General information for g337.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable isocitrate dehydrogenase [NAD] subunit beta, mitochondrial.
Parent gene
- The parent gene g337 is located on chr_3: 2792304..2793648 (+ 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 | g337 | g337.t1 | TSS | g337.t1 | 2792206 | 2792206 |
| chr_3 | g337 | g337.t1 | isoform | g337.t1 | 2792304 | 2793648 |
| chr_3 | g337 | g337.t1 | exon | g337.t1.exon1 | 2792304 | 2792345 |
| chr_3 | g337 | g337.t1 | cds | g337.t1.CDS1 | 2792304 | 2792345 |
| chr_3 | g337 | g337.t1 | exon | g337.t1.exon2 | 2792471 | 2793181 |
| chr_3 | g337 | g337.t1 | cds | g337.t1.CDS2 | 2792471 | 2793181 |
| chr_3 | g337 | g337.t1 | exon | g337.t1.exon3 | 2793238 | 2793363 |
| chr_3 | g337 | g337.t1 | cds | g337.t1.CDS3 | 2793238 | 2793363 |
| chr_3 | g337 | g337.t1 | exon | g337.t1.exon4 | 2793418 | 2793648 |
| chr_3 | g337 | g337.t1 | cds | g337.t1.CDS4 | 2793418 | 2793648 |
| chr_3 | g337 | g337.t1 | TTS | g337.t1 | 2794071 | 2794071 |
Sequences
>g337.t1 Gene=g337 Length=1110
ATGTCTCTTCTGACAAGAAATGTTGCTAGATGCTTGATTCAAGTCTCATCGCGCAATATT
CACTCAACTGCTGCTCTAGCAAATCCTCCAACGAAGCCTCAACAACGCGTCAAGTGCACT
TTAATTCCTGGCGATGGTGTCGGACCAGAATTGATTTATTCAGTACAAGAAGTTTTCAAG
GCTGCAGATGTACCAGTTGATTTTGAGCCTTTCTTCTTGTCAGAAGTTAATCCAGCACTT
AGTGCTCCTCTTGAGACTGTTGTAGAATCGATTAACAGAAACAAGATTTGCTTAAAGGGA
ATTTTAGCAACACCTGATTACAGTCATACTGGAGAATTACAAACACTCAATATGAAACTC
AGAAATGAGTTAGATTTATATGCAAACGTTGTACATGTTGCATCTTTACCGGGTGTTAAA
ACTCGTCATCAAGGAATCGATGCTGTTGTAATTCGTGAACAGACAGAAGGTGAATATTCT
GCACAAGAACATGAGACTGTGCCAGGTGTTGTTGAGTGCTTAAAAGTTGTCACTGAAGCT
AAATCATTGCGAATTGCCAAGTTTGCATTTGATTATGCTGTCAAGCACAACAGAAAGAAG
GTCACTGCTATTCACAAGGCTAATATCATGAAACTGGGCGATGGACTTTTCTTAAGAAGT
TGCGAAAAAATGGCAAAATTGTATCCTAGAATTCAATTTGAAAAAATGATTGTCGATAAT
GCCACAATGCAACTTGTTTCTAATCCACATCAATTTGATGTCATGGTAACACCTAATTTA
TACGGTAACATCATTGATAATATTTCATCAGGATTAGTCGGTGGCGCAGGTGTTGTTTCT
GGTGCCTCTTATTCTGCTTCGCATGTTGTTTATGAACCTGGTGCACGTCACACATTCTCA
GAAGCTGTAGGCAAAAATATTGCAAATCCAACAGCCATGTTACTTTGTGCATCGAAAATG
CTCCGCCATATTAATTTATTACATTATTCTCAACAAATTTATACCGCTGTCAACAATGTA
TTGAAAGCAGGAAAAGTACGTACCAAAGATCTTGGTGGTAATGCAACAACTAATGAATTT
ACAAAGGCTGTTATTCTCAGTCTTAAGTAA
>g337.t1 Gene=g337 Length=369
MSLLTRNVARCLIQVSSRNIHSTAALANPPTKPQQRVKCTLIPGDGVGPELIYSVQEVFK
AADVPVDFEPFFLSEVNPALSAPLETVVESINRNKICLKGILATPDYSHTGELQTLNMKL
RNELDLYANVVHVASLPGVKTRHQGIDAVVIREQTEGEYSAQEHETVPGVVECLKVVTEA
KSLRIAKFAFDYAVKHNRKKVTAIHKANIMKLGDGLFLRSCEKMAKLYPRIQFEKMIVDN
ATMQLVSNPHQFDVMVTPNLYGNIIDNISSGLVGGAGVVSGASYSASHVVYEPGARHTFS
EAVGKNIANPTAMLLCASKMLRHINLLHYSQQIYTAVNNVLKAGKVRTKDLGGNATTNEF
TKAVILSLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g337.t1 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 22 | 369 | 1.3E-124 |
| 2 | g337.t1 | PANTHER | PTHR11835:SF42 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL | 24 | 367 | 1.4E-151 |
| 3 | g337.t1 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 24 | 367 | 1.4E-151 |
| 1 | g337.t1 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 39 | 364 | 1.2E-71 |
| 7 | g337.t1 | ProSitePatterns | PS00470 | Isocitrate and isopropylmalate dehydrogenases signature. | 259 | 278 | - |
| 8 | g337.t1 | SMART | SM01329 | Iso_dh_2 | 38 | 364 | 1.2E-141 |
| 4 | g337.t1 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 23 | 365 | 1.13E-103 |
| 5 | g337.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
| 9 | g337.t1 | TIGRFAM | TIGR00175 | mito_nad_idh: isocitrate dehydrogenase, NAD-dependent | 35 | 366 | 9.2E-148 |
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.
