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.t9 TTS g17272.t9 12999507 12999507
chr_4 g17272 g17272.t9 isoform g17272.t9 12999580 13002602
chr_4 g17272 g17272.t9 exon g17272.t9.exon1 12999580 13000179
chr_4 g17272 g17272.t9 cds g17272.t9.CDS1 12999580 13000179
chr_4 g17272 g17272.t9 exon g17272.t9.exon2 13000490 13000827
chr_4 g17272 g17272.t9 cds g17272.t9.CDS2 13000490 13000827
chr_4 g17272 g17272.t9 exon g17272.t9.exon3 13000906 13001185
chr_4 g17272 g17272.t9 cds g17272.t9.CDS3 13000906 13001185
chr_4 g17272 g17272.t9 exon g17272.t9.exon4 13002588 13002602
chr_4 g17272 g17272.t9 cds g17272.t9.CDS4 13002588 13002602
chr_4 g17272 g17272.t9 TSS g17272.t9 13002690 13002690

Sequences

>g17272.t9 Gene=g17272 Length=1233
ATGGCACTTTCTAAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAATC
ACACCAAGATTATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGAA
ATTCAAGCAACAGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCAT
GACAGAACTGGAGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCTG
AATCACTCAATTCCTGAACATTGTGGTGGTCACAAATTGTCGACTTTTACGACTTCTTAT
GGTTGCACTGGTATTGAAACGGCTATGGAAGGATCTGGTCTAGGTCAGACTCCCGTAGTT
TTAGCTGGTAACAAGGAACAACAAAAGAAATACCTTGGACGTCTTGTTGAACAACCATTA
GTTGCAGCTTATTGCGTTACAGAACCATCAGCTGGTTCAGATGTTAATGGAATTAAATCA
AAAGCTGTCAAAAAAGGCGACGAATATATTTTGAATGGACAAAAAATGTGGATCACAAAT
GGTGGTGTTGCCAATTGGTATTTTGTACTTGCAAGAACAGCCGAAGATCCCAAAGCACCT
GCATCAAAAGCTTTTACTGGATTTATTGTTGAGCGTGAATGGCCAGGCGTAACTCTTGGA
CGTAAAGAAATCAACATGGGACAACGTGCAAGTGACACTCGTGGTATAACATTTGAAGAT
GTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGGTGCTGGATTTAAAATTGCAATG
TCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGGTGCAACAGGTTTAGCACAGCGA
GCCTACGATGAAGCATTAAAATATTCACTTGAACGTAAAACTTTTGGTGTTCCAATTGCA
CAACATCAAGCAATTCAATTTATGCTTGCTGATATGGCAATTGGTGTTGAACTGTCAAGA
CTGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGGAAGAAGAAATTCATATGAAGCT
TCAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAAAATTGCAACTGATGCAGTTCAA
ATATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGTTGAAAAACTCATGAGAGATGCC
AAAATTTACCAAATTTATGAAGGAACATCACAAATTCAACGACTGATTATTTCTAGAAAT
GCTTTTGAACGTGCTAAGGAAATGAATAAGTAA

>g17272.t9 Gene=g17272 Length=410
MALSKISSLIRPFGSRAFSITPRLCNESGPSFALSEEQREIQATARKFTREEIIPVAAHH
DRTGEYPWAIIKKAWELGLLNHSIPEHCGGHKLSTFTTSYGCTGIETAMEGSGLGQTPVV
LAGNKEQQKKYLGRLVEQPLVAAYCVTEPSAGSDVNGIKSKAVKKGDEYILNGQKMWITN
GGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQRASDTRGITFED
VRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEALKYSLERKTFGVPIA
QHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKCFAADMANKIATDAVQ
IFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERAKEMNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g17272.t9 Gene3D G3DSA:1.10.540.10 - 23 141 7.8E-32
11 g17272.t9 Gene3D G3DSA:2.40.110.10 - 142 258 1.0E-44
12 g17272.t9 Gene3D G3DSA:1.20.140.10 - 259 410 1.2E-53
4 g17272.t9 PANTHER PTHR48083 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 33 406 3.2E-167
5 g17272.t9 PANTHER PTHR48083:SF2 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 33 406 3.2E-167
3 g17272.t9 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 35 137 1.1E-18
1 g17272.t9 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 143 241 1.2E-25
2 g17272.t9 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 253 401 2.1E-50
9 g17272.t9 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 145 157 -
8 g17272.t9 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 360 379 -
6 g17272.t9 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 31 264 2.36E-72
7 g17272.t9 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 251 403 1.48E-56

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

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. There were no conditions that were differentially expressed