Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable medium-chain specific acyl-CoA 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_4 g17272 g17272.t4 TTS g17272.t4 12999507 12999507
chr_4 g17272 g17272.t4 isoform g17272.t4 12999580 13000672
chr_4 g17272 g17272.t4 exon g17272.t4.exon1 12999580 13000179
chr_4 g17272 g17272.t4 cds g17272.t4.CDS1 12999580 13000179
chr_4 g17272 g17272.t4 exon g17272.t4.exon2 13000490 13000672
chr_4 g17272 g17272.t4 cds g17272.t4.CDS2 13000490 13000597
chr_4 g17272 g17272.t4 TSS g17272.t4 NA NA

Sequences

>g17272.t4 Gene=g17272 Length=783
GCTGGTTCAGATGTTAATGGAATTAAATCAAAAGCTGTCAAAAAAGGCGACGAATATATT
TTGAATGGACAAAAAATGTGGATCACAAATGGTGGTGTTGCCAATTGGTATTTTGTACTT
GCAAGAACAGCCGAAGATCCCAAAGCACCTGCATCAAAAGCTTTTACTGGATTTATTGTT
GAGCGTGAATGGCCAGGCGTAACTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCA
AGTGACACTCGTGGTATAACATTTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTC
GGTGAAGGTGCTGGATTTAAAATTGCAATGTCAACATTTGACCTCACTCGACCACCAGTT
GCTGCAGGTGCAACAGGTTTAGCACAGCGAGCCTACGATGAAGCATTAAAATATTCACTT
GAACGTAAAACTTTTGGTGTTCCAATTGCACAACATCAAGCAATTCAATTTATGCTTGCT
GATATGGCAATTGGTGTTGAACTGTCAAGACTGAGTTGGTGGAGAGCTGCTTGGGAGGTG
GACCAAGGAAGAAGAAATTCATATGAAGCTTCAATTTCAAAATGTTTTGCTGCTGACATG
GCTAATAAAATTGCAACTGATGCAGTTCAAATATTTGGTGGAAATGGTTTCAATTCAGAA
TATCCAGTTGAAAAACTCATGAGAGATGCCAAAATTTACCAAATTTATGAAGGAACATCA
CAAATTCAACGACTGATTATTTCTAGAAATGCTTTTGAACGTGCTAAGGAAATGAATAAG
TAA

>g17272.t4 Gene=g17272 Length=235
MWITNGGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQRASDTRG
ITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEALKYSLERKTF
GVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKCFAADMANKIA
TDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERAKEMNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g17272.t4 Gene3D G3DSA:2.40.110.10 - 1 83 1.5E-26
9 g17272.t4 Gene3D G3DSA:1.20.140.10 - 84 235 3.0E-54
3 g17272.t4 PANTHER PTHR48083 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 2 230 1.4E-107
4 g17272.t4 PANTHER PTHR48083:SF21 ACYL COA DEHYDROGENASE 2 230 1.4E-107
1 g17272.t4 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 1 66 1.1E-10
2 g17272.t4 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 78 226 5.1E-51
7 g17272.t4 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 185 204 -
5 g17272.t4 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 1 89 6.15E-27
6 g17272.t4 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 76 228 3.54E-57

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:0016627 oxidoreductase activity, acting on the CH-CH group of donors MF
GO:0003995 acyl-CoA dehydrogenase activity MF
GO:0055114 NA NA

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