Gene loci information

Transcript annotation

  • This transcript has been annotated as Short-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 g14410 g14410.t8 TTS g14410.t8 355402 355402
chr_4 g14410 g14410.t8 isoform g14410.t8 355761 356959
chr_4 g14410 g14410.t8 exon g14410.t8.exon1 355761 356471
chr_4 g14410 g14410.t8 cds g14410.t8.CDS1 355762 356471
chr_4 g14410 g14410.t8 exon g14410.t8.exon2 356526 356819
chr_4 g14410 g14410.t8 cds g14410.t8.CDS2 356526 356819
chr_4 g14410 g14410.t8 exon g14410.t8.exon3 356929 356959
chr_4 g14410 g14410.t8 cds g14410.t8.CDS3 356929 356959
chr_4 g14410 g14410.t8 TSS g14410.t8 357084 357084

Sequences

>g14410.t8 Gene=g14410 Length=1036
ATGTTTACTATTAGACAATCATTCAAATTTGCTTCATCAATCAATGCTCGTTCAATTGTG
TCCCTCTCGCATCTTCCTGAGACTCATCAAATGTTGTATAAGACATGTCGTGATTTTGCT
GATAATGAGTTAGCACCAATTGCTAAACAAATTGATAAAGAACATCGATATCCATCGGAG
CAAGTTAAGAAAATGGGTGAACTTGGTTTACTTGCGATTGCTATTCCTGAAAAATATGGA
GGAACAGGGCTTGATTATCTTGCTTATGCTATTGGCATGGAAGAAATTTCTCGAGGTTGT
GCTACTTGTGGTGTCATTATGACTGTCAACAACACTTTATATTTGGGACCAGTTAAAAAT
TTTGGTAACGAAGCTCAAAAAAAAGAATTTTTAACTCCTTACACTGATGGTGACAAGATT
GGATGTTTTGCATTATCTGAGCCTGGAAATGGAAGTGATGCTGCAGCTGCTTCTACTACA
GCAAAACTTGTTGGTGATAAATGGGTTTTAAATGGTACCAAAAATTGGATAACAAATGGT
CCTGATGCTTCAGCTGCAATTGTTTTTGCTACCACTGATAAAAAATTAAAACACAAAGGT
ATTTCAGCTTTTATTGTAGAGCGTGGTATACCAGGATTTAGTTATGGCAAGAAAGAAGAT
AAATTGGGTATAAGAGGTAGTTCAACATGCTCTTTGATTTTTGATGACTGTGCTATACCT
AAAGAAAATATTCTCGGTGAAGAAGGATTTGGATTTAAAATTGCAATGAAAACATTAGAT
GAGGGCCGAATTGGAATAGCAGGGCAAGCATTAGGCATTGCTCAAGCATCATTAGAATGT
GCAGTTGATTATGCAAATAAGAGAATCGCATTTGGAAATCCTATAAGCAAAATGCAAACA
ATACAAAATAAAATAGCCGATATGGCAATGAGAATTGAAGCAGCAAGATTACTAACCTGG
AGAGCTGCTGTGTTGAAAGATGAAGGTAAATCAATAACAAAAGAAGCTGCTATGGCAAAA
TTAGCTGCTAGTGAAA

>g14410.t8 Gene=g14410 Length=345
MFTIRQSFKFASSINARSIVSLSHLPETHQMLYKTCRDFADNELAPIAKQIDKEHRYPSE
QVKKMGELGLLAIAIPEKYGGTGLDYLAYAIGMEEISRGCATCGVIMTVNNTLYLGPVKN
FGNEAQKKEFLTPYTDGDKIGCFALSEPGNGSDAAAASTTAKLVGDKWVLNGTKNWITNG
PDASAAIVFATTDKKLKHKGISAFIVERGIPGFSYGKKEDKLGIRGSSTCSLIFDDCAIP
KENILGEEGFGFKIAMKTLDEGRIGIAGQALGIAQASLECAVDYANKRIAFGNPISKMQT
IQNKIADMAMRIEAARLLTWRAAVLKDEGKSITKEAAMAKLAASE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g14410.t8 Gene3D G3DSA:1.10.540.10 - 18 140 3.5E-40
10 g14410.t8 Gene3D G3DSA:2.40.110.10 - 141 254 1.7E-44
11 g14410.t8 Gene3D G3DSA:1.20.140.10 - 255 345 7.6E-30
4 g14410.t8 PANTHER PTHR43884:SF12 ISOVALERYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED 21 345 3.2E-125
5 g14410.t8 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 21 345 3.2E-125
13 g14410.t8 PIRSF PIRSF016578 PIGM 17 131 5.8E-7
12 g14410.t8 PIRSF PIRSF016578 PIGM 150 344 1.1E-8
3 g14410.t8 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 27 138 1.7E-33
1 g14410.t8 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 142 237 1.3E-28
2 g14410.t8 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 251 345 2.5E-26
8 g14410.t8 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 144 156 -
6 g14410.t8 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 24 262 3.66E-86
7 g14410.t8 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 247 345 1.77E-33

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.

Raw TPM values