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.t7 TTS g17272.t7 12999507 12999507
chr_4 g17272 g17272.t7 isoform g17272.t7 12999580 13002602
chr_4 g17272 g17272.t7 exon g17272.t7.exon1 12999580 13000166
chr_4 g17272 g17272.t7 cds g17272.t7.CDS1 12999580 13000137
chr_4 g17272 g17272.t7 exon g17272.t7.exon2 13000490 13000827
chr_4 g17272 g17272.t7 exon g17272.t7.exon3 13000885 13001185
chr_4 g17272 g17272.t7 exon g17272.t7.exon4 13002588 13002602
chr_4 g17272 g17272.t7 TSS g17272.t7 13002690 13002690

Sequences

>g17272.t7 Gene=g17272 Length=1241
ATGGCACTTTCTAAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAATC
ACACCAAGATTATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGAA
ATTCAAGCAACAGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCAT
GACAGAACTGGAGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCTG
AATCACTCAATTCCTGAACATTGTGGTGGTCACAAATTGTCGACTTTTACGACTTGTTTA
ATTGCTGAAGAATTAGCTTATGGTTGCACTGGTATTGAAACGGCTATGGAAGGATCTGGT
CTAGGTCAGACTCCCGTAGTTTTAGCTGGTAACAAGGAACAACAAAAGAAATACCTTGGA
CGTCTTGTTGAACAACCATTAGTTGCAGCTTATTGCGTTACAGAACCATCAGCTGGTTCA
GATGTTAATGGAATTAAATCAAAAGCTGTCAAAAAAGGCGACGAATATATTTTGAATGGA
CAAAAAATGTGGATCACAAATGGTGGTGTTGCCAATTGGTATTTTGTACTTGCAAGAACA
GCCGAAGATCCCAAAGCACCTGCATCAAAAGCTTTTACTGGATTTATTGTTGAGGCGTAA
CTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCAAGTGACACTCGTGGTATAACAT
TTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGGTGCTGGATTTAAAA
TTGCAATGTCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGGTGCAACAGGTTTAG
CACAGCGAGCCTACGATGAAGCATTAAAATATTCACTTGAACGTAAAACTTTTGGTGTTC
CAATTGCACAACATCAAGCAATTCAATTTATGCTTGCTGATATGGCAATTGGTGTTGAAC
TGTCAAGACTGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGGAAGAAGAAATTCAT
ATGAAGCTTCAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAAAATTGCAACTGATG
CAGTTCAAATATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGTTGAAAAACTCATGA
GAGATGCCAAAATTTACCAAATTTATGAAGGAACATCACAAATTCAACGACTGATTATTT
CTAGAAATGCTTTTGAACGTGCTAAGGAAATGAATAAGTAA

>g17272.t7 Gene=g17272 Length=185
MGQRASDTRGITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEA
LKYSLERKTFGVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKC
FAADMANKIATDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERA
KEMNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17272.t7 Gene3D G3DSA:2.40.110.10 - 1 33 3.5E-8
8 g17272.t7 Gene3D G3DSA:1.20.140.10 - 34 185 1.4E-54
2 g17272.t7 PANTHER PTHR48083 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 1 180 1.2E-83
3 g17272.t7 PANTHER PTHR48083:SF21 ACYL COA DEHYDROGENASE 1 180 1.2E-83
1 g17272.t7 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 28 176 2.4E-51
6 g17272.t7 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 135 154 -
4 g17272.t7 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 1 38 3.38E-8
5 g17272.t7 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 26 178 1.61E-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