General information for g12936.t1
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.t1 | isoform | g12936.t1 | 27007127 | 27009301 |
| chr_1 | g12936 | g12936.t1 | exon | g12936.t1.exon1 | 27007127 | 27008041 |
| chr_1 | g12936 | g12936.t1 | cds | g12936.t1.CDS1 | 27007127 | 27008041 |
| chr_1 | g12936 | g12936.t1 | exon | g12936.t1.exon2 | 27008206 | 27008393 |
| chr_1 | g12936 | g12936.t1 | cds | g12936.t1.CDS2 | 27008206 | 27008393 |
| chr_1 | g12936 | g12936.t1 | exon | g12936.t1.exon3 | 27009094 | 27009199 |
| chr_1 | g12936 | g12936.t1 | cds | g12936.t1.CDS3 | 27009094 | 27009199 |
| chr_1 | g12936 | g12936.t1 | exon | g12936.t1.exon4 | 27009266 | 27009301 |
| chr_1 | g12936 | g12936.t1 | cds | g12936.t1.CDS4 | 27009266 | 27009301 |
| chr_1 | g12936 | g12936.t1 | TSS | g12936.t1 | 27009367 | 27009367 |
| chr_1 | g12936 | g12936.t1 | TTS | g12936.t1 | NA | NA |
Sequences
>g12936.t1 Gene=g12936 Length=1245
ATGAACAGATTGATTACAAAATTACCTATTCGATCGATGATGGGTGCAGCACTCAAAAAC
CAATCAAGAATGATGAGTGGCTCAGTAGGAATTAAGCCATTATTATCGCTTACTGAGGAT
GAATTAGCCATGAAAGAGACAGTCGCAAAATTCGCTCAAGAACAAATTAAGCCGCTTGTT
GCAAAAATGGATGAAGAACATAAGATGGATGAAGGTTTAGTGAGAAAACTTTTTGAAAAT
GGATTTATGGGAATTGAGGCAGATCCAGAATATGGCGGTTCAGGATGTAACTTTTTAACA
ATGATGATCGTTGTTGAAGAACTCAGCAAAGTCGATCCAGCTGTTGCTGCACTCGTTGAT
ATTCACAGTACATTAGTTGTAAATCTATTAAATGATTTGGGAACAAAGGCTCAAAAGGAA
AAGTATTTGACAAAAATTTGCACAGAACACACTGCTAGTTTTGCATTATCAGAACCTTCA
TCAGGATCAGATGCATTTGCATTGAAAACAGCTGCAAAAAAAGATGGAAATCACTACATT
CTTAATGGTACAAAAATGTGGATTTCTAATTCGGATTTATCAGGAACTTTCATTATTATG
GCTAATGCTGATCCTTCAAAGGGTTATAAAGGTATTACAGCATTTATTGTAGAAAGAGAC
ATGGAAGGTTTCACTGTTGGCAAGAAAGAGAAGAAACTTGGAATTTGTGCTTCAGGAACA
TGCATGCTTCATCTTGATAATGTGCGAGTACCAGAAGAAAACATTTTGGGTGAATTTGGA
AAAGGATATGCATATTCAGCATCAATTTTAAATGAAGGCAGAATCGGAATTGCAGCTCAA
ATGGTTGGTTGTGCACAAGGTGCATTTGATGCAACAATGCCATATCTTCTTGAACGAAAA
CAATTTGGTAAAGAAATTTACAGTTTCCAAGGCATGCAATATCAAGTTGCTGAAGTTGCA
TCTGAAATTGAAGCCGCACGTTTAATGTATTACAATGCTGCTCGTATGAAGGAAAATGGA
ATGCCATTCACTAAAGAAGCAGCAATGGCAAAATACATTGCATCAGAAGTTGCTCAAAAA
GCTACTGTCAGATGTGTTGATTGGATGGGTGGTGTCGGATTTACAAAAGATTTCCCACAA
GAAAAATTCTATAGAGACTGTAAGATCGGTGCAATTTATGAGGGCACAAGCAATATGCAA
TTAAGTACAATCGCCAAGCTTTTAAGAAAGGAGTATGAAAGTTAA
>g12936.t1 Gene=g12936 Length=414
MNRLITKLPIRSMMGAALKNQSRMMSGSVGIKPLLSLTEDELAMKETVAKFAQEQIKPLV
AKMDEEHKMDEGLVRKLFENGFMGIEADPEYGGSGCNFLTMMIVVEELSKVDPAVAALVD
IHSTLVVNLLNDLGTKAQKEKYLTKICTEHTASFALSEPSSGSDAFALKTAAKKDGNHYI
LNGTKMWISNSDLSGTFIIMANADPSKGYKGITAFIVERDMEGFTVGKKEKKLGICASGT
CMLHLDNVRVPEENILGEFGKGYAYSASILNEGRIGIAAQMVGCAQGAFDATMPYLLERK
QFGKEIYSFQGMQYQVAEVASEIEAARLMYYNAARMKENGMPFTKEAAMAKYIASEVAQK
ATVRCVDWMGGVGFTKDFPQEKFYRDCKIGAIYEGTSNMQLSTIAKLLRKEYES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g12936.t1 | CDD | cd01158 | SCAD_SBCAD | 39 | 410 | 0.0 |
| 10 | g12936.t1 | Gene3D | G3DSA:1.10.540.10 | - | 34 | 152 | 3.0E-35 |
| 11 | g12936.t1 | Gene3D | G3DSA:2.40.110.10 | - | 153 | 264 | 1.6E-39 |
| 12 | g12936.t1 | Gene3D | G3DSA:1.20.140.10 | - | 265 | 414 | 3.1E-50 |
| 4 | g12936.t1 | PANTHER | PTHR43884:SF1 | SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL | 20 | 412 | 8.6E-189 |
| 5 | g12936.t1 | PANTHER | PTHR43884 | ACYL-COA DEHYDROGENASE | 20 | 412 | 8.6E-189 |
| 13 | g12936.t1 | PIRSF | PIRSF016578 | PIGM | 35 | 411 | 4.5E-24 |
| 3 | g12936.t1 | Pfam | PF02771 | Acyl-CoA dehydrogenase, N-terminal domain | 38 | 148 | 3.8E-29 |
| 1 | g12936.t1 | Pfam | PF02770 | Acyl-CoA dehydrogenase, middle domain | 153 | 248 | 3.2E-25 |
| 2 | g12936.t1 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 260 | 406 | 5.4E-43 |
| 9 | g12936.t1 | ProSitePatterns | PS00072 | Acyl-CoA dehydrogenases signature 1. | 155 | 167 | - |
| 8 | g12936.t1 | ProSitePatterns | PS00073 | Acyl-CoA dehydrogenases signature 2. | 367 | 386 | - |
| 6 | g12936.t1 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 36 | 273 | 1.96E-74 |
| 7 | g12936.t1 | SUPERFAMILY | SSF47203 | Acyl-CoA dehydrogenase C-terminal domain-like | 258 | 412 | 1.93E-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 transcript has been annotated with K09478 (short-chain 2-methylacyl-CoA dehydrogenase)
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.
