General information for g2739.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial.
Parent gene
- The parent gene g2739 is located on chr_3: 19939642..19940855 (+ 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 | g2739 | g2739.t1 | TSS | g2739.t1 | 19938544 | 19938544 |
| chr_3 | g2739 | g2739.t1 | isoform | g2739.t1 | 19938614 | 19940104 |
| chr_3 | g2739 | g2739.t1 | exon | g2739.t1.exon1 | 19938614 | 19938643 |
| chr_3 | g2739 | g2739.t1 | cds | g2739.t1.CDS1 | 19938614 | 19938643 |
| chr_3 | g2739 | g2739.t1 | exon | g2739.t1.exon2 | 19939007 | 19939566 |
| chr_3 | g2739 | g2739.t1 | cds | g2739.t1.CDS2 | 19939007 | 19939566 |
| chr_3 | g2739 | g2739.t1 | exon | g2739.t1.exon3 | 19939627 | 19940104 |
| chr_3 | g2739 | g2739.t1 | cds | g2739.t1.CDS3 | 19939627 | 19940104 |
| chr_3 | g2739 | g2739.t1 | TTS | g2739.t1 | 19940861 | 19940861 |
Sequences
>g2739.t1 Gene=g2739 Length=1068
ATGCAAGCGACAAGATTTTTCAAGAAATTGATCACGCCATCAGGATGTGTAAGAAATTTT
GCTTCGCAGACAAAGAAAGTAACATTGATTCCAGGCGATGGAATCGGACCGGAAATCAGT
GCAGCTGTGCAAAAGATTTTCGCAACTGCTCAAGTCCCAATTGAATGGGAAAGTGTTGAT
GTGACGCCTGTAAGAAATCCCGATGGTCGTTTCGGTATTCCTCAAGCTGCAATTGATTCG
GTTAATCGAAATAAAGTTGGCTTAAAAGGGCCATTGATGACACCAGTCGGCAAGGGACAT
CGATCATTGAATTTAGCTCTTAGAAAAGAATTTGATCTCTATGCAAATGTTAGACCTTGC
AGAAGCCTTGAAGGCTACAAAACTCTCTATGATGACGTCGATGTTGTTACAATCAGAGAA
AATACTGAAGGCGAGTACTCTGGTATTGAGCACGAAATTGTTGATGGTGTCGTTCAAAGT
ATCAAATTGATTACCGAAGAGGCCTCAAAACGTGTTGCCGAATATGCCTTCCAATATGCA
AAGGAAAATCATCGTTCAAAAGTAACTGTCGTACACAAAGCTAATATCATGCGTATGTCT
GATGGTCTTTTCTTACGTTGTTGTCGTGAGACTGCTGATAAATTTCCAGAAATTAAATTT
GAGGAAAGATACCTTGATACTGTCTGCTTAAATATGGTACAAGATCCACGTCAATATGAT
GTTCTTGTTATGCCAAACTTGTATGGTGATATTTTGTCAGACATGTGTGCTGGCTTAGTT
GGTGGTCTCGGACTTACACCCTCTGGAAATATTGGTCTTGGTGGTGCACTTTTTGAAAGT
GTTCATGGTACAGCTCCTGATATTGCTGGCAAGGATTTGGCAAATCCAACTGCTCTTCTT
CTGTCGGCTGTTATGATGCTTCGTCATATGGAAATGAACGATAAAGCTGATAAAATTCAG
AAAGCATGCTTCGAGACCATAAAAGAAGGCAAATATCTCACTGGAGATTTAGGTGGAAAG
GCAAAGTGCTCTGAATTTACAAATGCTATTTGTGAAAAATTAGCTTAA
>g2739.t1 Gene=g2739 Length=355
MQATRFFKKLITPSGCVRNFASQTKKVTLIPGDGIGPEISAAVQKIFATAQVPIEWESVD
VTPVRNPDGRFGIPQAAIDSVNRNKVGLKGPLMTPVGKGHRSLNLALRKEFDLYANVRPC
RSLEGYKTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEASKRVAEYAFQYA
KENHRSKVTVVHKANIMRMSDGLFLRCCRETADKFPEIKFEERYLDTVCLNMVQDPRQYD
VLVMPNLYGDILSDMCAGLVGGLGLTPSGNIGLGGALFESVHGTAPDIAGKDLANPTALL
LSAVMMLRHMEMNDKADKIQKACFETIKEGKYLTGDLGGKAKCSEFTNAICEKLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2739.t1 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 21 | 355 | 8.0E-147 |
| 2 | g2739.t1 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 17 | 352 | 5.5E-186 |
| 3 | g2739.t1 | PANTHER | PTHR11835:SF34 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL | 17 | 352 | 5.5E-186 |
| 1 | g2739.t1 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 26 | 350 | 5.9E-109 |
| 6 | g2739.t1 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 246 | 265 | - |
| 5 | g2739.t1 | SMART | SM01329 | Iso_dh_2 | 26 | 350 | 9.7E-180 |
| 4 | g2739.t1 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 22 | 354 | 2.2E-125 |
| 8 | g2739.t1 | TIGRFAM | TIGR00175 | mito_nad_idh: isocitrate dehydrogenase, NAD-dependent | 23 | 354 | 1.4E-152 |
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:0006099 | tricarboxylic acid cycle | BP |
| 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:0004449 | isocitrate dehydrogenase (NAD+) activity | MF |
| GO:0051287 | NAD binding | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K00030 (isocitrate dehydrogenase (NAD+))
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.
