Gene loci information

Transcript annotation

  • This transcript has been annotated as Short/branched 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_1 g12935 g12935.t20 TTS g12935.t20 27004441 27004441
chr_1 g12935 g12935.t20 isoform g12935.t20 27004491 27005877
chr_1 g12935 g12935.t20 exon g12935.t20.exon1 27004491 27005083
chr_1 g12935 g12935.t20 cds g12935.t20.CDS1 27004491 27005083
chr_1 g12935 g12935.t20 exon g12935.t20.exon2 27005474 27005593
chr_1 g12935 g12935.t20 cds g12935.t20.CDS2 27005474 27005593
chr_1 g12935 g12935.t20 exon g12935.t20.exon3 27005687 27005780
chr_1 g12935 g12935.t20 cds g12935.t20.CDS3 27005687 27005780
chr_1 g12935 g12935.t20 exon g12935.t20.exon4 27005842 27005877
chr_1 g12935 g12935.t20 cds g12935.t20.CDS4 27005842 27005877
chr_1 g12935 g12935.t20 TSS g12935.t20 27005976 27005976

Sequences

>g12935.t20 Gene=g12935 Length=843
ATGAATTACTTAAGGAAACTATCAGCTATCAATCATATAACGCGAGCATTATCAATAACA
TCGCGAAAAAATTCACATTTTTCACCGTTAACAGTTTTATCAGACGATGAACTTATGATG
AAAGAGACATTTGCCAAGTTTGCAAGGGAAAAAATTGCACCAAAAGTCAGAGAAATGGAA
CAAAACCATAAACAAGATCCAGAAATCATTAAAGGATTATTTGAAAATGGTTTTATGGGA
ATTGAAATTGAGAAGAATATGGAAGGCTTATCGATTGGCAAAAAGGAAGATAAATTAGGA
TTAGTTGCTTCAGGAACATGCATGATTCATCTTGATAATGTGCGAGTGCCAGAAGAAAAC
ATTTTGGGTGAATTTGGAAAAGGATATGCATATGCTGCAGGTTTTTTAAATGAAGGCAGA
ATCGGAATTGGTGCTCAAATGGTTGGTTGTGCACAAGGTGCATTTGATGCTACTATCCCA
TATCTTCTTGAGCGTAAACAATTTGGACAAAACATTTACGATTTTCAAGGAATGCAATTT
CAAATTGCTGAAGTCGCAACACAAATTGAAGCAGGAAGATTATTAACTTATAATGCAGCT
CGCTTGCAAGAAGCAGGTAAACCATTTTTAAAAGAGGCAGCAATGGCAAAACTCTTTTGC
TCAAGAATGGCACAATTTGTTAGCAGTCAATGTGTTGATTGGATGGGTGGTGTCGGATTT
ACAAAAGATTTTCCACAAGAGAAATTTTACAGAGATTCCAAAGCTAGTACAATTTATGAG
GGTACAAGTAATATTCAAATGAGTACAATTGCTAAAATTATTAGAAAAGAATATTCTTCA
TGA

>g12935.t20 Gene=g12935 Length=280
MNYLRKLSAINHITRALSITSRKNSHFSPLTVLSDDELMMKETFAKFAREKIAPKVREME
QNHKQDPEIIKGLFENGFMGIEIEKNMEGLSIGKKEDKLGLVASGTCMIHLDNVRVPEEN
ILGEFGKGYAYAAGFLNEGRIGIGAQMVGCAQGAFDATIPYLLERKQFGQNIYDFQGMQF
QIAEVATQIEAGRLLTYNAARLQEAGKPFLKEAAMAKLFCSRMAQFVSSQCVDWMGGVGF
TKDFPQEKFYRDSKASTIYEGTSNIQMSTIAKIIRKEYSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12935.t20 Gene3D G3DSA:1.10.540.10 - 29 94 1.4E-12
12 g12935.t20 Gene3D G3DSA:1.20.140.10 - 104 277 2.9E-55
4 g12935.t20 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 17 86 1.1E-117
6 g12935.t20 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 17 86 1.1E-117
3 g12935.t20 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 84 278 1.1E-117
5 g12935.t20 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 84 278 1.1E-117
2 g12935.t20 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 34 92 6.4E-8
1 g12935.t20 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 126 272 2.3E-46
10 g12935.t20 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 233 252 -
8 g12935.t20 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 32 89 9.73E-7
7 g12935.t20 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 83 139 2.62E-15
9 g12935.t20 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 124 278 1.93E-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. There were no conditions that were differentially expressed