General information for g5582.t18
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.t18 | TSS | g5582.t18 | 10396252 | 10396252 |
| chr_2 | g5582 | g5582.t18 | isoform | g5582.t18 | 10396340 | 10398678 |
| chr_2 | g5582 | g5582.t18 | exon | g5582.t18.exon1 | 10396340 | 10396843 |
| chr_2 | g5582 | g5582.t18 | cds | g5582.t18.CDS1 | 10396804 | 10396843 |
| chr_2 | g5582 | g5582.t18 | exon | g5582.t18.exon2 | 10396901 | 10397779 |
| chr_2 | g5582 | g5582.t18 | cds | g5582.t18.CDS2 | 10396901 | 10397779 |
| chr_2 | g5582 | g5582.t18 | exon | g5582.t18.exon3 | 10397836 | 10397911 |
| chr_2 | g5582 | g5582.t18 | cds | g5582.t18.CDS3 | 10397836 | 10397911 |
| chr_2 | g5582 | g5582.t18 | exon | g5582.t18.exon4 | 10398603 | 10398678 |
| chr_2 | g5582 | g5582.t18 | cds | g5582.t18.CDS4 | 10398603 | 10398603 |
| chr_2 | g5582 | g5582.t18 | TTS | g5582.t18 | 10398686 | 10398686 |
Sequences
>g5582.t18 Gene=g5582 Length=1535
ATGGCGCTTGCTGTTCGATTTGCAAAGCAATCAACTGAGAAGTTGTCACCGCTCTTGAGA
AGAGTAAGTGTTGATTTAATGAAAAAAATTGTTAGATAACTATTTTTCTCGAGTCCTTCA
AGTTTTTGCGATTTATTTATATTCTTATTTTTCCTGTAATTTGCTGTTACTCGTAAATGT
CACGGGTTTGAATGAAGATATAAAATGTATAAATTTTTCAATGACATTGATTAATAATTA
TTATTAATTACATTATATGATTCTGTGAAAATAATGGAATATCTTAAATGAAAAATTGTT
TTTCTAGAACTTCTGCTCTGCATACGAATTGCAACACAAAAATCCTATTCAAAAACGAAT
TGCTGCAATCCCAAAAGCTCAAGTAAGTTTTTATTTTATGATACAATTATAACAGATAAT
GTTTCTATTTATTGTTTTAGTATGGAGGTAGACACACGGTCACAATGCTCCCTGGTGGTG
GAATCGGATTAGAGCTCTCAAACTATGTTCGAGAAATTTTCCGCTATGCAGGTGTTCCTG
TTGATTTTGAAGTTATTGATATAGATCCAAATAGCGAAACCAATGATGATTTAGATTATG
CAATTACATCAATTAAACGTAATGGTGTTGCAATTAAGGGAAATATTGAGACAAAAAGTG
AAGCAACTGGAATTATCTCAAGAAATGTTGCATTGCGAAATGAATTAGATTTGTTTGTCA
ATGTATTGCATTGCAAATCATATCCTGGTGTGAGATCTCACCATAAAGACATTGATTTAA
TTGTTGTACGTCAAAATACAGAAGGTGAGTATGCGATGTTGGAACACGAGTCAGTGCGAG
GTGTTGTTGAGTCATTGAAAATTATAACTGTGGAAGCTAGTGAGAGATTAAGTCGATTTG
CATTCGAATATGCTCGCAAAAATGGTCGCAAGAAGGTGACAACTATTCATAAAGCTAACA
TCATGAAGCTCTCCGATGGATGCTTCCTAGAAACTTCAAAGCGTATTGCCAAAGAATATC
CAGATATCGAGCACAATAATATGATTATTGACAATACATGCATGCAATTGGTGGCAAAGC
CTCAACAATTTGATGTTCTTTTAACAACTAATTTGTATGGATCAATTTGCACAAATGTAA
TTTGTGGATTAGTTGGAGGAGCTGGTTTATATAGCGGACGTAACTATGGTGATCATTATG
CTGTCTTTGAGCCAGGCACACGTAACACAGGAAGCTCAATTGCTGGAAAGAATATTTGCA
ATCCTTTTGCAATGCTTAATGCAAGTGTTGACATGTTGAATCATCTTGGTCATACTCAAC
ATGCAAATGCCATCTCTACAGCCATATACGAGACAATTGTCAAAGATAAAATTCATACAG
CCGACCTTGGTGGAACTGCATCTTCAACCGATTGTATTCAAAATGTGTTGAAGCATCTTG
CAGCTGGACAAGTTTCTTGATTTAAAATACTGAAAAACTAATAATTTATTATTTATTGTT
AAAAACATGAAATAAAGAAGAAAGAAAAAAGACAC
>g5582.t18 Gene=g5582 Length=331
MLPGGGIGLELSNYVREIFRYAGVPVDFEVIDIDPNSETNDDLDYAITSIKRNGVAIKGN
IETKSEATGIISRNVALRNELDLFVNVLHCKSYPGVRSHHKDIDLIVVRQNTEGEYAMLE
HESVRGVVESLKIITVEASERLSRFAFEYARKNGRKKVTTIHKANIMKLSDGCFLETSKR
IAKEYPDIEHNNMIIDNTCMQLVAKPQQFDVLLTTNLYGSICTNVICGLVGGAGLYSGRN
YGDHYAVFEPGTRNTGSSIAGKNICNPFAMLNASVDMLNHLGHTQHANAISTAIYETIVK
DKIHTADLGGTASSTDCIQNVLKHLAAGQVS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5582.t18 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 1 | 330 | 0 |
| 2 | g5582.t18 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 1 | 326 | 0 |
| 3 | g5582.t18 | PANTHER | PTHR11835:SF60 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, MITOCHONDRIAL | 1 | 326 | 0 |
| 1 | g5582.t18 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 2 | 313 | 0 |
| 5 | g5582.t18 | SMART | SM01329 | Iso_dh_2 | 1 | 321 | 0 |
| 4 | g5582.t18 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 1 | 325 | 0 |
| 7 | g5582.t18 | TIGRFAM | TIGR00175 | mito_nad_idh: isocitrate dehydrogenase, NAD-dependent | 1 | 325 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5582/g5582.t18; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5582.t18.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. There were no conditions that were differentially expressed