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.t18 isoform g12936.t18 27007127 27009301
chr_1 g12936 g12936.t18 exon g12936.t18.exon1 27007127 27008041
chr_1 g12936 g12936.t18 cds g12936.t18.CDS1 27007127 27008041
chr_1 g12936 g12936.t18 exon g12936.t18.exon2 27008224 27008393
chr_1 g12936 g12936.t18 cds g12936.t18.CDS2 27008224 27008393
chr_1 g12936 g12936.t18 exon g12936.t18.exon3 27009094 27009301
chr_1 g12936 g12936.t18 cds g12936.t18.CDS3 27009094 27009199
chr_1 g12936 g12936.t18 TSS g12936.t18 27009367 27009367
chr_1 g12936 g12936.t18 TTS g12936.t18 NA NA

Sequences

>g12936.t18 Gene=g12936 Length=1293
ATGAACAGATTGATTACAAAATTACCTATTCGATCGGTAAGAATAAGAAGAACTAGAAAA
CATAGAAAAATGAAAAATTCAACATTAATCATTTAAATATAGATGATGGGTGCAGCACTC
AAAAACCAATCAAGAATGATGAGTGGCTCAGTAGGAATTAAGCCATTATTATCGCTTACT
GAGGATGAATTAGCCATGAAAGAGACAGTCGCAAAATTCGCTCAAGAACAAATTAAGCCG
CTTGTTGCAAAAATGGATGAAGAACATAAGATGGATGAAGGTTTAGTGAGAAAACTTTTT
GAAAATGGATTTATGGGAATTGAGGCAGATCCAGAATATGGCGGTTCAGGATGTAACTTT
TTAACAATGATGATCGTTGTCGATCCAGCTGTTGCTGCACTCGTTGATATTCACAGTACA
TTAGTTGTAAATCTATTAAATGATTTGGGAACAAAGGCTCAAAAGGAAAAGTATTTGACA
AAAATTTGCACAGAACACACTGCTAGTTTTGCATTATCAGAACCTTCATCAGGATCAGAT
GCATTTGCATTGAAAACAGCTGCAAAAAAAGATGGAAATCACTACATTCTTAATGGTACA
AAAATGTGGATTTCTAATTCGGATTTATCAGGAACTTTCATTATTATGGCTAATGCTGAT
CCTTCAAAGGGTTATAAAGGTATTACAGCATTTATTGTAGAAAGAGACATGGAAGGTTTC
ACTGTTGGCAAGAAAGAGAAGAAACTTGGAATTTGTGCTTCAGGAACATGCATGCTTCAT
CTTGATAATGTGCGAGTACCAGAAGAAAACATTTTGGGTGAATTTGGAAAAGGATATGCA
TATTCAGCATCAATTTTAAATGAAGGCAGAATCGGAATTGCAGCTCAAATGGTTGGTTGT
GCACAAGGTGCATTTGATGCAACAATGCCATATCTTCTTGAACGAAAACAATTTGGTAAA
GAAATTTACAGTTTCCAAGGCATGCAATATCAAGTTGCTGAAGTTGCATCTGAAATTGAA
GCCGCACGTTTAATGTATTACAATGCTGCTCGTATGAAGGAAAATGGAATGCCATTCACT
AAAGAAGCAGCAATGGCAAAATACATTGCATCAGAAGTTGCTCAAAAAGCTACTGTCAGA
TGTGTTGATTGGATGGGTGGTGTCGGATTTACAAAAGATTTCCCACAAGAAAAATTCTAT
AGAGACTGTAAGATCGGTGCAATTTATGAGGGCACAAGCAATATGCAATTAAGTACAATC
GCCAAGCTTTTAAGAAAGGAGTATGAAAGTTAA

>g12936.t18 Gene=g12936 Length=396
MMGAALKNQSRMMSGSVGIKPLLSLTEDELAMKETVAKFAQEQIKPLVAKMDEEHKMDEG
LVRKLFENGFMGIEADPEYGGSGCNFLTMMIVVDPAVAALVDIHSTLVVNLLNDLGTKAQ
KEKYLTKICTEHTASFALSEPSSGSDAFALKTAAKKDGNHYILNGTKMWISNSDLSGTFI
IMANADPSKGYKGITAFIVERDMEGFTVGKKEKKLGICASGTCMLHLDNVRVPEENILGE
FGKGYAYSASILNEGRIGIAAQMVGCAQGAFDATMPYLLERKQFGKEIYSFQGMQYQVAE
VASEIEAARLMYYNAARMKENGMPFTKEAAMAKYIASEVAQKATVRCVDWMGGVGFTKDF
PQEKFYRDCKIGAIYEGTSNMQLSTIAKLLRKEYES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12936.t18 CDD cd01158 SCAD_SBCAD 27 392 0.0
10 g12936.t18 Gene3D G3DSA:1.10.540.10 - 22 134 1.9E-27
11 g12936.t18 Gene3D G3DSA:2.40.110.10 - 135 246 1.5E-39
12 g12936.t18 Gene3D G3DSA:1.20.140.10 - 247 396 2.8E-50
4 g12936.t18 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 8 394 6.7E-182
5 g12936.t18 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 8 394 6.7E-182
14 g12936.t18 PIRSF PIRSF016578 PIGM 23 102 0.18
13 g12936.t18 PIRSF PIRSF016578 PIGM 136 393 4.4E-18
3 g12936.t18 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 26 130 6.4E-22
1 g12936.t18 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 135 230 2.9E-25
2 g12936.t18 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 242 388 4.9E-43
9 g12936.t18 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 137 149 -
8 g12936.t18 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 349 368 -
6 g12936.t18 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 24 255 2.49E-70
7 g12936.t18 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 240 394 1.77E-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

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