General information for g8419.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial.
Parent gene
- The parent gene g8419 is located on chr_2: 30359833..30362659 (- 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 | g8419 | g8419.t6 | TTS | g8419.t6 | 30358907 | 30358907 |
| chr_2 | g8419 | g8419.t6 | isoform | g8419.t6 | 30358954 | 30360641 |
| chr_2 | g8419 | g8419.t6 | exon | g8419.t6.exon1 | 30358954 | 30359138 |
| chr_2 | g8419 | g8419.t6 | cds | g8419.t6.CDS1 | 30358954 | 30359138 |
| chr_2 | g8419 | g8419.t6 | exon | g8419.t6.exon2 | 30359826 | 30360174 |
| chr_2 | g8419 | g8419.t6 | cds | g8419.t6.CDS2 | 30359826 | 30360174 |
| chr_2 | g8419 | g8419.t6 | exon | g8419.t6.exon3 | 30360232 | 30360507 |
| chr_2 | g8419 | g8419.t6 | cds | g8419.t6.CDS3 | 30360232 | 30360507 |
| chr_2 | g8419 | g8419.t6 | exon | g8419.t6.exon4 | 30360570 | 30360641 |
| chr_2 | g8419 | g8419.t6 | cds | g8419.t6.CDS4 | 30360570 | 30360641 |
| chr_2 | g8419 | g8419.t6 | TSS | g8419.t6 | 30360766 | 30360766 |
Sequences
>g8419.t6 Gene=g8419 Length=882
ATGTCATCAGGAAACGTTATTAATCATGTCACAATCATTGGTGCTGGCCTAATGGGCTCT
GGCATAGCTCAGGTGGCTGCATCATCCGGTCATAAAGTTACAATGGTTGAATTGGACTCT
AAACTTCTTGACAAGGCACAGAAAAACATTGAAAAAAGTTTAGAAAGAGTTGCCAAGAAA
CAATTCAAAGGCGAGGAGGATAAAATTGCCGGCTTTGTGAATGAATCAATAAGCAGAATT
TCTGGATCAACTGACTTAAATTCTGTTGTTAAAGATACTGATTTGGTCATTGAAGCAATT
GTTGAAAACCTTGAAGTTAAGCAGAAACTTTTTGGACAAATCGATGGAGTAGCAAAACCA
TCAACAATTTTTGCTTCAAACACTTCATCAATTCCAATTAAAGACATTGCAAAAAGCACT
TCACGTCTTGATAGATTCTGTGGGCTTCACTTTTTCAATCCAGTTCCAGTCATGAAGTTA
CTTGAAGTTATTAGAATTCCTGAAACTTCCGACGCAACTTACAATGCAGCAATGGAATTT
GGAAAGAAAGTTGGCAAGACTTGTGTCACATGCAAAGATACACCTGGATTTATTGTCAAT
CGTCTTTTGGTACCATATATGGCTGAAGCAGTACGAATGCTAGAACGAGGTGATGCTACG
GCAAGAGATATTGATACTGCCATGAAATTAGGAGCAGCAATGGGACCTTTTGAGCTGAGC
GATTACGTTGGTTTGGACACAACAAAATTCATCTTAGATGGCTGGAGTAAAAATTATCCA
GACAATCCATTATTCAAAACAATTCCAATGTTGACAAAACTCGTTGAAGAAGGAAAATTA
GGAATGAAAACAGGCGAAGGATTTTATAAATATCAAAAATAA
>g8419.t6 Gene=g8419 Length=293
MSSGNVINHVTIIGAGLMGSGIAQVAASSGHKVTMVELDSKLLDKAQKNIEKSLERVAKK
QFKGEEDKIAGFVNESISRISGSTDLNSVVKDTDLVIEAIVENLEVKQKLFGQIDGVAKP
STIFASNTSSIPIKDIAKSTSRLDRFCGLHFFNPVPVMKLLEVIRIPETSDATYNAAMEF
GKKVGKTCVTCKDTPGFIVNRLLVPYMAEAVRMLERGDATARDIDTAMKLGAAMGPFELS
DYVGLDTTKFILDGWSKNYPDNPLFKTIPMLTKLVEEGKLGMKTGEGFYKYQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8419.t6 | Coils | Coil | Coil | 43 | 63 | - |
| 6 | g8419.t6 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 199 | 6.9E-79 |
| 7 | g8419.t6 | Gene3D | G3DSA:1.10.1040.10 | - | 203 | 292 | 2.6E-34 |
| 3 | g8419.t6 | PANTHER | PTHR43561 | - | 5 | 292 | 3.6E-128 |
| 9 | g8419.t6 | PIRSF | PIRSF000105 | HCDH | 2 | 293 | 1.4E-97 |
| 2 | g8419.t6 | Pfam | PF02737 | 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain | 9 | 194 | 1.3E-64 |
| 1 | g8419.t6 | Pfam | PF00725 | 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain | 196 | 291 | 4.0E-31 |
| 11 | g8419.t6 | ProSitePatterns | PS00067 | 3-hydroxyacyl-CoA dehydrogenase signature. | 193 | 217 | - |
| 4 | g8419.t6 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 7 | 195 | 3.54E-62 |
| 5 | g8419.t6 | SUPERFAMILY | SSF48179 | 6-phosphogluconate dehydrogenase C-terminal domain-like | 195 | 293 | 5.02E-30 |
| 10 | g8419.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 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:0070403 | NAD+ binding | MF |
| GO:0006631 | fatty acid metabolic process | BP |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00022 (3-hydroxyacyl-CoA dehydrogenase)
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