Gene loci information

Transcript annotation

  • This transcript has been annotated as Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial.

Parent gene

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.t11 TTS g8419.t11 30358907 30358907
chr_2 g8419 g8419.t11 isoform g8419.t11 30359833 30360641
chr_2 g8419 g8419.t11 exon g8419.t11.exon1 30359833 30360174
chr_2 g8419 g8419.t11 cds g8419.t11.CDS1 30359833 30360174
chr_2 g8419 g8419.t11 exon g8419.t11.exon2 30360232 30360507
chr_2 g8419 g8419.t11 cds g8419.t11.CDS2 30360232 30360507
chr_2 g8419 g8419.t11 exon g8419.t11.exon3 30360570 30360641
chr_2 g8419 g8419.t11 cds g8419.t11.CDS3 30360570 30360641
chr_2 g8419 g8419.t11 TSS g8419.t11 30360766 30360766

Sequences

>g8419.t11 Gene=g8419 Length=690
ATGTCATCAGGAAACGTTATTAATCATGTCACAATCATTGGTGCTGGCCTAATGGGCTCT
GGCATAGCTCAGGTGGCTGCATCATCCGGTCATAAAGTTACAATGGTTGAATTGGACTCT
AAACTTCTTGACAAGGCACAGAAAAACATTGAAAAAAGTTTAGAAAGAGTTGCCAAGAAA
CAATTCAAAGGCGAGGAGGATAAAATTGCCGGCTTTGTGAATGAATCAATAAGCAGAATT
TCTGGATCAACTGACTTAAATTCTGTTGTTAAAGATACTGATTTGGTCATTGAAGCAATT
GTTGAAAACCTTGAAGTTAAGCAGAAACTTTTTGGACAAATCGATGGAGTAGCAAAACCA
TCAACAATTTTTGCTTCAAACACTTCATCAATTCCAATTAAAGACATTGCAAAAAGCACT
TCACGTCTTGATAGATTCTGTGGGCTTCACTTTTTCAATCCAGTTCCAGTCATGAAGTTA
CTTGAAGTTATTAGAATTCCTGAAACTTCCGACGCAACTTACAATGCAGCAATGGAATTT
GGAAAGAAAGTTGGCAAGACTTGTGTCACATGCAAAGATACACCTGGATTTATTGTCAAT
CGTCTTTTGGTACCATATATGGCTGAAGCAGTACGAATGCTAGAACGAGGTGATGCTACG
GCAAGAGATATTGATACTGCCATGAAATTA

>g8419.t11 Gene=g8419 Length=230
MSSGNVINHVTIIGAGLMGSGIAQVAASSGHKVTMVELDSKLLDKAQKNIEKSLERVAKK
QFKGEEDKIAGFVNESISRISGSTDLNSVVKDTDLVIEAIVENLEVKQKLFGQIDGVAKP
STIFASNTSSIPIKDIAKSTSRLDRFCGLHFFNPVPVMKLLEVIRIPETSDATYNAAMEF
GKKVGKTCVTCKDTPGFIVNRLLVPYMAEAVRMLERGDATARDIDTAMKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8419.t11 Coils Coil Coil 43 63 -
6 g8419.t11 Gene3D G3DSA:3.40.50.720 - 1 197 3.1E-79
7 g8419.t11 Gene3D G3DSA:1.10.1040.10 - 198 230 8.1E-10
3 g8419.t11 PANTHER PTHR43561 - 5 230 1.4E-97
9 g8419.t11 PIRSF PIRSF000105 HCDH 2 230 5.4E-81
2 g8419.t11 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 9 194 6.1E-65
1 g8419.t11 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 196 230 2.7E-10
11 g8419.t11 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature. 193 217 -
4 g8419.t11 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 7 195 1.62E-62
5 g8419.t11 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 192 229 1.96E-9
10 g8419.t11 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 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.

Raw TPM values