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.t6 isoform g12936.t6 27006842 27008215
chr_1 g12936 g12936.t6 exon g12936.t6.exon1 27006842 27006867
chr_1 g12936 g12936.t6 exon g12936.t6.exon2 27006963 27008041
chr_1 g12936 g12936.t6 cds g12936.t6.CDS1 27007127 27007816
chr_1 g12936 g12936.t6 exon g12936.t6.exon3 27008206 27008215
chr_1 g12936 g12936.t6 TSS g12936.t6 NA NA
chr_1 g12936 g12936.t6 TTS g12936.t6 NA NA

Sequences

>g12936.t6 Gene=g12936 Length=1115
ACTCAGCAAAGTCGATCCAGCTGTTGCTGCACTCGTTGATATTCACAGTACATTAGTTGT
AAATCTATTAAATGATTTGGGAACAAAGGCTCAAAAGGAAAAGTATTTGACAAAAATTTG
CACAGAACACACTGCTAGTTTTGCATTATCAGAACCTTCATCAGGATCAGATGCATTTGC
ATTGAAAACAGCTGCAAAAAAAGATGGAAATCACTACATTCTTAATGGTACAAAAATGTG
GATTTCTAATTCGGATTTATCAGGAACTTTCATTATTATGGCTAATGCTGATCCTTCAAA
GGGTTATAAAGGTATTACAGCATTTATTGTAGAAAGAGACATGGAAGGTTTCACTGTTGG
CAAGAAAGAGAAGAAACTTGGAATTTGTGCTTCAGGAACATGCATGCTTCATCTTGATAA
TGTGCGAGTACCAGAAGAAAACATTTTGGGTGAATTTGGAAAAGGATATGCATATTCAGC
ATCAATTTTAAATGAAGGCAGAATCGGAATTGCAGCTCAAATGGTTGGTTGTGCACAAGG
TGCATTTGATGCAACAATGCCATATCTTCTTGAACGAAAACAATTTGGTAAAGAAATTTA
CAGTTTCCAAGGCATGCAATATCAAGTTGCTGAAGTTGCATCTGAAATTGAAGCCGCACG
TTTAATGTATTACAATGCTGCTCGTATGAAGGAAAATGGAATGCCATTCACTAAAGAAGC
AGCAATGGCAAAATACATTGCATCAGAAGTTGCTCAAAAAGCTACTGTCAGATGTGTTGA
TTGGATGGGTGGTGTCGGATTTACAAAAGATTTCCCACAAGAAAAATTCTATAGAGACTG
TAAGATCGGTGCAATTTATGAGGGCACAAGCAATATGCAATTAAGTACAATCGCCAAGCT
TTTAAGAAAGGAGTATGAAAGTTAAATGAATATTTTTAACAAAACCTGATAAAAGTGCAT
TTAAATTGGATGCTTGTTTATGCATTCAATTCTTTTCATTACTATAAAAGTCTGTAAAAC
ATATTTTACTATGATATTTTTGTGTCCGTTTTCTTATTGTACTTTGAGTTTAAATAAAAT
TAGTCCCGATACTTTGATAAAAGCCATAAAAGTCC

>g12936.t6 Gene=g12936 Length=229
MWISNSDLSGTFIIMANADPSKGYKGITAFIVERDMEGFTVGKKEKKLGICASGTCMLHL
DNVRVPEENILGEFGKGYAYSASILNEGRIGIAAQMVGCAQGAFDATMPYLLERKQFGKE
IYSFQGMQYQVAEVASEIEAARLMYYNAARMKENGMPFTKEAAMAKYIASEVAQKATVRC
VDWMGGVGFTKDFPQEKFYRDCKIGAIYEGTSNMQLSTIAKLLRKEYES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12936.t6 Gene3D G3DSA:2.40.110.10 - 1 78 1.2E-22
9 g12936.t6 Gene3D G3DSA:1.20.140.10 - 79 229 6.9E-51
3 g12936.t6 PANTHER PTHR43884:SF1 SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 1 227 9.2E-118
4 g12936.t6 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 1 227 9.2E-118
1 g12936.t6 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 1 63 1.2E-10
2 g12936.t6 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 75 221 1.2E-43
7 g12936.t6 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 182 201 -
5 g12936.t6 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 1 88 5.37E-27
6 g12936.t6 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 73 227 4.19E-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: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