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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for ACAA1

check button Gene summary
Gene informationGene symbol

ACAA1

Gene ID

30

Gene nameacetyl-CoA acyltransferase 1
SynonymsACAA|PTHIO|THIO
Cytomap

3p22.2

Type of geneprotein-coding
Description3-ketoacyl-CoA thiolase, peroxisomalacetyl-Coenzyme A acyltransferase 1beta-ketothiolaseperoxisomal 3-oxoacyl-CoA thiolaseperoxisomal 3-oxoacyl-Coenzyme A thiolasetesticular tissue protein Li 197
Modification date20180523
UniProtAcc

P09110

ContextPubMed: ACAA1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for ACAA1 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for ACAA1

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for ACAA1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_382439338167316:38167372:38167652:38167832:38168000:3816808538167652:38167832ENSG00000060971.13ENST00000450296.1,ENST00000333167.8,ENST00000421218.1
exon_skip_382442338167316:38167372:38167652:38168191:38169276:3816935738167652:38168191ENSG00000060971.13ENST00000480865.1,ENST00000411549.1
exon_skip_382446338167316:38167372:38168000:38168191:38169276:3816935738168000:38168191ENSG00000060971.13ENST00000452171.1,ENST00000301810.7
exon_skip_382452338168000:38168191:38169276:38169357:38170780:3817087938169276:38169357ENSG00000060971.13ENST00000450296.1,ENST00000444607.2,ENST00000447223.1,ENST00000480865.1,ENST00000333167.8,ENST00000440176.1,ENST00000452171.1,ENST00000469559.1,ENST00000423611.1,ENST00000411549.1,ENST00000544624.1
exon_skip_382453338168000:38168191:38169276:38169357:38173086:3817312938169276:38169357ENSG00000060971.13ENST00000301810.7,ENST00000421218.1
exon_skip_382455338169276:38169357:38170780:38170879:38173086:3817312938170780:38170879ENSG00000060971.13ENST00000447223.1,ENST00000480865.1,ENST00000333167.8,ENST00000452171.1,ENST00000469559.1
exon_skip_382456338169276:38169357:38170780:38170879:38173416:3817343738170780:38170879ENSG00000060971.13ENST00000444607.2,ENST00000440176.1,ENST00000423611.1,ENST00000418880.1,ENST00000411549.1,ENST00000544624.1
exon_skip_382457338169276:38169357:38173086:38173129:38173416:3817343738173086:38173129ENSG00000060971.13ENST00000301810.7,ENST00000421218.1
exon_skip_382458338170819:38170879:38173086:38173129:38173416:3817343738173086:38173129ENSG00000060971.13ENST00000447223.1,ENST00000480865.1,ENST00000333167.8,ENST00000452171.1,ENST00000469559.1
exon_skip_382459338170780:38170879:38173416:38173496:38175442:3817550038173416:38173496ENSG00000060971.13ENST00000444607.2,ENST00000440176.1,ENST00000465181.1,ENST00000411549.1,ENST00000544624.1
exon_skip_382460338173416:38173496:38175442:38175500:38178082:3817811538175442:38175500ENSG00000060971.13ENST00000444607.2,ENST00000333167.8,ENST00000301810.7,ENST00000421218.1,ENST00000411549.1
exon_skip_382462338175442:38175500:38175999:38176043:38178082:3817811538175999:38176043ENSG00000060971.13ENST00000460424.1,ENST00000447223.1,ENST00000440176.1,ENST00000544624.1
exon_skip_382463338175886:38176043:38176674:38176785:38178082:3817817638176674:38176785ENSG00000060971.13ENST00000489559.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for ACAA1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_382439338167316:38167372:38167652:38167832:38168000:3816808538167652:38167832ENSG00000060971.13ENST00000333167.8,ENST00000450296.1,ENST00000421218.1
exon_skip_382442338167316:38167372:38167652:38168191:38169276:3816935738167652:38168191ENSG00000060971.13ENST00000411549.1,ENST00000480865.1
exon_skip_382446338167316:38167372:38168000:38168191:38169276:3816935738168000:38168191ENSG00000060971.13ENST00000301810.7,ENST00000452171.1
exon_skip_382452338168000:38168191:38169276:38169357:38170780:3817087938169276:38169357ENSG00000060971.13ENST00000333167.8,ENST00000411549.1,ENST00000469559.1,ENST00000480865.1,ENST00000450296.1,ENST00000452171.1,ENST00000440176.1,ENST00000544624.1,ENST00000444607.2,ENST00000423611.1,ENST00000447223.1
exon_skip_382453338168000:38168191:38169276:38169357:38173086:3817312938169276:38169357ENSG00000060971.13ENST00000301810.7,ENST00000421218.1
exon_skip_382455338169276:38169357:38170780:38170879:38173086:3817312938170780:38170879ENSG00000060971.13ENST00000333167.8,ENST00000469559.1,ENST00000480865.1,ENST00000452171.1,ENST00000447223.1
exon_skip_382456338169276:38169357:38170780:38170879:38173416:3817343738170780:38170879ENSG00000060971.13ENST00000411549.1,ENST00000440176.1,ENST00000544624.1,ENST00000444607.2,ENST00000423611.1,ENST00000418880.1
exon_skip_382457338169276:38169357:38173086:38173129:38173416:3817343738173086:38173129ENSG00000060971.13ENST00000301810.7,ENST00000421218.1
exon_skip_382458338170819:38170879:38173086:38173129:38173416:3817343738173086:38173129ENSG00000060971.13ENST00000333167.8,ENST00000469559.1,ENST00000480865.1,ENST00000452171.1,ENST00000447223.1
exon_skip_382459338170780:38170879:38173416:38173496:38175442:3817550038173416:38173496ENSG00000060971.13ENST00000411549.1,ENST00000440176.1,ENST00000544624.1,ENST00000444607.2,ENST00000465181.1
exon_skip_382460338173416:38173496:38175442:38175500:38178082:3817811538175442:38175500ENSG00000060971.13ENST00000333167.8,ENST00000301810.7,ENST00000411549.1,ENST00000421218.1,ENST00000444607.2
exon_skip_382462338175442:38175500:38175999:38176043:38178082:3817811538175999:38176043ENSG00000060971.13ENST00000440176.1,ENST00000544624.1,ENST00000447223.1,ENST00000460424.1
exon_skip_382463338175886:38176043:38176674:38176785:38178082:3817817638176674:38176785ENSG00000060971.13ENST00000489559.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for ACAA1

