General information for g5582.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial.
Parent gene
- The parent gene g5582 is located on chr_2: 10397560..10398678 (+ 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_2 | g5582 | g5582.t13 | TSS | g5582.t13 | 10396252 | 10396252 |
| chr_2 | g5582 | g5582.t13 | isoform | g5582.t13 | 10396340 | 10398678 |
| chr_2 | g5582 | g5582.t13 | exon | g5582.t13.exon1 | 10396340 | 10396402 |
| chr_2 | g5582 | g5582.t13 | cds | g5582.t13.CDS1 | 10396340 | 10396402 |
| chr_2 | g5582 | g5582.t13 | exon | g5582.t13.exon2 | 10396647 | 10396721 |
| chr_2 | g5582 | g5582.t13 | cds | g5582.t13.CDS2 | 10396647 | 10396721 |
| chr_2 | g5582 | g5582.t13 | exon | g5582.t13.exon3 | 10396780 | 10396843 |
| chr_2 | g5582 | g5582.t13 | cds | g5582.t13.CDS3 | 10396780 | 10396843 |
| chr_2 | g5582 | g5582.t13 | exon | g5582.t13.exon4 | 10396901 | 10397779 |
| chr_2 | g5582 | g5582.t13 | cds | g5582.t13.CDS4 | 10396901 | 10397779 |
| chr_2 | g5582 | g5582.t13 | exon | g5582.t13.exon5 | 10397836 | 10397911 |
| chr_2 | g5582 | g5582.t13 | cds | g5582.t13.CDS5 | 10397836 | 10397911 |
| chr_2 | g5582 | g5582.t13 | exon | g5582.t13.exon6 | 10398603 | 10398678 |
| chr_2 | g5582 | g5582.t13 | cds | g5582.t13.CDS6 | 10398603 | 10398603 |
| chr_2 | g5582 | g5582.t13 | TTS | g5582.t13 | 10398686 | 10398686 |
Sequences
>g5582.t13 Gene=g5582 Length=1233
ATGGCGCTTGCTGTTCGATTTGCAAAGCAATCAACTGAGAAGTTGTCACCGCTCTTGAGA
AGAAACTTCTGCTCTGCATACGAATTGCAACACAAAAATCCTATTCAAAAACGAATTGCT
GCAATCCCAAAAGCTCAATATGGAGGTAGACACACGGTCACAATGCTCCCTGGTGGTGGA
ATCGGATTAGAGCTCTCAAACTATGTTCGAGAAATTTTCCGCTATGCAGGTGTTCCTGTT
GATTTTGAAGTTATTGATATAGATCCAAATAGCGAAACCAATGATGATTTAGATTATGCA
ATTACATCAATTAAACGTAATGGTGTTGCAATTAAGGGAAATATTGAGACAAAAAGTGAA
GCAACTGGAATTATCTCAAGAAATGTTGCATTGCGAAATGAATTAGATTTGTTTGTCAAT
GTATTGCATTGCAAATCATATCCTGGTGTGAGATCTCACCATAAAGACATTGATTTAATT
GTTGTACGTCAAAATACAGAAGGTGAGTATGCGATGTTGGAACACGAGTCAGTGCGAGGT
GTTGTTGAGTCATTGAAAATTATAACTGTGGAAGCTAGTGAGAGATTAAGTCGATTTGCA
TTCGAATATGCTCGCAAAAATGGTCGCAAGAAGGTGACAACTATTCATAAAGCTAACATC
ATGAAGCTCTCCGATGGATGCTTCCTAGAAACTTCAAAGCGTATTGCCAAAGAATATCCA
GATATCGAGCACAATAATATGATTATTGACAATACATGCATGCAATTGGTGGCAAAGCCT
CAACAATTTGATGTTCTTTTAACAACTAATTTGTATGGATCAATTTGCACAAATGTAATT
TGTGGATTAGTTGGAGGAGCTGGTTTATATAGCGGACGTAACTATGGTGATCATTATGCT
GTCTTTGAGCCAGGCACACGTAACACAGGAAGCTCAATTGCTGGAAAGAATATTTGCAAT
CCTTTTGCAATGCTTAATGCAAGTGTTGACATGTTGAATCATCTTGGTCATACTCAACAT
GCAAATGCCATCTCTACAGCCATATACGAGACAATTGTCAAAGATAAAATTCATACAGCC
GACCTTGGTGGAACTGCATCTTCAACCGATTGTATTCAAAATGTGTTGAAGCATCTTGCA
GCTGGACAAGTTTCTTGATTTAAAATACTGAAAAACTAATAATTTATTATTTATTGTTAA
AAACATGAAATAAAGAAGAAAGAAAAAAGACAC
>g5582.t13 Gene=g5582 Length=385
MALAVRFAKQSTEKLSPLLRRNFCSAYELQHKNPIQKRIAAIPKAQYGGRHTVTMLPGGG
IGLELSNYVREIFRYAGVPVDFEVIDIDPNSETNDDLDYAITSIKRNGVAIKGNIETKSE
ATGIISRNVALRNELDLFVNVLHCKSYPGVRSHHKDIDLIVVRQNTEGEYAMLEHESVRG
VVESLKIITVEASERLSRFAFEYARKNGRKKVTTIHKANIMKLSDGCFLETSKRIAKEYP
DIEHNNMIIDNTCMQLVAKPQQFDVLLTTNLYGSICTNVICGLVGGAGLYSGRNYGDHYA
VFEPGTRNTGSSIAGKNICNPFAMLNASVDMLNHLGHTQHANAISTAIYETIVKDKIHTA
DLGGTASSTDCIQNVLKHLAAGQVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5582.t13 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 37 | 384 | 0 |
| 2 | g5582.t13 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 31 | 380 | 0 |
| 3 | g5582.t13 | PANTHER | PTHR11835:SF60 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL | 31 | 380 | 0 |
| 1 | g5582.t13 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 52 | 367 | 0 |
| 5 | g5582.t13 | SMART | SM01329 | Iso_dh_2 | 52 | 375 | 0 |
| 4 | g5582.t13 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 43 | 379 | 0 |
| 7 | g5582.t13 | TIGRFAM | TIGR00175 | mito_nad_idh: isocitrate dehydrogenase, NAD-dependent | 48 | 379 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5582/g5582.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5582.t13.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006099 | tricarboxylic acid cycle | BP |
| 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: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.
