General information for g2739.t2
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.t2 | TSS | g2739.t2 | 19938544 | 19938544 |
| chr_3 | g2739 | g2739.t2 | isoform | g2739.t2 | 19938614 | 19939566 |
| chr_3 | g2739 | g2739.t2 | exon | g2739.t2.exon1 | 19938614 | 19938643 |
| chr_3 | g2739 | g2739.t2 | cds | g2739.t2.CDS1 | 19938614 | 19938643 |
| chr_3 | g2739 | g2739.t2 | exon | g2739.t2.exon2 | 19939007 | 19939566 |
| chr_3 | g2739 | g2739.t2 | cds | g2739.t2.CDS2 | 19939007 | 19939564 |
| chr_3 | g2739 | g2739.t2 | TTS | g2739.t2 | 19940515 | 19940515 |
Sequences
>g2739.t2 Gene=g2739 Length=590
ATGCAAGCGACAAGATTTTTCAAGAAATTGATCACGCCATCAGGATGTGTAAGAAATTTT
GCTTCGCAGACAAAGAAAGTAACATTGATTCCAGGCGATGGAATCGGACCGGAAATCAGT
GCAGCTGTGCAAAAGATTTTCGCAACTGCTCAAGTCCCAATTGAATGGGAAAGTGTTGAT
GTGACGCCTGTAAGAAATCCCGATGGTCGTTTCGGTATTCCTCAAGCTGCAATTGATTCG
GTTAATCGAAATAAAGTTGGCTTAAAAGGGCCATTGATGACACCAGTCGGCAAGGGACAT
CGATCATTGAATTTAGCTCTTAGAAAAGAATTTGATCTCTATGCAAATGTTAGACCTTGC
AGAAGCCTTGAAGGCTACAAAACTCTCTATGATGACGTCGATGTTGTTACAATCAGAGAA
AATACTGAAGGCGAGTACTCTGGTATTGAGCACGAAATTGTTGATGGTGTCGTTCAAAGT
ATCAAATTGATTACCGAAGAGGCCTCAAAACGTGTTGCCGAATATGCCTTCCAATATGCA
AAGGAAAATCATCGTTCAAAAGTAACTGTCGTACACAAAGCTAATATCAT
>g2739.t2 Gene=g2739 Length=196
MQATRFFKKLITPSGCVRNFASQTKKVTLIPGDGIGPEISAAVQKIFATAQVPIEWESVD
VTPVRNPDGRFGIPQAAIDSVNRNKVGLKGPLMTPVGKGHRSLNLALRKEFDLYANVRPC
RSLEGYKTLYDDVDVVTIRENTEGEYSGIEHEIVDGVVQSIKLITEEASKRVAEYAFQYA
KENHRSKVTVVHKANI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2739.t2 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 9 | 196 | 0 |
| 2 | g2739.t2 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 17 | 196 | 0 |
| 3 | g2739.t2 | PANTHER | PTHR11835:SF34 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, MITOCHONDRIAL | 17 | 196 | 0 |
| 1 | g2739.t2 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 26 | 196 | 0 |
| 5 | g2739.t2 | SMART | SM01329 | Iso_dh_2 | 26 | 196 | 0 |
| 4 | g2739.t2 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 22 | 196 | 0 |
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:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 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.
