General information for g12935.t19
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 g12935 is located on chr_1: 27004491..27006329 (- 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 | g12935 | g12935.t19 | isoform | g12935.t19 | 27004428 | 27005083 |
| chr_1 | g12935 | g12935.t19 | exon | g12935.t19.exon1 | 27004428 | 27005083 |
| chr_1 | g12935 | g12935.t19 | TTS | g12935.t19 | 27004441 | 27004441 |
| chr_1 | g12935 | g12935.t19 | cds | g12935.t19.CDS1 | 27004491 | 27005075 |
| chr_1 | g12935 | g12935.t19 | TSS | g12935.t19 | 27005976 | 27005976 |
Sequences
>g12935.t19 Gene=g12935 Length=656
AGAAGAATATGGAAGGCTTATCGATTGGCAAAAAGGAAGATAAATTAGGATTAGTTGCTT
CAGGAACATGCATGATTCATCTTGATAATGTGCGAGTGCCAGAAGAAAACATTTTGGGTG
AATTTGGAAAAGGATATGCATATGCTGCAGGTTTTTTAAATGAAGGCAGAATCGGAATTG
GTGCTCAAATGGTTGGTTGTGCACAAGGTGCATTTGATGCTACTATCCCATATCTTCTTG
AGCGTAAACAATTTGGACAAAACATTTACGATTTTCAAGGAATGCAATTTCAAATTGCTG
AAGTCGCAACACAAATTGAAGCAGGAAGATTATTAACTTATAATGCAGCTCGCTTGCAAG
AAGCAGGTAAACCATTTTTAAAAGAGGCAGCAATGGCAAAACTCTTTTGCTCAAGAATGG
CACAATTTGTTAGCAGTCAATGTGTTGATTGGATGGGTGGTGTCGGATTTACAAAAGATT
TTCCACAAGAGAAATTTTACAGAGATTCCAAAGCTAGTACAATTTATGAGGGTACAAGTA
ATATTCAAATGAGTACAATTGCTAAAATTATTAGAAAAGAATATTCTTCATGATTGATGC
TACTTATAATTTTTATTAAAAGTTTAATAGAATATTCATAATATTATAAACTCAAT
>g12935.t19 Gene=g12935 Length=194
MEGLSIGKKEDKLGLVASGTCMIHLDNVRVPEENILGEFGKGYAYAAGFLNEGRIGIGAQ
MVGCAQGAFDATIPYLLERKQFGQNIYDFQGMQFQIAEVATQIEAGRLLTYNAARLQEAG
KPFLKEAAMAKLFCSRMAQFVSSQCVDWMGGVGFTKDFPQEKFYRDSKASTIYEGTSNIQ
MSTIAKIIRKEYSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12935.t19 | Gene3D | G3DSA:2.40.110.10 | - | 1 | 42 | 6.1E-10 |
| 8 | g12935.t19 | Gene3D | G3DSA:1.20.140.10 | - | 43 | 192 | 9.3E-53 |
| 2 | g12935.t19 | PANTHER | PTHR43884:SF1 | SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL | 1 | 192 | 5.7E-97 |
| 3 | g12935.t19 | PANTHER | PTHR43884 | ACYL-COA DEHYDROGENASE | 1 | 192 | 5.7E-97 |
| 1 | g12935.t19 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 40 | 186 | 7.9E-47 |
| 6 | g12935.t19 | ProSitePatterns | PS00073 | Acyl-CoA dehydrogenases signature 2. | 147 | 166 | - |
| 4 | g12935.t19 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 2 | 53 | 4.45E-14 |
| 5 | g12935.t19 | SUPERFAMILY | SSF47203 | Acyl-CoA dehydrogenase C-terminal domain-like | 38 | 192 | 6.28E-53 |
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.
