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.t4 TTS g14410.t4 355402 355402
chr_4 g14410 g14410.t4 isoform g14410.t4 355467 356959
chr_4 g14410 g14410.t4 exon g14410.t4.exon1 355467 355479
chr_4 g14410 g14410.t4 cds g14410.t4.CDS1 355469 355479
chr_4 g14410 g14410.t4 exon g14410.t4.exon2 355589 355679
chr_4 g14410 g14410.t4 cds g14410.t4.CDS2 355589 355679
chr_4 g14410 g14410.t4 exon g14410.t4.exon3 355738 356471
chr_4 g14410 g14410.t4 cds g14410.t4.CDS3 355738 356471
chr_4 g14410 g14410.t4 exon g14410.t4.exon4 356526 356959
chr_4 g14410 g14410.t4 cds g14410.t4.CDS4 356526 356760
chr_4 g14410 g14410.t4 TSS g14410.t4 357084 357084

Sequences

>g14410.t4 Gene=g14410 Length=1272
ATGTTTACTATTAGACAATCATTCAAATTTGGTAAATTAAATAAAGAAATTCATAATTGA
ACTTTGGACCTTTTAACTAATTTTTGATATTAAAATTATAAATTCAAATAAATGACCTCA
AAATAATTTATTTCCTTCAGCTTCATCAATCAATGCTCGTTCAATTGTGTCCCTCTCGCA
TCTTCCTGAGACTCATCAAATGTTGTATAAGACATGTCGTGATTTTGCTGATAATGAGTT
AGCACCAATTGCTAAACAAATTGATAAAGAACATCGATATCCATCGGAGCAAGTTAAGAA
AATGGGTGAACTTGGTTTACTTGCGATTGCTATTCCTGAAAAATATGGAGGAACAGGGCT
TGATTATCTTGCTTATGCTATTGGCATGGAAGAAATTTCTCGAGGTTGTGCTACTTGTGG
TGTCATTATGACTGTCAACAACACTTTATATTTGGGACCAGTTAAAAATTTTGGTAACGA
AGCTCAAAAAAAAGAATTTTTAACTCCTTACACTGATGGTGACAAGATTGGATGTTTTGC
ATTATCTGAGCCTGGAAATGGAAGTGATGCTGCAGCTGCTTCTACTACAGCAAAACTTGT
TGGTGATAAATGGGTTTTAAATGGTACCAAAAATTGGATAACAAATGGTCCTGATGCTTC
AGCTGCAATTGTTTTTGCTACCACTGATAAAAAATTAAAACACAAAGGTATTTCAGCTTT
TATTGTAGAGCGTGGTATACCAGGATTTAGTTATGGCAAGAAAGAAGATAAATTGGGTAT
AAGAGGTAGTTCAACATGCTCTTTGATTTTTGATGACTGTGCTATACCTAAAGAAAATAT
TCTCGGTGAAGAAGGATTTGGATTTAAAATTGCAATGAAAACATTAGATGAGGGCCGAAT
TGGAATAGCAGGGCAAGCATTAGGCATTGCTCAAGCATCATTAGAATGTGCAGTTGATTA
TGCAAATAAGAGAATCGCATTTGGAAATCCTATAAGCAAAATGCAAACAATACAAAATAA
AATAGCCGATATGGCAATGAGAATTGAAGCAGCAAGATTACTAACCTGGAGAGCTGCTGT
GTTGAAAGATGAAGGTAAATCAATAACAAAAGAAGCTGCTATGGCAAAATTAGCTGCTAG
TGAAACTGCAACTTTCTGTTCCCATCAAGCAATACAAATTCTTGGTGGTATGGGATACGT
AACAGATATGCCAGCAGAACGTCATTATAGAGATGCAAGAATAACTGAAATTTATGAAGA
ATGTCACAATAA

>g14410.t4 Gene=g14410 Length=357
MLYKTCRDFADNELAPIAKQIDKEHRYPSEQVKKMGELGLLAIAIPEKYGGTGLDYLAYA
IGMEEISRGCATCGVIMTVNNTLYLGPVKNFGNEAQKKEFLTPYTDGDKIGCFALSEPGN
GSDAAAASTTAKLVGDKWVLNGTKNWITNGPDASAAIVFATTDKKLKHKGISAFIVERGI
PGFSYGKKEDKLGIRGSSTCSLIFDDCAIPKENILGEEGFGFKIAMKTLDEGRIGIAGQA
LGIAQASLECAVDYANKRIAFGNPISKMQTIQNKIADMAMRIEAARLLTWRAAVLKDEGK
SITKEAAMAKLAASETATFCSHQAIQILGGMGYVTDMPAERHYRDARITEIYEECHN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14410.t4 CDD cd01158 SCAD_SBCAD 1 353 0.0
10 g14410.t4 Gene3D G3DSA:1.10.540.10 - 1 110 1.4E-37
11 g14410.t4 Gene3D G3DSA:2.40.110.10 - 111 224 1.9E-44
12 g14410.t4 Gene3D G3DSA:1.20.140.10 - 225 357 9.8E-49
4 g14410.t4 PANTHER PTHR43884:SF26 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN-RELATED 1 353 5.6E-145
5 g14410.t4 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 1 353 5.6E-145
13 g14410.t4 PIRSF PIRSF016578 PIGM 6 101 1.1E-6
14 g14410.t4 PIRSF PIRSF016578 PIGM 116 351 5.0E-13
3 g14410.t4 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 1 108 2.1E-31
1 g14410.t4 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 112 207 1.4E-28
2 g14410.t4 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 221 353 1.5E-42
9 g14410.t4 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 114 126 -
8 g14410.t4 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 326 345 -
6 g14410.t4 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 1 232 5.76E-84
7 g14410.t4 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 217 354 6.44E-52

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