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 g12936 g12936.t13 isoform g12936.t13 27006968 27009301
chr_1 g12936 g12936.t13 exon g12936.t13.exon1 27006968 27007656
chr_1 g12936 g12936.t13 cds g12936.t13.CDS1 27007127 27007656
chr_1 g12936 g12936.t13 exon g12936.t13.exon2 27007741 27008041
chr_1 g12936 g12936.t13 cds g12936.t13.CDS2 27007741 27008041
chr_1 g12936 g12936.t13 exon g12936.t13.exon3 27008206 27008393
chr_1 g12936 g12936.t13 cds g12936.t13.CDS3 27008206 27008393
chr_1 g12936 g12936.t13 exon g12936.t13.exon4 27009094 27009199
chr_1 g12936 g12936.t13 cds g12936.t13.CDS4 27009094 27009199
chr_1 g12936 g12936.t13 exon g12936.t13.exon5 27009266 27009301
chr_1 g12936 g12936.t13 cds g12936.t13.CDS5 27009266 27009301
chr_1 g12936 g12936.t13 TSS g12936.t13 27009367 27009367
chr_1 g12936 g12936.t13 TTS g12936.t13 NA NA

Sequences

>g12936.t13 Gene=g12936 Length=1320
ATGAACAGATTGATTACAAAATTACCTATTCGATCGATGATGGGTGCAGCACTCAAAAAC
CAATCAAGAATGATGAGTGGCTCAGTAGGAATTAAGCCATTATTATCGCTTACTGAGGAT
GAATTAGCCATGAAAGAGACAGTCGCAAAATTCGCTCAAGAACAAATTAAGCCGCTTGTT
GCAAAAATGGATGAAGAACATAAGATGGATGAAGGTTTAGTGAGAAAACTTTTTGAAAAT
GGATTTATGGGAATTGAGGCAGATCCAGAATATGGCGGTTCAGGATGTAACTTTTTAACA
ATGATGATCGTTGTTGAAGAACTCAGCAAAGTCGATCCAGCTGTTGCTGCACTCGTTGAT
ATTCACAGTACATTAGTTGTAAATCTATTAAATGATTTGGGAACAAAGGCTCAAAAGGAA
AAGTATTTGACAAAAATTTGCACAGAACACACTGCTAGTTTTGCATTATCAGAACCTTCA
TCAGGATCAGATGCATTTGCATTGAAAACAGCTGCAAAAAAAGATGGAAATCACTACATT
CTTAATGGTACAAAAATGTGGATTTCTAATTCGGATTTATCAGGAACTTTCATTATTATG
GCTAATGCTGATCCTTCAAAGGGTTATAAAGGAACATGCATGCTTCATCTTGATAATGTG
CGAGTACCAGAAGAAAACATTTTGGGTGAATTTGGAAAAGGATATGCATATTCAGCATCA
ATTTTAAATGAAGGCAGAATCGGAATTGCAGCTCAAATGGTTGGTTGTGCACAAGGTGCA
TTTGATGCAACAATGCCATATCTTCTTGAACGAAAACAATTTGGTAAAGAAATTTACAGT
TTCCAAGGCATGCAATATCAAGTTGCTGAAGTTGCATCTGAAATTGAAGCCGCACGTTTA
ATGTATTACAATGCTGCTCGTATGAAGGAAAATGGAATGCCATTCACTAAAGAAGCAGCA
ATGGCAAAATACATTGCATCAGAAGTTGCTCAAAAAGCTACTGTCAGATGTGTTGATTGG
ATGGGTGGTGTCGGATTTACAAAAGATTTCCCACAAGAAAAATTCTATAGAGACTGTAAG
ATCGGTGCAATTTATGAGGGCACAAGCAATATGCAATTAAGTACAATCGCCAAGCTTTTA
AGAAAGGAGTATGAAAGTTAAATGAATATTTTTAACAAAACCTGATAAAAGTGCATTTAA
ATTGGATGCTTGTTTATGCATTCAATTCTTTTCATTACTATAAAAGTCTGTAAAACATAT
TTTACTATGATATTTTTGTGTCCGTTTTCTTATTGTACTTTGAGTTTAAATAAAATTAGT

>g12936.t13 Gene=g12936 Length=386
MNRLITKLPIRSMMGAALKNQSRMMSGSVGIKPLLSLTEDELAMKETVAKFAQEQIKPLV
AKMDEEHKMDEGLVRKLFENGFMGIEADPEYGGSGCNFLTMMIVVEELSKVDPAVAALVD
IHSTLVVNLLNDLGTKAQKEKYLTKICTEHTASFALSEPSSGSDAFALKTAAKKDGNHYI
LNGTKMWISNSDLSGTFIIMANADPSKGYKGTCMLHLDNVRVPEENILGEFGKGYAYSAS
ILNEGRIGIAAQMVGCAQGAFDATMPYLLERKQFGKEIYSFQGMQYQVAEVASEIEAARL
MYYNAARMKENGMPFTKEAAMAKYIASEVAQKATVRCVDWMGGVGFTKDFPQEKFYRDCK
IGAIYEGTSNMQLSTIAKLLRKEYES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g12936.t13 Gene3D G3DSA:1.10.540.10 - 34 152 2.7E-35
13 g12936.t13 Gene3D G3DSA:2.40.110.10 - 153 213 6.7E-19
14 g12936.t13 Gene3D G3DSA:1.20.140.10 - 214 384 3.2E-53
4 g12936.t13 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 20 213 1.9E-165
6 g12936.t13 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 20 213 1.9E-165
5 g12936.t13 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 212 384 1.9E-165
7 g12936.t13 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 212 384 1.9E-165
16 g12936.t13 PIRSF PIRSF016578 PIGM 35 227 2.8E-7
15 g12936.t13 PIRSF PIRSF016578 PIGM 211 383 1.4E-10
3 g12936.t13 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 38 148 3.3E-29
1 g12936.t13 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 153 215 6.3E-14
2 g12936.t13 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 232 378 4.7E-43
11 g12936.t13 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 155 167 -
10 g12936.t13 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 339 358 -
8 g12936.t13 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 36 245 4.97E-59
9 g12936.t13 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 230 384 1.61E-50

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