General information for g10682.t16
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.t16 | TSS | g10682.t16 | 11292240 | 11292240 |
| chr_1 | g10682 | g10682.t16 | isoform | g10682.t16 | 11292739 | 11295009 |
| chr_1 | g10682 | g10682.t16 | exon | g10682.t16.exon1 | 11292739 | 11292811 |
| chr_1 | g10682 | g10682.t16 | exon | g10682.t16.exon2 | 11292879 | 11292965 |
| chr_1 | g10682 | g10682.t16 | exon | g10682.t16.exon3 | 11293198 | 11293391 |
| chr_1 | g10682 | g10682.t16 | exon | g10682.t16.exon4 | 11294093 | 11295009 |
| chr_1 | g10682 | g10682.t16 | cds | g10682.t16.CDS1 | 11294236 | 11295009 |
| chr_1 | g10682 | g10682.t16 | TTS | g10682.t16 | 11295205 | 11295205 |
Sequences
>g10682.t16 Gene=g10682 Length=1271
GTCAAATAATCATTCCATTACTTGAAAACAGAATAAAAAGATGTCTCAAAAAATTAAAGT
TGATAATCCAGTTGATGTCCTTGGTGACGAGATGACGCGGATTATTTGGGATAGCATCAA
AGAAAAACTGATTCTTCCATTTCTCGATATTGAACTCAAGGTATTTGACCTTGGAATTGA
ATACAGAGATCAAACAAACGATCAAGTTACTATTGATTGTGCCAATGCAATTAAACAATA
TAATGTCGGTATTAAATGTGCAACAATCACTCCAGATGAAGCTCGTGTAAAAGAGTTTAA
TCTGAAACAAATGTGGAAATCACCAAATGGCACTATAAGAAATATTTTAGGTGACTGGTT
TTAGGGAAGCTATTATTTGTAATAATATTCCAAGACTTGTCCCAGGATGGATCAAGCCAA
TAATTATCGGTCGTCATGCTCATGCAGATCAATATCGTGCTACAGATTTTGTCGTAAACT
CTCCAGGAAAATTAGAAATGGTTTTCACTCCAACTGATGGAAGTGCTCAACAACGATATA
CTGTCAATGAATATAAAGGACCAGGCGTTGCACTTGGCATGTACAACACTCAAGAATCAA
TTAGAGATTTCGCTCACTCTTCATTCAAGTATGCTTTGGATCGAAAAATGCCACTTTATA
TGAGTACTAAGAATACAATTTTGAAGAAATATGACGGCTACTTCAAGGACATTTTTCAAG
AGCTCTATGATACACAATATAAGACCGATTTTGAAGCACAAGGATTATGGTATGAACACC
GTCTTATTGATGACATGGTTGCTTATTGCTTGAAGAGTGAGGGAGGCTATGTTTGGGCTT
GTAAAAACTACGACGGGGACGTGCAATCTGATACAGTTGCCCAGGGATACGGTAGTCTTG
GTTTAATGACAAGCGTTTTAATTGCACCTGACGGTAAAACTGTTGAAGCTGAAGCAGCTC
ATGGAACTGTTACTCGTCATTATCGTCAATATCAACAAGGAAAAGAAACAAGTACTAATC
CAATTGCCTCAATATTTGCATGGACTCGCGGTTTACTTCATCGTGCAGCTCTAGACAATA
ATGCAGAACTCAAGAAATTCTGTGAAACATTAGAGAAAGTTTGTATCGATACAATTGAGA
GTGGATTTATGACAAAAGATTTGGCAATTTGTGTTAAGGGATCTATGAGTGCAGTAAAAC
GCGAAGATTATCTTGAAACATTTGAGTTTATGGAAAAACTTGCTGATAATTTGAAAAAAG
CCCTCGCATGA
>g10682.t16 Gene=g10682 Length=257
MVFTPTDGSAQQRYTVNEYKGPGVALGMYNTQESIRDFAHSSFKYALDRKMPLYMSTKNT
ILKKYDGYFKDIFQELYDTQYKTDFEAQGLWYEHRLIDDMVAYCLKSEGGYVWACKNYDG
DVQSDTVAQGYGSLGLMTSVLIAPDGKTVEAEAAHGTVTRHYRQYQQGKETSTNPIASIF
AWTRGLLHRAALDNNAELKKFCETLEKVCIDTIESGFMTKDLAICVKGSMSAVKREDYLE
TFEFMEKLADNLKKALA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10682.t16 | Coils | Coil | Coil | 235 | 257 | - |
| 5 | g10682.t16 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 1 | 257 | 1.3E-134 |
| 2 | g10682.t16 | PANTHER | PTHR11822:SF21 | ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL | 1 | 256 | 2.6E-131 |
| 3 | g10682.t16 | PANTHER | PTHR11822 | NADP-SPECIFIC ISOCITRATE DEHYDROGENASE | 1 | 256 | 2.6E-131 |
| 1 | g10682.t16 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 20 | 236 | 6.4E-50 |
| 7 | g10682.t16 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 117 | 136 | - |
| 8 | g10682.t16 | SMART | SM01329 | Iso_dh_2 | 2 | 248 | 7.8E-27 |
| 4 | g10682.t16 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 1 | 256 | 1.54E-97 |
| 9 | g10682.t16 | TIGRFAM | TIGR00127 | nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent | 1 | 256 | 1.4E-134 |
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. There were no conditions that were differentially expressed