General information for g17272.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable medium-chain specific acyl-CoA dehydrogenase, mitochondrial.
Parent gene
- The parent gene g17272 is located on chr_4: 13000759..13006689 (- 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_4 | g17272 | g17272.t10 | TTS | g17272.t10 | 12999507 | 12999507 |
| chr_4 | g17272 | g17272.t10 | isoform | g17272.t10 | 12999580 | 13002602 |
| chr_4 | g17272 | g17272.t10 | exon | g17272.t10.exon1 | 12999580 | 13000179 |
| chr_4 | g17272 | g17272.t10 | cds | g17272.t10.CDS1 | 12999580 | 13000179 |
| chr_4 | g17272 | g17272.t10 | exon | g17272.t10.exon2 | 13000490 | 13000827 |
| chr_4 | g17272 | g17272.t10 | cds | g17272.t10.CDS2 | 13000490 | 13000597 |
| chr_4 | g17272 | g17272.t10 | exon | g17272.t10.exon3 | 13000919 | 13001185 |
| chr_4 | g17272 | g17272.t10 | exon | g17272.t10.exon4 | 13002588 | 13002602 |
| chr_4 | g17272 | g17272.t10 | TSS | g17272.t10 | 13002690 | 13002690 |
Sequences
>g17272.t10 Gene=g17272 Length=1220
ATGGCACTTTCTAAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAATC
ACACCAAGATTATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGAA
ATTCAAGCAACAGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCAT
GACAGAACTGGAGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCTG
AATCACTCAATTCCTGAACATTGTGGTGGTCACAAATTGTCGCTTATGGTTGCACTGGTA
TTGAAACGGCTATGGAAGGATCTGGTCTAGGTCAGACTCCCGTAGTTTTAGCTGGTAACA
AGGAACAACAAAAGAAATACCTTGGACGTCTTGTTGAACAACCATTAGTTGCAGCTTATT
GCGTTACAGAACCATCAGCTGGTTCAGATGTTAATGGAATTAAATCAAAAGCTGTCAAAA
AAGGCGACGAATATATTTTGAATGGACAAAAAATGTGGATCACAAATGGTGGTGTTGCCA
ATTGGTATTTTGTACTTGCAAGAACAGCCGAAGATCCCAAAGCACCTGCATCAAAAGCTT
TTACTGGATTTATTGTTGAGCGTGAATGGCCAGGCGTAACTCTTGGACGTAAAGAAATCA
ACATGGGACAACGTGCAAGTGACACTCGTGGTATAACATTTGAAGATGTTCGAATTCCAA
AAGAAAATGTTTTACTCGGTGAAGGTGCTGGATTTAAAATTGCAATGTCAACATTTGACC
TCACTCGACCACCAGTTGCTGCAGGTGCAACAGGTTTAGCACAGCGAGCCTACGATGAAG
CATTAAAATATTCACTTGAACGTAAAACTTTTGGTGTTCCAATTGCACAACATCAAGCAA
TTCAATTTATGCTTGCTGATATGGCAATTGGTGTTGAACTGTCAAGACTGAGTTGGTGGA
GAGCTGCTTGGGAGGTGGACCAAGGAAGAAGAAATTCATATGAAGCTTCAATTTCAAAAT
GTTTTGCTGCTGACATGGCTAATAAAATTGCAACTGATGCAGTTCAAATATTTGGTGGAA
ATGGTTTCAATTCAGAATATCCAGTTGAAAAACTCATGAGAGATGCCAAAATTTACCAAA
TTTATGAAGGAACATCACAAATTCAACGACTGATTATTTCTAGAAATGCTTTTGAACGTG
CTAAGGAAATGAATAAGTAA
>g17272.t10 Gene=g17272 Length=235
MWITNGGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQRASDTRG
ITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEALKYSLERKTF
GVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKCFAADMANKIA
TDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERAKEMNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g17272.t10 | Gene3D | G3DSA:2.40.110.10 | - | 1 | 83 | 1.5E-26 |
| 9 | g17272.t10 | Gene3D | G3DSA:1.20.140.10 | - | 84 | 235 | 3.0E-54 |
| 3 | g17272.t10 | PANTHER | PTHR48083 | MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED | 2 | 230 | 1.4E-107 |
| 4 | g17272.t10 | PANTHER | PTHR48083:SF21 | ACYL COA DEHYDROGENASE | 2 | 230 | 1.4E-107 |
| 1 | g17272.t10 | Pfam | PF02770 | Acyl-CoA dehydrogenase, middle domain | 1 | 66 | 1.1E-10 |
| 2 | g17272.t10 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 78 | 226 | 5.1E-51 |
| 7 | g17272.t10 | ProSitePatterns | PS00073 | Acyl-CoA dehydrogenases signature 2. | 185 | 204 | - |
| 5 | g17272.t10 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 1 | 89 | 6.15E-27 |
| 6 | g17272.t10 | SUPERFAMILY | SSF47203 | Acyl-CoA dehydrogenase C-terminal domain-like | 76 | 228 | 3.54E-57 |
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.
