Iso_dh_2 10 322 2.7E-72
7 g10682.t4 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like 2 330 4.42E-119
15 g10682.t4 TIGRFAM TIGR00127 nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent 71 330 2.7E-136

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.

Raw TPM values