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.t9 TTS g8420.t9 30360761 30360761
chr_2 g8420 g8420.t9 isoform g8420.t9 30360946 30362014
chr_2 g8420 g8420.t9 exon g8420.t9.exon1 30360946 30361137
chr_2 g8420 g8420.t9 cds g8420.t9.CDS1 30361112 30361137
chr_2 g8420 g8420.t9 exon g8420.t9.exon2 30361253 30361874
chr_2 g8420 g8420.t9 cds g8420.t9.CDS2 30361253 30361874
chr_2 g8420 g8420.t9 exon g8420.t9.exon3 30361937 30362014
chr_2 g8420 g8420.t9 cds g8420.t9.CDS3 30361937 30362014
chr_2 g8420 g8420.t9 TSS g8420.t9 30362073 30362073

Sequences

>g8420.t9 Gene=g8420 Length=892
ATGACTTCAAATATTGAAAATATCAAAAATGTAGTTGTTGTTGGTGCTGGTTTGATGGGC
TCTGGCATTGCAGGAATGGCAGCAGTCGCTGGATTTCAAGTCACGATTGTTGATTTAGAT
AAAAAGCTACTTGAGAAATCTAAGGAACAAATTGCAATCACACTTGAACGTGTAGGACGT
AAAAAATTTAAACAAAATGAGACTAAAATTAATGAATTTATTCAGAATTCATTGAGAAAT
ATTTCTGATTCAACAGATTTATTAGAGGTTGTAAAAAATGCTGACATCGTCATTGAAGCA
ATTGTGGAAAATTTAGAAGCAAAACAAAAAATGTTTCAATCAATTGATAAAATTGCAAAA
CCTTCAGCAATTTTTGCATCAAATACATCAGCATTGCCAATTAGAGAAATTTCAAAAAAT
TCAACAAGACTTGATCGATTTTGTGGTTTGCATTTCTTTAATCCCGTGGCTGTCATGAAA
TTACTTGAAGTAATTAGAATTCCTGAAACAAGTGAAACAACTTATAAGACTGTGATGGAT
TTTGGTGCTAAAATGGGAAAAACTTGTGTAACATGTAAAGATACGCCTGGCTTTATTGTT
AATCGATTGTTATTGCCTTATATGTCTGAATCAGTGAGAATGTTAGAACGAGGTGATGCA
AGTAAGGAAGATATTGACATGGCTATGAAATTGGGAGCAGAAGTAAATTTTTCAAGGCCC
ATTTGAGCTAAGTGACTTAGTTGGAATTGACACTATGAAAAATGCTCGAGATTTTTATCA
TCGTATGGCACCAGAAAATGAGCTTTTTTTTCCAAGTCCTTTGATTAATAAAATGGTTCA
GGAAGGAAAACTTGGATTGAAGACTGGTGAAGGATTTTATAATTACAAATAA

>g8420.t9 Gene=g8420 Length=241
MTSNIENIKNVVVVGAGLMGSGIAGMAAVAGFQVTIVDLDKKLLEKSKEQIAITLERVGR
KKFKQNETKINEFIQNSLRNISDSTDLLEVVKNADIVIEAIVENLEAKQKMFQSIDKIAK
PSAIFASNTSALPIREISKNSTRLDRFCGLHFFNPVAVMKLLEVIRIPETSETTYKTVMD
FGAKMGKTCVTCKDTPGFIVNRLLLPYMSESVRMLERGDASKEDIDMAMKLGAEVNFSRP
I

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g8420.t9 Gene3D G3DSA:3.40.50.720 - 1 198 3.8E-74
7 g8420.t9 Gene3D G3DSA:1.10.1040.10 - 199 239 4.3E-9
3 g8420.t9 PANTHER PTHR43561 - 5 233 1.2E-88
11 g8420.t9 PIRSF PIRSF000105 HCDH 3 238 4.0E-77
2 g8420.t9 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 10 195 3.1E-59
1 g8420.t9 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 197 234 2.6E-10
9 g8420.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
10 g8420.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 37 -
8 g8420.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 38 241 -
13 g8420.t9 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature. 194 218 -
4 g8420.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 7 196 1.2E-57
5 g8420.t9 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 193 233 2.3E-9
12 g8420.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -

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. There were no conditions that were differentially expressed