General information for g17272.t1
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.t1 | TTS | g17272.t1 | 12999507 | 12999507 |
| chr_4 | g17272 | g17272.t1 | isoform | g17272.t1 | 12999580 | 13002602 |
| chr_4 | g17272 | g17272.t1 | exon | g17272.t1.exon1 | 12999580 | 13000179 |
| chr_4 | g17272 | g17272.t1 | cds | g17272.t1.CDS1 | 12999580 | 13000179 |
| chr_4 | g17272 | g17272.t1 | exon | g17272.t1.exon2 | 13000490 | 13000827 |
| chr_4 | g17272 | g17272.t1 | cds | g17272.t1.CDS2 | 13000490 | 13000827 |
| chr_4 | g17272 | g17272.t1 | exon | g17272.t1.exon3 | 13000885 | 13001185 |
| chr_4 | g17272 | g17272.t1 | cds | g17272.t1.CDS3 | 13000885 | 13001185 |
| chr_4 | g17272 | g17272.t1 | exon | g17272.t1.exon4 | 13002588 | 13002602 |
| chr_4 | g17272 | g17272.t1 | cds | g17272.t1.CDS4 | 13002588 | 13002602 |
| chr_4 | g17272 | g17272.t1 | TSS | g17272.t1 | 13002690 | 13002690 |
Sequences
>g17272.t1 Gene=g17272 Length=1254
ATGGCACTTTCTAAGATTTCATCATTAATTCGCCCATTTGGATCACGAGCATTTTCAATC
ACACCAAGATTATGTAATGAATCTGGACCATCATTTGCTCTTTCTGAAGAACAACGTGAA
ATTCAAGCAACAGCAAGAAAATTTACTCGTGAAGAAATCATTCCAGTTGCAGCACATCAT
GACAGAACTGGAGAATATCCATGGGCAATTATCAAGAAAGCTTGGGAACTTGGATTGCTG
AATCACTCAATTCCTGAACATTGTGGTGGTCACAAATTGTCGACTTTTACGACTTGTTTA
ATTGCTGAAGAATTAGCTTATGGTTGCACTGGTATTGAAACGGCTATGGAAGGATCTGGT
CTAGGTCAGACTCCCGTAGTTTTAGCTGGTAACAAGGAACAACAAAAGAAATACCTTGGA
CGTCTTGTTGAACAACCATTAGTTGCAGCTTATTGCGTTACAGAACCATCAGCTGGTTCA
GATGTTAATGGAATTAAATCAAAAGCTGTCAAAAAAGGCGACGAATATATTTTGAATGGA
CAAAAAATGTGGATCACAAATGGTGGTGTTGCCAATTGGTATTTTGTACTTGCAAGAACA
GCCGAAGATCCCAAAGCACCTGCATCAAAAGCTTTTACTGGATTTATTGTTGAGCGTGAA
TGGCCAGGCGTAACTCTTGGACGTAAAGAAATCAACATGGGACAACGTGCAAGTGACACT
CGTGGTATAACATTTGAAGATGTTCGAATTCCAAAAGAAAATGTTTTACTCGGTGAAGGT
GCTGGATTTAAAATTGCAATGTCAACATTTGACCTCACTCGACCACCAGTTGCTGCAGGT
GCAACAGGTTTAGCACAGCGAGCCTACGATGAAGCATTAAAATATTCACTTGAACGTAAA
ACTTTTGGTGTTCCAATTGCACAACATCAAGCAATTCAATTTATGCTTGCTGATATGGCA
ATTGGTGTTGAACTGTCAAGACTGAGTTGGTGGAGAGCTGCTTGGGAGGTGGACCAAGGA
AGAAGAAATTCATATGAAGCTTCAATTTCAAAATGTTTTGCTGCTGACATGGCTAATAAA
ATTGCAACTGATGCAGTTCAAATATTTGGTGGAAATGGTTTCAATTCAGAATATCCAGTT
GAAAAACTCATGAGAGATGCCAAAATTTACCAAATTTATGAAGGAACATCACAAATTCAA
CGACTGATTATTTCTAGAAATGCTTTTGAACGTGCTAAGGAAATGAATAAGTAA
>g17272.t1 Gene=g17272 Length=417
MALSKISSLIRPFGSRAFSITPRLCNESGPSFALSEEQREIQATARKFTREEIIPVAAHH
DRTGEYPWAIIKKAWELGLLNHSIPEHCGGHKLSTFTTCLIAEELAYGCTGIETAMEGSG
LGQTPVVLAGNKEQQKKYLGRLVEQPLVAAYCVTEPSAGSDVNGIKSKAVKKGDEYILNG
QKMWITNGGVANWYFVLARTAEDPKAPASKAFTGFIVEREWPGVTLGRKEINMGQRASDT
RGITFEDVRIPKENVLLGEGAGFKIAMSTFDLTRPPVAAGATGLAQRAYDEALKYSLERK
TFGVPIAQHQAIQFMLADMAIGVELSRLSWWRAAWEVDQGRRNSYEASISKCFAADMANK
IATDAVQIFGGNGFNSEYPVEKLMRDAKIYQIYEGTSQIQRLIISRNAFERAKEMNK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g17272.t1 | Gene3D | G3DSA:1.10.540.10 | - | 23 | 148 | 5.8E-41 |
| 11 | g17272.t1 | Gene3D | G3DSA:2.40.110.10 | - | 149 | 265 | 1.1E-44 |
| 12 | g17272.t1 | Gene3D | G3DSA:1.20.140.10 | - | 266 | 417 | 1.3E-53 |
| 4 | g17272.t1 | PANTHER | PTHR48083 | MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-RELATED | 33 | 413 | 5.0E-176 |
| 5 | g17272.t1 | PANTHER | PTHR48083:SF2 | MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL | 33 | 413 | 5.0E-176 |
| 14 | g17272.t1 | PIRSF | PIRSF016578 | PIGM | 30 | 112 | 3.9E-4 |
| 13 | g17272.t1 | PIRSF | PIRSF016578 | PIGM | 158 | 398 | 1.9E-9 |
| 3 | g17272.t1 | Pfam | PF02771 | Acyl-CoA dehydrogenase, N-terminal domain | 35 | 144 | 3.0E-27 |
| 1 | g17272.t1 | Pfam | PF02770 | Acyl-CoA dehydrogenase, middle domain | 150 | 248 | 1.3E-25 |
| 2 | g17272.t1 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 260 | 408 | 2.1E-50 |
| 9 | g17272.t1 | ProSitePatterns | PS00072 | Acyl-CoA dehydrogenases signature 1. | 152 | 164 | - |
| 8 | g17272.t1 | ProSitePatterns | PS00073 | Acyl-CoA dehydrogenases signature 2. | 367 | 386 | - |
| 6 | g17272.t1 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 31 | 271 | 4.45E-78 |
| 7 | g17272.t1 | SUPERFAMILY | SSF47203 | Acyl-CoA dehydrogenase C-terminal domain-like | 258 | 410 | 1.55E-56 |
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 K00249 (acyl-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.
