General information for g429.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Isocitrate dehydrogenase [NADP], mitochondrial.
Parent gene
- The parent gene g429 is located on chr_3: 3321162..3327884 (- 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_3 | g429 | g429.t6 | TTS | g429.t6 | 3321026 | 3321026 |
| chr_3 | g429 | g429.t6 | isoform | g429.t6 | 3321162 | 3324039 |
| chr_3 | g429 | g429.t6 | exon | g429.t6.exon1 | 3321162 | 3322309 |
| chr_3 | g429 | g429.t6 | cds | g429.t6.CDS1 | 3321162 | 3322121 |
| chr_3 | g429 | g429.t6 | exon | g429.t6.exon2 | 3322446 | 3322513 |
| chr_3 | g429 | g429.t6 | exon | g429.t6.exon3 | 3323952 | 3324039 |
| chr_3 | g429 | g429.t6 | TSS | g429.t6 | 3324139 | 3324139 |
Sequences
>g429.t6 Gene=g429 Length=1304
ATGGCTTTTGCATTGAGTAAAATTGCCAAGTGCATCAATAAAAATGCACTTGTCACTCCT
TTATCATCAGCAATGTCATCAAGAAACTACTCTAGTGGAAGCCGAGTTGAAGTAGCAAAA
CCAGTTGTTGAAATGGACGGAGATGAAATGACTCGCAGAAATTGATTTTCCCATATGTCA
AAGTTGAATGTCTCTATTATGATCTTGGTTTGCCATATCGTGATCAGACAGACGATCAAG
TTACAATTGATGCAGCTCATGCAATCTTGAAGCACAATGTAGGCATTAAGTGTGCAACTA
TCACTCCCGATGAACAACGTGTTGAGGAATTCAAATTGAAAAAAATGTGGTTGTCACCAA
ATGGTACCATAAGAAACATTTTGGGTGGCACTGTGTTCCGTGAGCCAATTTTGTGCAAAA
ATATTCCACGTCTTGTCCCAGGCTGGACAAATCCTATCGTAATTGGACGTCATGCTTTCG
GTGATCAATACAGAGCTAAAGATTTAGTAATTTCAAAACCTGGCACAGTTTCACTCAAAT
TTGTCGGCGATGACGGTAAAGTTGAAGAGACTGAAGTTTTCCACTTCAAAAATGGAGGTG
TAATGCTTGGCATGTATAACACTGATGATTCAATTGCTGCATTCGCTCATTCATCATTCC
AAGTCGCTTTGCAAAAGGGATGGCCACTTTATATGAGTACCAAAAATACTATTCTTAAGA
AATACGATGGTCGCTTCAAAGATATCTTCCAAGAAATTTACGAAAAGCACTACGAAGCTA
AATTTAATGAAGCTAAAATTTGGTATGAACATCGTTTGATTGATGACATGGTTGCACAAG
CTTTAAAATCATCAGGCAAATTTGTATGGGCTTGTAAAAACTACGATGGTGATGTACAGT
CAGATATTGTTGCCCAAGGTTACGGTAGTTTAGGTTTAATGACAAGTGTTTTGATGTGTC
CTGATGGTAAAACAATTGAAGCTGAAGCTGCTCACGGAACTGTCACACGTCATTTTCGAC
AACATCAACAAGGAAAACCAACAAGCACTAATCCTATTGCTTCAATCTTTGCATGGACTC
GAGGTTTCGAGCATCGTGCTAAACTCGATAACAATCCAGTTCTCGCTAGATTCGCTCAAT
CACTCGAAAAAGCATGCATTGACACAGTTGAGTCTGGAAAAATGACAAAAGATTTGGCTG
GTTGTATTCATGGTTTAAGTAACGTTAAAGAAGGCATGTACTTGAACACAGAAGATTTCT
TACAAGCTATTGCTGAAGAATTGAATCGCTCATGGAAAAAATAA
>g429.t6 Gene=g429 Length=319
MWLSPNGTIRNILGGTVFREPILCKNIPRLVPGWTNPIVIGRHAFGDQYRAKDLVISKPG
TVSLKFVGDDGKVEETEVFHFKNGGVMLGMYNTDDSIAAFAHSSFQVALQKGWPLYMSTK
NTILKKYDGRFKDIFQEIYEKHYEAKFNEAKIWYEHRLIDDMVAQALKSSGKFVWACKNY
DGDVQSDIVAQGYGSLGLMTSVLMCPDGKTIEAEAAHGTVTRHFRQHQQGKPTSTNPIAS
IFAWTRGFEHRAKLDNNPVLARFAQSLEKACIDTVESGKMTKDLAGCIHGLSNVKEGMYL
NTEDFLQAIAEELNRSWKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g429.t6 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 1 | 319 | 1.3E-174 |
| 2 | g429.t6 | PANTHER | PTHR11822:SF21 | ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL | 1 | 317 | 7.3E-170 |
| 3 | g429.t6 | PANTHER | PTHR11822 | NADP-SPECIFIC ISOCITRATE DEHYDROGENASE | 1 | 317 | 7.3E-170 |
| 1 | g429.t6 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 5 | 308 | 2.8E-61 |
| 6 | g429.t6 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 179 | 198 | - |
| 5 | g429.t6 | SMART | SM01329 | Iso_dh_2 | 2 | 309 | 3.9E-70 |
| 4 | g429.t6 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 1 | 316 | 1.82E-120 |
| 8 | g429.t6 | TIGRFAM | TIGR00127 | nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent | 1 | 316 | 4.6E-168 |
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