General information for g12936.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial.
Parent gene
- The parent gene g12936 is located on chr_1: 27007515..27009301 (- strand)
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.t17 | isoform | g12936.t17 | 27007127 | 27009301 |
| chr_1 | g12936 | g12936.t17 | exon | g12936.t17.exon1 | 27007127 | 27008153 |
| chr_1 | g12936 | g12936.t17 | cds | g12936.t17.CDS1 | 27007127 | 27007816 |
| chr_1 | g12936 | g12936.t17 | exon | g12936.t17.exon2 | 27009094 | 27009199 |
| chr_1 | g12936 | g12936.t17 | exon | g12936.t17.exon3 | 27009266 | 27009301 |
| chr_1 | g12936 | g12936.t17 | TSS | g12936.t17 | 27009367 | 27009367 |
| chr_1 | g12936 | g12936.t17 | TTS | g12936.t17 | NA | NA |
Sequences
>g12936.t17 Gene=g12936 Length=1169
ATGAACAGATTGATTACAAAATTACCTATTCGATCGATGATGGGTGCAGCACTCAAAAAC
CAATCAAGAATGATGAGTGGCTCAGTAGGAATTAAGCCATTATTATCGCTTACTGAGGAT
GAATTAGCCATGAAAGAGACAGAAGTCTTAAATTCAAGGTTGAATGTTAGTTAATTGATG
TTCGCATGTAGTTTGACATATACATGCATATGTATTGTTTAGTTTAATAATAATGATTTT
TTAATGAAAAACAGGTCGATCCAGCTGTTGCTGCACTCGTTGATATTCACAGTACATTAG
TTGTAAATCTATTAAATGATTTGGGAACAAAGGCTCAAAAGGAAAAGTATTTGACAAAAA
TTTGCACAGAACACACTGCTAGTTTTGCATTATCAGAACCTTCATCAGGATCAGATGCAT
TTGCATTGAAAACAGCTGCAAAAAAAGATGGAAATCACTACATTCTTAATGGTACAAAAA
TGTGGATTTCTAATTCGGATTTATCAGGAACTTTCATTATTATGGCTAATGCTGATCCTT
CAAAGGGTTATAAAGGTATTACAGCATTTATTGTAGAAAGAGACATGGAAGGTTTCACTG
TTGGCAAGAAAGAGAAGAAACTTGGAATTTGTGCTTCAGGAACATGCATGCTTCATCTTG
ATAATGTGCGAGTACCAGAAGAAAACATTTTGGGTGAATTTGGAAAAGGATATGCATATT
CAGCATCAATTTTAAATGAAGGCAGAATCGGAATTGCAGCTCAAATGGTTGGTTGTGCAC
AAGGTGCATTTGATGCAACAATGCCATATCTTCTTGAACGAAAACAATTTGGTAAAGAAA
TTTACAGTTTCCAAGGCATGCAATATCAAGTTGCTGAAGTTGCATCTGAAATTGAAGCCG
CACGTTTAATGTATTACAATGCTGCTCGTATGAAGGAAAATGGAATGCCATTCACTAAAG
AAGCAGCAATGGCAAAATACATTGCATCAGAAGTTGCTCAAAAAGCTACTGTCAGATGTG
TTGATTGGATGGGTGGTGTCGGATTTACAAAAGATTTCCCACAAGAAAAATTCTATAGAG
ACTGTAAGATCGGTGCAATTTATGAGGGCACAAGCAATATGCAATTAAGTACAATCGCCA
AGCTTTTAAGAAAGGAGTATGAAAGTTAA
>g12936.t17 Gene=g12936 Length=229
MWISNSDLSGTFIIMANADPSKGYKGITAFIVERDMEGFTVGKKEKKLGICASGTCMLHL
DNVRVPEENILGEFGKGYAYSASILNEGRIGIAAQMVGCAQGAFDATMPYLLERKQFGKE
IYSFQGMQYQVAEVASEIEAARLMYYNAARMKENGMPFTKEAAMAKYIASEVAQKATVRC
VDWMGGVGFTKDFPQEKFYRDCKIGAIYEGTSNMQLSTIAKLLRKEYES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12936.t17 | Gene3D | G3DSA:2.40.110.10 | - | 1 | 78 | 1.2E-22 |
| 9 | g12936.t17 | Gene3D | G3DSA:1.20.140.10 | - | 79 | 229 | 6.9E-51 |
| 3 | g12936.t17 | PANTHER | PTHR43884:SF1 | SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL | 1 | 227 | 9.2E-118 |
| 4 | g12936.t17 | PANTHER | PTHR43884 | ACYL-COA DEHYDROGENASE | 1 | 227 | 9.2E-118 |
| 1 | g12936.t17 | Pfam | PF02770 | Acyl-CoA dehydrogenase, middle domain | 1 | 63 | 1.2E-10 |
| 2 | g12936.t17 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 75 | 221 | 1.2E-43 |
| 7 | g12936.t17 | ProSitePatterns | PS00073 | Acyl-CoA dehydrogenases signature 2. | 182 | 201 | - |
| 5 | g12936.t17 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 1 | 88 | 5.37E-27 |
| 6 | g12936.t17 | 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. There were no conditions that were differentially expressed