General information for g17272.t3
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.t3 | isoform | g17272.t3 | 12999507 | 13000172 |
| chr_4 | g17272 | g17272.t3 | TTS | g17272.t3 | 12999507 | 12999507 |
| chr_4 | g17272 | g17272.t3 | exon | g17272.t3.exon1 | 12999507 | 13000172 |
| chr_4 | g17272 | g17272.t3 | cds | g17272.t3.CDS1 | 12999580 | 13000137 |
| chr_4 | g17272 | g17272.t3 | TSS | g17272.t3 | NA | NA |
Sequences
>g17272.t3 Gene=g17272 Length=666
GGCCAGGCGTAACTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCAAGTGACACTC
GTGGTATAACATTTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGGTG
CTGGATTTAAAATTGCAATGTCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGGTG
CAACAGGTTTAGCACAGCGAGCCTACGATGAAGCATTAAAATATTCACTTGAACGTAAAA
CTTTTGGTGTTCCAATTGCACAACATCAAGCAATTCAATTTATGCTTGCTGATATGGCAA
TTGGTGTTGAACTGTCAAGACTGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGGAA
GAAGAAATTCATATGAAGCTTCAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAAAA
TTGCAACTGATGCAGTTCAAATATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGTTG
AAAAACTCATGAGAGATGCCAAAATTTACCAAATTTATGAAGGAACATCACAAATTCAAC
GACTGATTATTTCTAGAAATGCTTTTGAACGTGCTAAGGAAATGAATAAGTAAATTTTTT
CCACAAAATTTTTCAAGTTCAATTTTTTAATAAATAAAGAAATTTTTGAATCAAAAGTGA
AATAAA
>g17272.t3 Gene=g17272 Length=185
MGQRASDTRGITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEA
LKYSLERKTFGVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKC
FAADMANKIATDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERA
KEMNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g17272.t3 | Gene3D | G3DSA:2.40.110.10 | - | 1 | 33 | 3.5E-8 |
| 8 | g17272.t3 | Gene3D | G3DSA:1.20.140.10 | - | 34 | 185 | 1.4E-54 |
| 2 | g17272.t3 | PANTHER | PTHR48083 | MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED | 1 | 180 | 1.2E-83 |
| 3 | g17272.t3 | PANTHER | PTHR48083:SF21 | ACYL COA DEHYDROGENASE | 1 | 180 | 1.2E-83 |
| 1 | g17272.t3 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 28 | 176 | 2.4E-51 |
| 6 | g17272.t3 | ProSitePatterns | PS00073 | Acyl-CoA dehydrogenases signature 2. | 135 | 154 | - |
| 4 | g17272.t3 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 1 | 38 | 3.38E-8 |
| 5 | g17272.t3 | SUPERFAMILY | SSF47203 | Acyl-CoA dehydrogenase C-terminal domain-like | 26 | 178 | 1.61E-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.
