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.t11 isoform g12936.t11 27006968 27008395
chr_1 g12936 g12936.t11 exon g12936.t11.exon1 27006968 27007731
chr_1 g12936 g12936.t11 cds g12936.t11.CDS1 27007127 27007731
chr_1 g12936 g12936.t11 exon g12936.t11.exon2 27008005 27008041
chr_1 g12936 g12936.t11 cds g12936.t11.CDS2 27008005 27008041
chr_1 g12936 g12936.t11 exon g12936.t11.exon3 27008206 27008395
chr_1 g12936 g12936.t11 cds g12936.t11.CDS3 27008206 27008349
chr_1 g12936 g12936.t11 TSS g12936.t11 27009367 27009367
chr_1 g12936 g12936.t11 TTS g12936.t11 NA NA

Sequences

>g12936.t11 Gene=g12936 Length=991
AGTCGCAAAATTCGCTCAAGAACAAATTAAGCCGCTTGTTGCAAAAATGGATGAAGAACA
TAAGATGGATGAAGGTTTAGTGAGAAAACTTTTTGAAAATGGATTTATGGGAATTGAGGC
AGATCCAGAATATGGCGGTTCAGGATGTAACTTTTTAACAATGATGATCGTTGTTGAAGA
ACTCAGCAAAGTCGATCCAGCTGTTGCTGCACTCGTTGATATTCACACATTTATTGTAGA
AAGAGACATGGAAGGTTTCACTGTTGGCAAGAAAGAGAAGAAACTTGGAATTTGTGCTTC
AGGAACATGCATGCTTCATCTTGATAATGTGCGAGTACCAGAAGAAAACATTTTGGGTGA
ATTTGGAAAAGGATATGCATATTCAGCATCAATTTTAAATGAAGGCAGAATCGGAATTGC
AGCTCAAATGGTTGGTTGTGCACAAGGTGCATTTGATGCAACAATGCCATATCTTCTTGA
ACGAAAACAATTTGGTAAAGAAATTTACAGTTTCCAAGGCATGCAATATCAAGTTGCTGA
AGTTGCATCTGAAATTGAAGCCGCACGTTTAATGTATTACAATGCTGCTCGTATGAAGGA
AAATGGAATGCCATTCACTAAAGAAGCAGCAATGGCAAAATACATTGCATCAGAAGTTGC
TCAAAAAGCTACTGTCAGATGTGTTGATTGGATGGGTGGTGTCGGATTTACAAAAGATTT
CCCACAAGAAAAATTCTATAGAGACTGTAAGATCGGTGCAATTTATGAGGGCACAAGCAA
TATGCAATTAAGTACAATCGCCAAGCTTTTAAGAAAGGAGTATGAAAGTTAAATGAATAT
TTTTAACAAAACCTGATAAAAGTGCATTTAAATTGGATGCTTGTTTATGCATTCAATTCT
TTTCATTACTATAAAAGTCTGTAAAACATATTTTACTATGATATTTTTGTGTCCGTTTTC
TTATTGTACTTTGAGTTTAAATAAAATTAGT

>g12936.t11 Gene=g12936 Length=261
MDEEHKMDEGLVRKLFENGFMGIEADPEYGGSGCNFLTMMIVVEELSKVDPAVAALVDIH
TFIVERDMEGFTVGKKEKKLGICASGTCMLHLDNVRVPEENILGEFGKGYAYSASILNEG
RIGIAAQMVGCAQGAFDATMPYLLERKQFGKEIYSFQGMQYQVAEVASEIEAARLMYYNA
ARMKENGMPFTKEAAMAKYIASEVAQKATVRCVDWMGGVGFTKDFPQEKFYRDCKIGAIY
EGTSNMQLSTIAKLLRKEYES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12936.t11 Gene3D G3DSA:1.10.540.10 - 1 83 4.3E-17
11 g12936.t11 Gene3D G3DSA:1.20.140.10 - 85 259 1.0E-53
3 g12936.t11 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 1 60 1.2E-120
5 g12936.t11 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 1 60 1.2E-120
4 g12936.t11 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 59 259 1.2E-120
6 g12936.t11 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 59 259 1.2E-120
2 g12936.t11 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 2 64 2.0E-12
1 g12936.t11 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 107 253 1.8E-43
9 g12936.t11 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 214 233 -
7 g12936.t11 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 2 107 8.07E-22
8 g12936.t11 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 105 259 6.28E-51

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