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.t1 TTS g14410.t1 355402 355402
chr_4 g14410 g14410.t1 isoform g14410.t1 355467 356959
chr_4 g14410 g14410.t1 exon g14410.t1.exon1 355467 355528
chr_4 g14410 g14410.t1 cds g14410.t1.CDS1 355467 355528
chr_4 g14410 g14410.t1 exon g14410.t1.exon2 355589 355679
chr_4 g14410 g14410.t1 cds g14410.t1.CDS2 355589 355679
chr_4 g14410 g14410.t1 exon g14410.t1.exon3 355738 356471
chr_4 g14410 g14410.t1 cds g14410.t1.CDS3 355738 356471
chr_4 g14410 g14410.t1 exon g14410.t1.exon4 356526 356819
chr_4 g14410 g14410.t1 cds g14410.t1.CDS4 356526 356819
chr_4 g14410 g14410.t1 exon g14410.t1.exon5 356929 356959
chr_4 g14410 g14410.t1 cds g14410.t1.CDS5 356929 356959
chr_4 g14410 g14410.t1 TSS g14410.t1 357084 357084

Sequences

>g14410.t1 Gene=g14410 Length=1212
ATGTTTACTATTAGACAATCATTCAAATTTGCTTCATCAATCAATGCTCGTTCAATTGTG
TCCCTCTCGCATCTTCCTGAGACTCATCAAATGTTGTATAAGACATGTCGTGATTTTGCT
GATAATGAGTTAGCACCAATTGCTAAACAAATTGATAAAGAACATCGATATCCATCGGAG
CAAGTTAAGAAAATGGGTGAACTTGGTTTACTTGCGATTGCTATTCCTGAAAAATATGGA
GGAACAGGGCTTGATTATCTTGCTTATGCTATTGGCATGGAAGAAATTTCTCGAGGTTGT
GCTACTTGTGGTGTCATTATGACTGTCAACAACACTTTATATTTGGGACCAGTTAAAAAT
TTTGGTAACGAAGCTCAAAAAAAAGAATTTTTAACTCCTTACACTGATGGTGACAAGATT
GGATGTTTTGCATTATCTGAGCCTGGAAATGGAAGTGATGCTGCAGCTGCTTCTACTACA
GCAAAACTTGTTGGTGATAAATGGGTTTTAAATGGTACCAAAAATTGGATAACAAATGGT
CCTGATGCTTCAGCTGCAATTGTTTTTGCTACCACTGATAAAAAATTAAAACACAAAGGT
ATTTCAGCTTTTATTGTAGAGCGTGGTATACCAGGATTTAGTTATGGCAAGAAAGAAGAT
AAATTGGGTATAAGAGGTAGTTCAACATGCTCTTTGATTTTTGATGACTGTGCTATACCT
AAAGAAAATATTCTCGGTGAAGAAGGATTTGGATTTAAAATTGCAATGAAAACATTAGAT
GAGGGCCGAATTGGAATAGCAGGGCAAGCATTAGGCATTGCTCAAGCATCATTAGAATGT
GCAGTTGATTATGCAAATAAGAGAATCGCATTTGGAAATCCTATAAGCAAAATGCAAACA
ATACAAAATAAAATAGCCGATATGGCAATGAGAATTGAAGCAGCAAGATTACTAACCTGG
AGAGCTGCTGTGTTGAAAGATGAAGGTAAATCAATAACAAAAGAAGCTGCTATGGCAAAA
TTAGCTGCTAGTGAAACTGCAACTTTCTGTTCCCATCAAGCAATACAAATTCTTGGTGGT
ATGGGATACGTAACAGATATGCCAGCAGAACGTCATTATAGAGATGCAAGAATAACTGAA
ATTTATGAAGGAACATCCGAAATTCAAAGACTTGTAATTGCTGGTCAAATACTTAAACAA
ATGTCACAATAA

>g14410.t1 Gene=g14410 Length=403
MFTIRQSFKFASSINARSIVSLSHLPETHQMLYKTCRDFADNELAPIAKQIDKEHRYPSE
QVKKMGELGLLAIAIPEKYGGTGLDYLAYAIGMEEISRGCATCGVIMTVNNTLYLGPVKN
FGNEAQKKEFLTPYTDGDKIGCFALSEPGNGSDAAAASTTAKLVGDKWVLNGTKNWITNG
PDASAAIVFATTDKKLKHKGISAFIVERGIPGFSYGKKEDKLGIRGSSTCSLIFDDCAIP
KENILGEEGFGFKIAMKTLDEGRIGIAGQALGIAQASLECAVDYANKRIAFGNPISKMQT
IQNKIADMAMRIEAARLLTWRAAVLKDEGKSITKEAAMAKLAASETATFCSHQAIQILGG
MGYVTDMPAERHYRDARITEIYEGTSEIQRLVIAGQILKQMSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14410.t1 CDD cd01158 SCAD_SBCAD 27 399 0.0
10 g14410.t1 Gene3D G3DSA:1.10.540.10 - 18 140 4.8E-40
11 g14410.t1 Gene3D G3DSA:2.40.110.10 - 141 254 2.4E-44
12 g14410.t1 Gene3D G3DSA:1.20.140.10 - 255 403 9.8E-55
4 g14410.t1 PANTHER PTHR43884:SF26 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN-RELATED 16 401 2.1E-155
5 g14410.t1 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 16 401 2.1E-155
13 g14410.t1 PIRSF PIRSF016578 PIGM 17 132 7.4E-7
14 g14410.t1 PIRSF PIRSF016578 PIGM 149 400 4.4E-13
3 g14410.t1 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 27 138 2.4E-33
1 g14410.t1 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 142 237 1.8E-28
2 g14410.t1 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 251 397 1.4E-49
9 g14410.t1 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 144 156 -
8 g14410.t1 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 356 375 -
6 g14410.t1 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 24 262 5.76E-86
7 g14410.t1 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 247 400 1.59E-59

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