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.t3 TTS g8419.t3 30358907 30358907
chr_2 g8419 g8419.t3 isoform g8419.t3 30358954 30360641
chr_2 g8419 g8419.t3 exon g8419.t3.exon1 30358954 30359144
chr_2 g8419 g8419.t3 cds g8419.t3.CDS1 30358954 30359144
chr_2 g8419 g8419.t3 exon g8419.t3.exon2 30359826 30360174
chr_2 g8419 g8419.t3 cds g8419.t3.CDS2 30359826 30360174
chr_2 g8419 g8419.t3 exon g8419.t3.exon3 30360232 30360641
chr_2 g8419 g8419.t3 cds g8419.t3.CDS3 30360232 30360477
chr_2 g8419 g8419.t3 TSS g8419.t3 30360766 30360766

Sequences

>g8419.t3 Gene=g8419 Length=950
ATGTCATCAGGAAACGTTATTAATCATGTCACAATCATTGGTGCTGGCCTAATGGGCTCT
GGCATAGCTCAGGTAAAAAATTACAAAGATTCAAAGTTCAAAGTCCAACAGTGTAAAATG
GAAAATATTTCTAGGTGGCTGCATCATCCGGTCATAAAGTTACAATGGTTGAATTGGACT
CTAAACTTCTTGACAAGGCACAGAAAAACATTGAAAAAAGTTTAGAAAGAGTTGCCAAGA
AACAATTCAAAGGCGAGGAGGATAAAATTGCCGGCTTTGTGAATGAATCAATAAGCAGAA
TTTCTGGATCAACTGACTTAAATTCTGTTGTTAAAGATACTGATTTGGTCATTGAAGCAA
TTGTTGAAAACCTTGAAGTTAAGCAGAAACTTTTTGGACAAATCGATGGAGTAGCAAAAC
CATCAACAATTTTTGCTTCAAACACTTCATCAATTCCAATTAAAGACATTGCAAAAAGCA
CTTCACGTCTTGATAGATTCTGTGGGCTTCACTTTTTCAATCCAGTTCCAGTCATGAAGT
TACTTGAAGTTATTAGAATTCCTGAAACTTCCGACGCAACTTACAATGCAGCAATGGAAT
TTGGAAAGAAAGTTGGCAAGACTTGTGTCACATGCAAAGATACACCTGGATTTATTGTCA
ATCGTCTTTTGGTACCATATATGGCTGAAGCAGTACGAATGCTAGAACGAGGTGATGCTA
CGGCAAGAGATATTGATACTGCCATGAAATTAGGAGCAGGCTACCCAATGGGACCTTTTG
AGCTGAGCGATTACGTTGGTTTGGACACAACAAAATTCATCTTAGATGGCTGGAGTAAAA
ATTATCCAGACAATCCATTATTCAAAACAATTCCAATGTTGACAAAACTCGTTGAAGAAG
GAAAATTAGGAATGAAAACAGGCGAAGGATTTTATAAATATCAAAAATAA

>g8419.t3 Gene=g8419 Length=261
MVELDSKLLDKAQKNIEKSLERVAKKQFKGEEDKIAGFVNESISRISGSTDLNSVVKDTD
LVIEAIVENLEVKQKLFGQIDGVAKPSTIFASNTSSIPIKDIAKSTSRLDRFCGLHFFNP
VPVMKLLEVIRIPETSDATYNAAMEFGKKVGKTCVTCKDTPGFIVNRLLVPYMAEAVRML
ERGDATARDIDTAMKLGAGYPMGPFELSDYVGLDTTKFILDGWSKNYPDNPLFKTIPMLT
KLVEEGKLGMKTGEGFYKYQK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g8419.t3 Coils Coil Coil 9 29 -
7 g8419.t3 Gene3D G3DSA:3.40.50.720 - 1 165 6.4E-63
8 g8419.t3 Gene3D G3DSA:1.10.1040.10 - 169 260 5.3E-38
3 g8419.t3 PANTHER PTHR43561 - 2 260 1.2E-117
10 g8419.t3 PIRSF PIRSF000105 HCDH 1 261 3.2E-85
2 g8419.t3 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 1 160 5.6E-50
1 g8419.t3 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 162 259 3.1E-35
6 g8419.t3 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature. 159 183 -
4 g8419.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 161 2.03E-46
5 g8419.t3 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 161 261 8.08E-35

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

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.

Raw TPM values