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.t5 TTS g17272.t5 12999507 12999507
chr_4 g17272 g17272.t5 isoform g17272.t5 12999580 13001189
chr_4 g17272 g17272.t5 exon g17272.t5.exon1 12999580 13000179
chr_4 g17272 g17272.t5 cds g17272.t5.CDS1 12999580 13000179
chr_4 g17272 g17272.t5 exon g17272.t5.exon2 13000490 13000827
chr_4 g17272 g17272.t5 cds g17272.t5.CDS2 13000490 13000798
chr_4 g17272 g17272.t5 exon g17272.t5.exon3 13000885 13001189
chr_4 g17272 g17272.t5 TSS g17272.t5 NA NA

Sequences

>g17272.t5 Gene=g17272 Length=1243
ATAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAATCACACCAAGATT
ATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGAAATTCAAGCAAC
AGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCATGACAGAACTGG
AGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCTGAATCACTCAAT
TCCTGAACATTGTGGTGGTCACAAATTGTCGACTTTTACGACTTGTTTAATTGCTGAAGA
ATTAGCTTATGGTTGCACTGGTATTGAAACGGCTATGGAAGGATCTGGTCTAGGTCAGAC
TCCCGTAGTTTTAGCTGGTAACAAGGAACAACAAAAGAAATACCTTGGACGTCTTGTTGA
ACAACCATTAGTTGCAGCTTATTGCGTTACAGAACCATCAGCTGGTTCAGATGTTAATGG
AATTAAATCAAAAGCTGTCAAAAAAGGCGACGAATATATTTTGAATGGACAAAAAATGTG
GATCACAAATGGTGGTGTTGCCAATTGGTATTTTGTACTTGCAAGAACAGCCGAAGATCC
CAAAGCACCTGCATCAAAAGCTTTTACTGGATTTATTGTTGAGCGTGAATGGCCAGGCGT
AACTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCAAGTGACACTCGTGGTATAAC
ATTTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGGTGCTGGATTTAA
AATTGCAATGTCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGGTGCAACAGGTTT
AGCACAGCGAGCCTACGATGAAGCATTAAAATATTCACTTGAACGTAAAACTTTTGGTGT
TCCAATTGCACAACATCAAGCAATTCAATTTATGCTTGCTGATATGGCAATTGGTGTTGA
ACTGTCAAGACTGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGGAAGAAGAAATTC
ATATGAAGCTTCAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAAAATTGCAACTGA
TGCAGTTCAAATATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGTTGAAAAACTCAT
GAGAGATGCCAAAATTTACCAAATTTATGAAGGAACATCACAAATTCAACGACTGATTAT
TTCTAGAAATGCTTTTGAACGTGCTAAGGAAATGAATAAGTAA

>g17272.t5 Gene=g17272 Length=302
MEGSGLGQTPVVLAGNKEQQKKYLGRLVEQPLVAAYCVTEPSAGSDVNGIKSKAVKKGDE
YILNGQKMWITNGGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQ
RASDTRGITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEALKY
SLERKTFGVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKCFAA
DMANKIATDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERAKEM
NK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g17272.t5 Gene3D G3DSA:2.40.110.10 - 34 150 5.4E-45
10 g17272.t5 Gene3D G3DSA:1.20.140.10 - 151 302 6.0E-54
3 g17272.t5 PANTHER PTHR48083 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 2 298 8.3E-141
4 g17272.t5 PANTHER PTHR48083:SF2 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 2 298 8.3E-141
1 g17272.t5 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 35 133 6.8E-26
2 g17272.t5 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 145 293 1.0E-50
8 g17272.t5 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 37 49 -
7 g17272.t5 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 252 271 -
5 g17272.t5 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 4 156 5.63E-54
6 g17272.t5 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 143 295 7.25E-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