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.t6 TTS g17272.t6 12999507 12999507
chr_4 g17272 g17272.t6 isoform g17272.t6 12999580 13002602
chr_4 g17272 g17272.t6 exon g17272.t6.exon1 12999580 12999853
chr_4 g17272 g17272.t6 cds g17272.t6.CDS1 12999849 12999853
chr_4 g17272 g17272.t6 exon g17272.t6.exon2 12999996 13000179
chr_4 g17272 g17272.t6 cds g17272.t6.CDS2 12999996 13000179
chr_4 g17272 g17272.t6 exon g17272.t6.exon3 13000490 13000827
chr_4 g17272 g17272.t6 cds g17272.t6.CDS3 13000490 13000827
chr_4 g17272 g17272.t6 exon g17272.t6.exon4 13000885 13001185
chr_4 g17272 g17272.t6 cds g17272.t6.CDS4 13000885 13001185
chr_4 g17272 g17272.t6 exon g17272.t6.exon5 13002588 13002602
chr_4 g17272 g17272.t6 cds g17272.t6.CDS5 13002588 13002602
chr_4 g17272 g17272.t6 TSS g17272.t6 13002690 13002690

Sequences

>g17272.t6 Gene=g17272 Length=1112
ATGGCACTTTCTAAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAATC
ACACCAAGATTATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGAA
ATTCAAGCAACAGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCAT
GACAGAACTGGAGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCTG
AATCACTCAATTCCTGAACATTGTGGTGGTCACAAATTGTCGACTTTTACGACTTGTTTA
ATTGCTGAAGAATTAGCTTATGGTTGCACTGGTATTGAAACGGCTATGGAAGGATCTGGT
CTAGGTCAGACTCCCGTAGTTTTAGCTGGTAACAAGGAACAACAAAAGAAATACCTTGGA
CGTCTTGTTGAACAACCATTAGTTGCAGCTTATTGCGTTACAGAACCATCAGCTGGTTCA
GATGTTAATGGAATTAAATCAAAAGCTGTCAAAAAAGGCGACGAATATATTTTGAATGGA
CAAAAAATGTGGATCACAAATGGTGGTGTTGCCAATTGGTATTTTGTACTTGCAAGAACA
GCCGAAGATCCCAAAGCACCTGCATCAAAAGCTTTTACTGGATTTATTGTTGAGCGTGAA
TGGCCAGGCGTAACTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCAAGTGACACT
CGTGGTATAACATTTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGGT
GCTGGATTTAAAATTGCAATGTCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGAC
TGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGGAAGAAGAAATTCATATGAAGCTT
CAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAAAATTGCAACTGATGCAGTTCAAA
TATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGTTGAAAAACTCATGAGAGATGCCA
AAATTTACCAAATTTATGAAGGAACATCACAAATTCAACGACTGATTATTTCTAGAAATG
CTTTTGAACGTGCTAAGGAAATGAATAAGTAA

>g17272.t6 Gene=g17272 Length=280
MALSKISSLIRPFGSRAFSITPRLCNESGPSFALSEEQREIQATARKFTREEIIPVAAHH
DRTGEYPWAIIKKAWELGLLNHSIPEHCGGHKLSTFTTCLIAEELAYGCTGIETAMEGSG
LGQTPVVLAGNKEQQKKYLGRLVEQPLVAAYCVTEPSAGSDVNGIKSKAVKKGDEYILNG
QKMWITNGGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQRASDT
RGITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17272.t6 Gene3D G3DSA:1.10.540.10 - 23 148 2.5E-41
8 g17272.t6 Gene3D G3DSA:2.40.110.10 - 149 269 4.6E-45
3 g17272.t6 PANTHER PTHR48083 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 33 279 2.5E-114
4 g17272.t6 PANTHER PTHR48083:SF2 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 33 279 2.5E-114
2 g17272.t6 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 35 144 1.3E-27
1 g17272.t6 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 150 248 5.8E-26
6 g17272.t6 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 152 164 -
5 g17272.t6 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 31 271 1.24E-78

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:0050660 flavin adenine dinucleotide binding 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. There were no conditions that were differentially expressed