General information for g337.t3
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.t3 | TSS | g337.t3 | 2792206 | 2792206 |
| chr_3 | g337 | g337.t3 | isoform | g337.t3 | 2792304 | 2793181 |
| chr_3 | g337 | g337.t3 | exon | g337.t3.exon1 | 2792304 | 2792345 |
| chr_3 | g337 | g337.t3 | cds | g337.t3.CDS1 | 2792304 | 2792345 |
| chr_3 | g337 | g337.t3 | exon | g337.t3.exon2 | 2792471 | 2793181 |
| chr_3 | g337 | g337.t3 | cds | g337.t3.CDS2 | 2792471 | 2793181 |
| chr_3 | g337 | g337.t3 | TTS | g337.t3 | 2794071 | 2794071 |
Sequences
>g337.t3 Gene=g337 Length=753
ATGTCTCTTCTGACAAGAAATGTTGCTAGATGCTTGATTCAAGTCTCATCGCGCAATATT
CACTCAACTGCTGCTCTAGCAAATCCTCCAACGAAGCCTCAACAACGCGTCAAGTGCACT
TTAATTCCTGGCGATGGTGTCGGACCAGAATTGATTTATTCAGTACAAGAAGTTTTCAAG
GCTGCAGATGTACCAGTTGATTTTGAGCCTTTCTTCTTGTCAGAAGTTAATCCAGCACTT
AGTGCTCCTCTTGAGACTGTTGTAGAATCGATTAACAGAAACAAGATTTGCTTAAAGGGA
ATTTTAGCAACACCTGATTACAGTCATACTGGAGAATTACAAACACTCAATATGAAACTC
AGAAATGAGTTAGATTTATATGCAAACGTTGTACATGTTGCATCTTTACCGGGTGTTAAA
ACTCGTCATCAAGGAATCGATGCTGTTGTAATTCGTGAACAGACAGAAGGTGAATATTCT
GCACAAGAACATGAGACTGTGCCAGGTGTTGTTGAGTGCTTAAAAGTTGTCACTGAAGCT
AAATCATTGCGAATTGCCAAGTTTGCATTTGATTATGCTGTCAAGCACAACAGAAAGAAG
GTCACTGCTATTCACAAGGCTAATATCATGAAACTGGGCGATGGACTTTTCTTAAGAAGT
TGCGAAAAAATGGCAAAATTGTATCCTAGAATTCAATTTGAAAAAATGATTGTCGATAAT
GCCACAATGCAACTTGTTTCTAATCCACATCAA
>g337.t3 Gene=g337 Length=251
MSLLTRNVARCLIQVSSRNIHSTAALANPPTKPQQRVKCTLIPGDGVGPELIYSVQEVFK
AADVPVDFEPFFLSEVNPALSAPLETVVESINRNKICLKGILATPDYSHTGELQTLNMKL
RNELDLYANVVHVASLPGVKTRHQGIDAVVIREQTEGEYSAQEHETVPGVVECLKVVTEA
KSLRIAKFAFDYAVKHNRKKVTAIHKANIMKLGDGLFLRSCEKMAKLYPRIQFEKMIVDN
ATMQLVSNPHQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g337.t3 | Gene3D | G3DSA:3.40.718.10 | Isopropylmalate Dehydrogenase | 22 | 251 | 5.4E-76 |
| 2 | g337.t3 | PANTHER | PTHR11835:SF42 | ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, MITOCHONDRIAL | 23 | 251 | 9.1E-96 |
| 3 | g337.t3 | PANTHER | PTHR11835 | DECARBOXYLATING DEHYDROGENASES-ISOCITRATE, ISOPROPYLMALATE, TARTRATE | 23 | 251 | 9.1E-96 |
| 1 | g337.t3 | Pfam | PF00180 | Isocitrate/isopropylmalate dehydrogenase | 39 | 251 | 2.2E-39 |
| 5 | g337.t3 | SMART | SM01329 | Iso_dh_2 | 38 | 251 | 2.9E-25 |
| 4 | g337.t3 | SUPERFAMILY | SSF53659 | Isocitrate/Isopropylmalate dehydrogenase-like | 23 | 251 | 2.26E-61 |
| 6 | g337.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
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.
