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.t11 TTS g17272.t11 12999507 12999507
chr_4 g17272 g17272.t11 isoform g17272.t11 12999580 13006689
chr_4 g17272 g17272.t11 exon g17272.t11.exon1 12999580 13000179
chr_4 g17272 g17272.t11 cds g17272.t11.CDS1 12999580 13000179
chr_4 g17272 g17272.t11 exon g17272.t11.exon2 13000490 13000827
chr_4 g17272 g17272.t11 cds g17272.t11.CDS2 13000490 13000827
chr_4 g17272 g17272.t11 exon g17272.t11.exon3 13000885 13001185
chr_4 g17272 g17272.t11 cds g17272.t11.CDS3 13000885 13001185
chr_4 g17272 g17272.t11 exon g17272.t11.exon4 13002588 13002674
chr_4 g17272 g17272.t11 cds g17272.t11.CDS4 13002588 13002602
chr_4 g17272 g17272.t11 TSS g17272.t11 13002690 13002690
chr_4 g17272 g17272.t11 exon g17272.t11.exon5 13006581 13006689

Sequences

>g17272.t11 Gene=g17272 Length=1435
TTAATTAGAAATTTTAACAAATTCATCTCTAAAAGCAATTGCAGTCAAAGCCTTTGAATG
TCCCAAATATTCTCTTTCGATGCTTTTTGTTTCAATTTTCCACAATCTCTGAACAACATC
AGACGTATAAATTTTTCTTTTTTCAAATTTTTTGGATTTTACTTTAATTTTTGTGGAAAT
TATGGCACTTTCTAAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAAT
CACACCAAGATTATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGA
AATTCAAGCAACAGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCA
TGACAGAACTGGAGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCT
GAATCACTCAATTCCTGAACATTGTGGTGGTCACAAATTGTCGACTTTTACGACTTGTTT
AATTGCTGAAGAATTAGCTTATGGTTGCACTGGTATTGAAACGGCTATGGAAGGATCTGG
TCTAGGTCAGACTCCCGTAGTTTTAGCTGGTAACAAGGAACAACAAAAGAAATACCTTGG
ACGTCTTGTTGAACAACCATTAGTTGCAGCTTATTGCGTTACAGAACCATCAGCTGGTTC
AGATGTTAATGGAATTAAATCAAAAGCTGTCAAAAAAGGCGACGAATATATTTTGAATGG
ACAAAAAATGTGGATCACAAATGGTGGTGTTGCCAATTGGTATTTTGTACTTGCAAGAAC
AGCCGAAGATCCCAAAGCACCTGCATCAAAAGCTTTTACTGGATTTATTGTTGAGCGTGA
ATGGCCAGGCGTAACTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCAAGTGACAC
TCGTGGTATAACATTTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGG
TGCTGGATTTAAAATTGCAATGTCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGG
TGCAACAGGTTTAGCACAGCGAGCCTACGATGAAGCATTAAAATATTCACTTGAACGTAA
AACTTTTGGTGTTCCAATTGCACAACATCAAGCAATTCAATTTATGCTTGCTGATATGGC
AATTGGTGTTGAACTGTCAAGACTGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGG
AAGAAGAAATTCATATGAAGCTTCAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAA
AATTGCAACTGATGCAGTTCAAATATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGT
TGAAAAACTCATGAGAGATGCCAAAATTTACCAAATTTATGAAGGAACATCACAAATTCA
ACGACTGATTATTTCTAGAAATGCTTTTGAACGTGCTAAGGAAATGAATAAGTAA

>g17272.t11 Gene=g17272 Length=417
MALSKISSLIRPFGSRAFSITPRLCNESGPSFALSEEQREIQATARKFTREEIIPVAAHH
DRTGEYPWAIIKKAWELGLLNHSIPEHCGGHKLSTFTTCLIAEELAYGCTGIETAMEGSG
LGQTPVVLAGNKEQQKKYLGRLVEQPLVAAYCVTEPSAGSDVNGIKSKAVKKGDEYILNG
QKMWITNGGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQRASDT
RGITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEALKYSLERK
TFGVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKCFAADMANK
IATDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERAKEMNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g17272.t11 Gene3D G3DSA:1.10.540.10 - 23 148 5.8E-41
11 g17272.t11 Gene3D G3DSA:2.40.110.10 - 149 265 1.1E-44
12 g17272.t11 Gene3D G3DSA:1.20.140.10 - 266 417 1.3E-53
4 g17272.t11 PANTHER PTHR48083 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 33 413 5.0E-176
5 g17272.t11 PANTHER PTHR48083:SF2 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 33 413 5.0E-176
14 g17272.t11 PIRSF PIRSF016578 PIGM 30 112 3.8E-4
13 g17272.t11 PIRSF PIRSF016578 PIGM 158 398 1.8E-9
3 g17272.t11 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 35 144 3.0E-27
1 g17272.t11 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 150 248 1.3E-25
2 g17272.t11 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 260 408 2.1E-50
9 g17272.t11 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 152 164 -
8 g17272.t11 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 367 386 -
6 g17272.t11 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 31 271 4.45E-78
7 g17272.t11 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 258 410 1.55E-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.

Raw TPM values