General information for g429.t1
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.t1 | TTS | g429.t1 | 3321026 | 3321026 |
| chr_3 | g429 | g429.t1 | isoform | g429.t1 | 3321162 | 3324039 |
| chr_3 | g429 | g429.t1 | exon | g429.t1.exon1 | 3321162 | 3322331 |
| chr_3 | g429 | g429.t1 | cds | g429.t1.CDS1 | 3321162 | 3322331 |
| chr_3 | g429 | g429.t1 | exon | g429.t1.exon2 | 3322446 | 3322513 |
| chr_3 | g429 | g429.t1 | cds | g429.t1.CDS2 | 3322446 | 3322513 |
| chr_3 | g429 | g429.t1 | exon | g429.t1.exon3 | 3323952 | 3324039 |
| chr_3 | g429 | g429.t1 | cds | g429.t1.CDS3 | 3323952 | 3324039 |
| chr_3 | g429 | g429.t1 | TSS | g429.t1 | 3324139 | 3324139 |
Sequences
>g429.t1 Gene=g429 Length=1326
ATGGCTTTTGCATTGAGTAAAATTGCCAAGTGCATCAATAAAAATGCACTTGTCACTCCT
TTATCATCAGCAATGTCATCAAGAAACTACTCTAGTGGAAGCCGAGTTGAAGTAGCAAAA
CCAGTTGTTGAAATGGACGGAGATGAAATGACTCGCATTATCTGGCAATTCATTAAAGAG
AAATTGATTTTCCCATATGTCAAAGTTGAATGTCTCTATTATGATCTTGGTTTGCCATAT
CGTGATCAGACAGACGATCAAGTTACAATTGATGCAGCTCATGCAATCTTGAAGCACAAT
GTAGGCATTAAGTGTGCAACTATCACTCCCGATGAACAACGTGTTGAGGAATTCAAATTG
AAAAAAATGTGGTTGTCACCAAATGGTACCATAAGAAACATTTTGGGTGGCACTGTGTTC
CGTGAGCCAATTTTGTGCAAAAATATTCCACGTCTTGTCCCAGGCTGGACAAATCCTATC
GTAATTGGACGTCATGCTTTCGGTGATCAATACAGAGCTAAAGATTTAGTAATTTCAAAA
CCTGGCACAGTTTCACTCAAATTTGTCGGCGATGACGGTAAAGTTGAAGAGACTGAAGTT
TTCCACTTCAAAAATGGAGGTGTAATGCTTGGCATGTATAACACTGATGATTCAATTGCT
GCATTCGCTCATTCATCATTCCAAGTCGCTTTGCAAAAGGGATGGCCACTTTATATGAGT
ACCAAAAATACTATTCTTAAGAAATACGATGGTCGCTTCAAAGATATCTTCCAAGAAATT
TACGAAAAGCACTACGAAGCTAAATTTAATGAAGCTAAAATTTGGTATGAACATCGTTTG
ATTGATGACATGGTTGCACAAGCTTTAAAATCATCAGGCAAATTTGTATGGGCTTGTAAA
AACTACGATGGTGATGTACAGTCAGATATTGTTGCCCAAGGTTACGGTAGTTTAGGTTTA
ATGACAAGTGTTTTGATGTGTCCTGATGGTAAAACAATTGAAGCTGAAGCTGCTCACGGA
ACTGTCACACGTCATTTTCGACAACATCAACAAGGAAAACCAACAAGCACTAATCCTATT
GCTTCAATCTTTGCATGGACTCGAGGTTTCGAGCATCGTGCTAAACTCGATAACAATCCA
GTTCTCGCTAGATTCGCTCAATCACTCGAAAAAGCATGCATTGACACAGTTGAGTCTGGA
AAAATGACAAAAGATTTGGCTGGTTGTATTCATGGTTTAAGTAACGTTAAAGAAGGCATG
TACTTGAACACAGAAGATTTCTTACAAGCTATTGCTGAAGAATTGAATCGCTCATGGAAA
AAATAA
>g429.t1 Gene=g429 Length=441
MAFALSKIAKCINKNALVTPLSSAMSSRNYSSGSRVEVAKPVVEMDGDEMTRIIWQFIKE
KLIFPYVKVECLYYDLGLPYRDQTDDQVTIDAAHAILKHNVGIKCATITPDEQRVEEFKL
KKMWLSPNGTIRNILGGTVFREPILCKNIPRLVPGWTNPIVIGRHAFGDQYRAKDLVISK
PGTVSLKFVGDDGKVEETEVFHFKNGGVMLGMYNTDDSIAAFAHSSFQVALQKGWPLYMS
TKNTILKKYDGRFKDIFQEIYEKHYEAKFNEAKIWYEHRLIDDMVAQALKSSGKFVWACK
NYDGDVQSDIVAQGYGSLGLMTSVLMCPDGKTIEAEAAHGTVTRHFRQHQQGKPTSTNPI
ASIFAWTRGFEHRAKLDNNPVLARFAQSLEKACIDTVESGKMTKDLAGCIHGLSNVKEGM
YLNTEDFLQAIAEELNRSWKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g429.t1 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 33 | 441 | 3.6E-227 |
| 2 | g429.t1 | PANTHER | PTHR11822:SF21 | ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL | 34 | 439 | 2.7E-221 |
| 3 | g429.t1 | PANTHER | PTHR11822 | NADP-SPECIFIC ISOCITRATE DEHYDROGENASE | 34 | 439 | 2.7E-221 |
| 6 | g429.t1 | PIRSF | PIRSF000108 | IDH_NADP | 15 | 441 | 9.2E-230 |
| 1 | g429.t1 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 38 | 430 | 1.3E-79 |
| 7 | g429.t1 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 301 | 320 | - |
| 8 | g429.t1 | SMART | SM01329 | Iso_dh_2 | 41 | 431 | 1.4E-135 |
| 4 | g429.t1 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 35 | 438 | 1.12E-155 |
| 9 | g429.t1 | TIGRFAM | TIGR00127 | nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent | 35 | 438 | 1.7E-218 |
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.
