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.t7 TTS g14410.t7 355402 355402
chr_4 g14410 g14410.t7 isoform g14410.t7 355467 357445
chr_4 g14410 g14410.t7 exon g14410.t7.exon1 355467 355528
chr_4 g14410 g14410.t7 cds g14410.t7.CDS1 355467 355528
chr_4 g14410 g14410.t7 exon g14410.t7.exon2 355589 355679
chr_4 g14410 g14410.t7 cds g14410.t7.CDS2 355589 355679
chr_4 g14410 g14410.t7 exon g14410.t7.exon3 355738 356471
chr_4 g14410 g14410.t7 cds g14410.t7.CDS3 355738 356471
chr_4 g14410 g14410.t7 exon g14410.t7.exon4 356526 356617
chr_4 g14410 g14410.t7 cds g14410.t7.CDS4 356526 356574
chr_4 g14410 g14410.t7 exon g14410.t7.exon5 356709 356819
chr_4 g14410 g14410.t7 TSS g14410.t7 357084 357084
chr_4 g14410 g14410.t7 exon g14410.t7.exon6 357285 357445

Sequences

>g14410.t7 Gene=g14410 Length=1251
TGAGTTCATAATTTATTTGTGGAATGTCTTGATAATATTTTATTACTGGCTTTATTGATA
TCTCTAAACAAAATTTTATTTTTAAATAACTTTTTAAATACTTACATGAATGTTTTGTAC
TGAAACTTTTAAAAGCAAGCATTTTTATTAAAATTTTGAAACTTCATCAATCAATGCTCG
TTCAATTGTGTCCCTCTCGCATCTTCCTGAGACTCATCAAATGTTGTATAAGACATGTCG
TGATTTTGCTGATAATGAGTTAGCACCAATTGATATGGAGGAACAGGGCTTGATTATCTT
GCTTATGCTATTGGCATGGAAGAAATTTCTCGAGGTTGTGCTACTTGTGGTGTCATTATG
ACTGTCAACAACACTTTATATTTGGGACCAGTTAAAAATTTTGGTAACGAAGCTCAAAAA
AAAGAATTTTTAACTCCTTACACTGATGGTGACAAGATTGGATGTTTTGCATTATCTGAG
CCTGGAAATGGAAGTGATGCTGCAGCTGCTTCTACTACAGCAAAACTTGTTGGTGATAAA
TGGGTTTTAAATGGTACCAAAAATTGGATAACAAATGGTCCTGATGCTTCAGCTGCAATT
GTTTTTGCTACCACTGATAAAAAATTAAAACACAAAGGTATTTCAGCTTTTATTGTAGAG
CGTGGTATACCAGGATTTAGTTATGGCAAGAAAGAAGATAAATTGGGTATAAGAGGTAGT
TCAACATGCTCTTTGATTTTTGATGACTGTGCTATACCTAAAGAAAATATTCTCGGTGAA
GAAGGATTTGGATTTAAAATTGCAATGAAAACATTAGATGAGGGCCGAATTGGAATAGCA
GGGCAAGCATTAGGCATTGCTCAAGCATCATTAGAATGTGCAGTTGATTATGCAAATAAG
AGAATCGCATTTGGAAATCCTATAAGCAAAATGCAAACAATACAAAATAAAATAGCCGAT
ATGGCAATGAGAATTGAAGCAGCAAGATTACTAACCTGGAGAGCTGCTGTGTTGAAAGAT
GAAGGTAAATCAATAACAAAAGAAGCTGCTATGGCAAAATTAGCTGCTAGTGAAACTGCA
ACTTTCTGTTCCCATCAAGCAATACAAATTCTTGGTGGTATGGGATACGTAACAGATATG
CCAGCAGAACGTCATTATAGAGATGCAAGAATAACTGAAATTTATGAAGGAACATCCGAA
ATTCAAAGACTTGTAATTGCTGGTCAAATACTTAAACAAATGTCACAATAA

>g14410.t7 Gene=g14410 Length=311
MEEISRGCATCGVIMTVNNTLYLGPVKNFGNEAQKKEFLTPYTDGDKIGCFALSEPGNGS
DAAAASTTAKLVGDKWVLNGTKNWITNGPDASAAIVFATTDKKLKHKGISAFIVERGIPG
FSYGKKEDKLGIRGSSTCSLIFDDCAIPKENILGEEGFGFKIAMKTLDEGRIGIAGQALG
IAQASLECAVDYANKRIAFGNPISKMQTIQNKIADMAMRIEAARLLTWRAAVLKDEGKSI
TKEAAMAKLAASETATFCSHQAIQILGGMGYVTDMPAERHYRDARITEIYEGTSEIQRLV
IAGQILKQMSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g14410.t7 Gene3D G3DSA:1.10.540.10 - 1 48 1.1E-113
10 g14410.t7 Gene3D G3DSA:2.40.110.10 - 49 156 1.1E-113
11 g14410.t7 Gene3D G3DSA:1.20.140.10 - 157 302 1.1E-113
4 g14410.t7 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 1 310 3.2E-126
3 g14410.t7 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 1 46 6.5E-7
1 g14410.t7 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 50 145 1.1E-28
2 g14410.t7 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 159 305 8.0E-50
8 g14410.t7 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 52 64 -
7 g14410.t7 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 264 283 -
5 g14410.t7 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 1 170 6.41E-63
6 g14410.t7 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 155 308 8.7E-60

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