General information for g10682.t1
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.t1 | TSS | g10682.t1 | 11292240 | 11292240 |
| chr_1 | g10682 | g10682.t1 | isoform | g10682.t1 | 11292779 | 11295009 |
| chr_1 | g10682 | g10682.t1 | exon | g10682.t1.exon1 | 11292779 | 11292814 |
| chr_1 | g10682 | g10682.t1 | cds | g10682.t1.CDS1 | 11292779 | 11292814 |
| chr_1 | g10682 | g10682.t1 | exon | g10682.t1.exon2 | 11292879 | 11292965 |
| chr_1 | g10682 | g10682.t1 | cds | g10682.t1.CDS2 | 11292879 | 11292965 |
| chr_1 | g10682 | g10682.t1 | exon | g10682.t1.exon3 | 11293198 | 11293387 |
| chr_1 | g10682 | g10682.t1 | cds | g10682.t1.CDS3 | 11293198 | 11293387 |
| chr_1 | g10682 | g10682.t1 | exon | g10682.t1.exon4 | 11293452 | 11293467 |
| chr_1 | g10682 | g10682.t1 | cds | g10682.t1.CDS4 | 11293452 | 11293467 |
| chr_1 | g10682 | g10682.t1 | exon | g10682.t1.exon5 | 11294103 | 11295009 |
| chr_1 | g10682 | g10682.t1 | cds | g10682.t1.CDS5 | 11294103 | 11295009 |
| chr_1 | g10682 | g10682.t1 | TTS | g10682.t1 | 11295205 | 11295205 |
Sequences
>g10682.t1 Gene=g10682 Length=1236
ATGTCTCAAAAAATTAAAGTTGATAATCCAGTTGTGGATGTCCTTGGTGACGAGATGACG
CGGATTATTTGGGATAGCATCAAAGAAAAACTGATTCTTCCATTTCTCGATATTGAACTC
AAGGTATTTGACCTTGGAATTGAATACAGAGATCAAACAAACGATCAAGTTACTATTGAT
TGTGCCAATGCAATTAAACAATATAATGTCGGTATTAAATGTGCAACAATCACTCCAGAT
GAAGCTCGTGTAAAAGAGTTTAATCTGAAACAAATGTGGAAATCACCAAATGGCACTATA
AGAAATATTTTAGGGGGGACTGTTTTTAGGGAAGCTATTATTTGTAATAATATTCCAAGA
CTTGTCCCAGGATGGATCAAGCCAATAATTATCGGTCGTCATGCTCATGCAGATCAATAT
CGTGCTACAGATTTTGTCGTAAACTCTCCAGGAAAATTAGAAATGGTTTTCACTCCAACT
GATGGAAGTGCTCAACAACGATATACTGTCAATGAATATAAAGGACCAGGCGTTGCACTT
GGCATGTACAACACTCAAGAATCAATTAGAGATTTCGCTCACTCTTCATTCAAGTATGCT
TTGGATCGAAAAATGCCACTTTATATGAGTACTAAGAATACAATTTTGAAGAAATATGAC
GGCTACTTCAAGGACATTTTTCAAGAGCTCTATGATACACAATATAAGACCGATTTTGAA
GCACAAGGATTATGGTATGAACACCGTCTTATTGATGACATGGTTGCTTATTGCTTGAAG
AGTGAGGGAGGCTATGTTTGGGCTTGTAAAAACTACGACGGGGACGTGCAATCTGATACA
GTTGCCCAGGGATACGGTAGTCTTGGTTTAATGACAAGCGTTTTAATTGCACCTGACGGT
AAAACTGTTGAAGCTGAAGCAGCTCATGGAACTGTTACTCGTCATTATCGTCAATATCAA
CAAGGAAAAGAAACAAGTACTAATCCAATTGCCTCAATATTTGCATGGACTCGCGGTTTA
CTTCATCGTGCAGCTCTAGACAATAATGCAGAACTCAAGAAATTCTGTGAAACATTAGAG
AAAGTTTGTATCGATACAATTGAGAGTGGATTTATGACAAAAGATTTGGCAATTTGTGTT
AAGGGATCTATGAGTGCAGTAAAACGCGAAGATTATCTTGAAACATTTGAGTTTATGGAA
AAACTTGCTGATAATTTGAAAAAAGCCCTCGCATGA
>g10682.t1 Gene=g10682 Length=411
MSQKIKVDNPVVDVLGDEMTRIIWDSIKEKLILPFLDIELKVFDLGIEYRDQTNDQVTID
CANAIKQYNVGIKCATITPDEARVKEFNLKQMWKSPNGTIRNILGGTVFREAIICNNIPR
LVPGWIKPIIIGRHAHADQYRATDFVVNSPGKLEMVFTPTDGSAQQRYTVNEYKGPGVAL
GMYNTQESIRDFAHSSFKYALDRKMPLYMSTKNTILKKYDGYFKDIFQELYDTQYKTDFE
AQGLWYEHRLIDDMVAYCLKSEGGYVWACKNYDGDVQSDTVAQGYGSLGLMTSVLIAPDG
KTVEAEAAHGTVTRHYRQYQQGKETSTNPIASIFAWTRGLLHRAALDNNAELKKFCETLE
KVCIDTIESGFMTKDLAICVKGSMSAVKREDYLETFEFMEKLADNLKKALA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10682.t1 | Coils | Coil | Coil | 389 | 409 | - |
| 5 | g10682.t1 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 1 | 411 | 4.2E-226 |
| 2 | g10682.t1 | PANTHER | PTHR11822:SF21 | ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL | 3 | 410 | 1.6E-223 |
| 3 | g10682.t1 | PANTHER | PTHR11822 | NADP-SPECIFIC ISOCITRATE DEHYDROGENASE | 3 | 410 | 1.6E-223 |
| 7 | g10682.t1 | PIRSF | PIRSF000108 | IDH_NADP | 1 | 411 | 2.0E-232 |
| 1 | g10682.t1 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 7 | 390 | 6.9E-77 |
| 8 | g10682.t1 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 271 | 290 | - |
| 9 | g10682.t1 | SMART | SM01329 | Iso_dh_2 | 10 | 402 | 5.3E-130 |
| 4 | g10682.t1 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 2 | 410 | 8.26E-159 |
| 10 | g10682.t1 | TIGRFAM | TIGR00127 | nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent | 3 | 410 | 2.8E-229 |
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.
