General information for g10682.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Isocitrate dehydrogenase [NADP] cytoplasmic.
Parent gene
- The parent gene g10682 is located on chr_1: 11294096..11295009 (+ strand)
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.t10 | TSS | g10682.t10 | 11292240 | 11292240 |
| chr_1 | g10682 | g10682.t10 | isoform | g10682.t10 | 11292275 | 11295009 |
| chr_1 | g10682 | g10682.t10 | exon | g10682.t10.exon1 | 11292275 | 11292303 |
| chr_1 | g10682 | g10682.t10 | exon | g10682.t10.exon2 | 11292736 | 11292814 |
| chr_1 | g10682 | g10682.t10 | cds | g10682.t10.CDS1 | 11292779 | 11292814 |
| chr_1 | g10682 | g10682.t10 | exon | g10682.t10.exon3 | 11292879 | 11292965 |
| chr_1 | g10682 | g10682.t10 | cds | g10682.t10.CDS2 | 11292879 | 11292965 |
| chr_1 | g10682 | g10682.t10 | exon | g10682.t10.exon4 | 11293198 | 11293391 |
| chr_1 | g10682 | g10682.t10 | cds | g10682.t10.CDS3 | 11293198 | 11293391 |
| chr_1 | g10682 | g10682.t10 | exon | g10682.t10.exon5 | 11294103 | 11295009 |
| chr_1 | g10682 | g10682.t10 | cds | g10682.t10.CDS4 | 11294103 | 11295009 |
| chr_1 | g10682 | g10682.t10 | TTS | g10682.t10 | 11295205 | 11295205 |
Sequences
>g10682.t10 Gene=g10682 Length=1296
ACTGGTCGAAACAGTTATTTCTGATTTCTATCGTCAAATAATCATTCCATTACTTGAAAA
CAGAATAAAAAGATGTCTCAAAAAATTAAAGTTGATAATCCAGTTGTGGATGTCCTTGGT
GACGAGATGACGCGGATTATTTGGGATAGCATCAAAGAAAAACTGATTCTTCCATTTCTC
GATATTGAACTCAAGGTATTTGACCTTGGAATTGAATACAGAGATCAAACAAACGATCAA
GTTACTATTGATTGTGCCAATGCAATTAAACAATATAATGTCGGTATTAAATGTGCAACA
ATCACTCCAGATGAAGCTCGTGTAAAAGAGTTTAATCTGAAACAAATGTGGAAATCACCA
AATGGCACTATAAGAAATATTTTAGGTGAGGAAGCTATTATTTGTAATAATATTCCAAGA
CTTGTCCCAGGATGGATCAAGCCAATAATTATCGGTCGTCATGCTCATGCAGATCAATAT
CGTGCTACAGATTTTGTCGTAAACTCTCCAGGAAAATTAGAAATGGTTTTCACTCCAACT
GATGGAAGTGCTCAACAACGATATACTGTCAATGAATATAAAGGACCAGGCGTTGCACTT
GGCATGTACAACACTCAAGAATCAATTAGAGATTTCGCTCACTCTTCATTCAAGTATGCT
TTGGATCGAAAAATGCCACTTTATATGAGTACTAAGAATACAATTTTGAAGAAATATGAC
GGCTACTTCAAGGACATTTTTCAAGAGCTCTATGATACACAATATAAGACCGATTTTGAA
GCACAAGGATTATGGTATGAACACCGTCTTATTGATGACATGGTTGCTTATTGCTTGAAG
AGTGAGGGAGGCTATGTTTGGGCTTGTAAAAACTACGACGGGGACGTGCAATCTGATACA
GTTGCCCAGGGATACGGTAGTCTTGGTTTAATGACAAGCGTTTTAATTGCACCTGACGGT
AAAACTGTTGAAGCTGAAGCAGCTCATGGAACTGTTACTCGTCATTATCGTCAATATCAA
CAAGGAAAAGAAACAAGTACTAATCCAATTGCCTCAATATTTGCATGGACTCGCGGTTTA
CTTCATCGTGCAGCTCTAGACAATAATGCAGAACTCAAGAAATTCTGTGAAACATTAGAG
AAAGTTTGTATCGATACAATTGAGAGTGGATTTATGACAAAAGATTTGGCAATTTGTGTT
AAGGGATCTATGAGTGCAGTAAAACGCGAAGATTATCTTGAAACATTTGAGTTTATGGAA
AAACTTGCTGATAATTTGAAAAAAGCCCTCGCATGA
>g10682.t10 Gene=g10682 Length=407
MSQKIKVDNPVVDVLGDEMTRIIWDSIKEKLILPFLDIELKVFDLGIEYRDQTNDQVTID
CANAIKQYNVGIKCATITPDEARVKEFNLKQMWKSPNGTIRNILGEEAIICNNIPRLVPG
WIKPIIIGRHAHADQYRATDFVVNSPGKLEMVFTPTDGSAQQRYTVNEYKGPGVALGMYN
TQESIRDFAHSSFKYALDRKMPLYMSTKNTILKKYDGYFKDIFQELYDTQYKTDFEAQGL
WYEHRLIDDMVAYCLKSEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLIAPDGKTVE
AEAAHGTVTRHYRQYQQGKETSTNPIASIFAWTRGLLHRAALDNNAELKKFCETLEKVCI
DTIESGFMTKDLAICVKGSMSAVKREDYLETFEFMEKLADNLKKALA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10682.t10 | Coils | Coil | Coil | 385 | 405 | - |
| 5 | g10682.t10 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 2 | 407 | 4.6E-219 |
| 2 | g10682.t10 | PANTHER | PTHR11822:SF21 | ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL | 3 | 406 | 2.2E-216 |
| 3 | g10682.t10 | PANTHER | PTHR11822 | NADP-SPECIFIC ISOCITRATE DEHYDROGENASE | 3 | 406 | 2.2E-216 |
| 7 | g10682.t10 | PIRSF | PIRSF000108 | IDH_NADP | 1 | 407 | 1.2E-224 |
| 1 | g10682.t10 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 7 | 386 | 4.0E-74 |
| 8 | g10682.t10 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 267 | 286 | - |
| 9 | g10682.t10 | SMART | SM01329 | Iso_dh_2 | 10 | 398 | 3.5E-122 |
| 4 | g10682.t10 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 2 | 406 | 4.8E-154 |
| 10 | g10682.t10 | TIGRFAM | TIGR00127 | nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent | 3 | 406 | 6.5E-222 |
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 transcript has been annotated with K00031 (isocitrate dehydrogenase)
Pathway
- This transcript belongs to the following pathways
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.
