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 g8420 g8420.t10 TTS g8420.t10 30360761 30360761
chr_2 g8420 g8420.t10 isoform g8420.t10 30360946 30362014
chr_2 g8420 g8420.t10 exon g8420.t10.exon1 30360946 30361097
chr_2 g8420 g8420.t10 cds g8420.t10.CDS1 30360946 30361097
chr_2 g8420 g8420.t10 exon g8420.t10.exon2 30361253 30362014
chr_2 g8420 g8420.t10 cds g8420.t10.CDS2 30361253 30361622
chr_2 g8420 g8420.t10 TSS g8420.t10 30362073 30362073

Sequences

>g8420.t10 Gene=g8420 Length=914
ATGACTTCAAATATTGAAAATATCAAAAATGTAGTTGTTGTTGGTGCTGGTTTGATGGGC
TCTGGCATTGCAGGAATGGTAAAAAAACTCGATAAAAAATTTCCCAAAAAAGTCCAAAGT
ACAAAAGATAATTTTATTAGGCAGCAGTCGCTGGATTTCAAGTCACGATTGTTGATTTAG
ATAAAAAGCTACTTGAGAAATCTAAGGAACAAATTGCAATCACACTTGAACGTGTAGGAC
GTAAAAAATTTAAACAAAATGAGACTAAAATTAATGAATTTATTCAGAATTCATTGAGAA
ATATTTCTGATTCAACAGATTTATTAGAGGTTGTAAAAAATGCTGACATCGTCATTGAAG
CAATTGTGGAAAATTTAGAAGCAAAACAAAAAATGTTTCAATCAATTGATAAAATTGCAA
AACCTTCAGCAATTTTTGCATCAAATACATCAGCATTGCCAATTAGAGAAATTTCAAAAA
ATTCAACAAGACTTGATCGATTTTGTGGTTTGCATTTCTTTAATCCCGTGGCTGTCATGA
AATTACTTGAAGTAATTAGAATTCCTGAAACAAGTGAAACAACTTATAAGACTGTGATGG
ATTTTGGTGCTAAAATGGGAAAAACTTGTGTAACATGTAAAGATACGCCTGGCTTTATTG
TTAATCGATTGTTATTGCCTTATATGTCTGAATCAGTGAGAATGTTAGAACGAGGTGATG
CAAGTAAGGAAGATATTGACATGGCTATGAAATTGGGAGCAGTTGGAATTGACACTATGA
AAAATGCTCGAGATTTTTATCATCGTATGGCACCAGAAAATGAGCTTTTTTTTCCAAGTC
CTTTGATTAATAAAATGGTTCAGGAAGGAAAACTTGGATTGAAGACTGGTGAAGGATTTT
ATAATTACAAATAA

>g8420.t10 Gene=g8420 Length=173
MFQSIDKIAKPSAIFASNTSALPIREISKNSTRLDRFCGLHFFNPVAVMKLLEVIRIPET
SETTYKTVMDFGAKMGKTCVTCKDTPGFIVNRLLLPYMSESVRMLERGDASKEDIDMAMK
LGAVGIDTMKNARDFYHRMAPENELFFPSPLINKMVQEGKLGLKTGEGFYNYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g8420.t10 Gene3D G3DSA:3.40.50.720 - 1 88 1.8E-36
8 g8420.t10 Gene3D G3DSA:1.10.1040.10 - 89 173 7.4E-21
3 g8420.t10 PANTHER PTHR43561 - 1 173 3.2E-66
2 g8420.t10 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 1 85 1.4E-29
1 g8420.t10 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 87 172 2.1E-18
6 g8420.t10 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature. 84 108 -
4 g8420.t10 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 86 7.88E-25
5 g8420.t10 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 86 172 2.3E-22

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