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003331673817308638173129Frame-shift
ENST000003331673817544238175500Frame-shift
ENST000003331673816765238167832In-frame
ENST000003331673816927638169357In-frame
ENST000003331673817078038170879In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003331673817308638173129Frame-shift
ENST000003331673817544238175500Frame-shift
ENST000003331673816765238167832In-frame
ENST000003331673816927638169357In-frame
ENST000003331673817078038170879In-frame

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Infer the effects of exon skipping event on protein functional features for ACAA1

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000033316718024243817078038170879620718149181
ENST0000033316718024243816927638169357719799182208
ENST00000333167180242438167652381678329911170272332

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000033316718024243817078038170879620718149181
ENST0000033316718024243816927638169357719799182208
ENST00000333167180242438167652381678329911170272332

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P09110149181149181Alternative sequenceID=VSP_046195;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
P09110149181143152Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P0911014918127424ChainID=PRO_0000034067;Note=3-ketoacyl-CoA thiolase%2C peroxisomal
P09110149181168170HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181172175HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181176178HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181181191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181172172Natural variantID=VAR_011904;Note=E->D;Dbxref=dbSNP:rs156265
P09110149181153155TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P0911018220827424ChainID=PRO_0000034067;Note=3-ketoacyl-CoA thiolase%2C peroxisomal
P09110182208181191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110182208196216HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332272331Alternative sequenceID=VSP_046196;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
P09110272332279289Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332302311Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P0911027233227424ChainID=PRO_0000034067;Note=3-ketoacyl-CoA thiolase%2C peroxisomal
P09110272332290296HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332314319HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332320332HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P09110149181149181Alternative sequenceID=VSP_046195;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
P09110149181143152Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P0911014918127424ChainID=PRO_0000034067;Note=3-ketoacyl-CoA thiolase%2C peroxisomal
P09110149181168170HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181172175HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181176178HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181181191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110149181172172Natural variantID=VAR_011904;Note=E->D;Dbxref=dbSNP:rs156265
P09110149181153155TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P0911018220827424ChainID=PRO_0000034067;Note=3-ketoacyl-CoA thiolase%2C peroxisomal
P09110182208181191HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110182208196216HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332272331Alternative sequenceID=VSP_046196;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334
P09110272332279289Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332302311Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P0911027233227424ChainID=PRO_0000034067;Note=3-ketoacyl-CoA thiolase%2C peroxisomal
P09110272332290296HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332314319HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK
P09110272332320332HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2IIK


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SNVs in the skipped exons for ACAA1

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
BLCATCGA-FD-A43X-01exon_skip_382460
38175443381755003817547338175474Frame_Shift_Ins-Cp.A98fs
BRCATCGA-A7-A0DB-01exon_skip_382460
38175443381755003817545338175453Nonsense_MutationGAp.Q105*
PAADTCGA-IB-7651-01exon_skip_382460
38175443381755003817548938175489Nonsense_MutationGAp.Q93*
PAADTCGA-IB-7651-01exon_skip_382460
38175443381755003817548938175489Nonsense_MutationGAp.Q93X
COADTCGA-AY-6197-01exon_skip_382457
exon_skip_382458
38173087381731293817308538173085Splice_SiteAG.

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SNU81_LARGE_INTESTINE38167653381681913816766538167665Missense_MutationACp.L329V
SNU81_LARGE_INTESTINE38167653381678323816766538167665Missense_MutationACp.L329V
SW1271_LUNG38167653381681913816778438167784Missense_MutationCAp.R289L
SW1271_LUNG38167653381678323816778438167784Missense_MutationCAp.R289L
HEC251_ENDOMETRIUM38169277381693573816931238169312Missense_MutationCAp.E197D
FUOV1_OVARY38169277381693573816931638169316Missense_MutationCTp.R196Q
SNU1040_LARGE_INTESTINE38169277381693573816933238169332Missense_MutationGAp.R191W
OE19_OESOPHAGUS38173087381731293817311138173111Missense_MutationGCp.S141C
LNCAPCLONEFGC_PROSTATE38173417381734963817344638173446Missense_MutationGAp.S125L
SNGM_ENDOMETRIUM38175443381755003817545638175456Missense_MutationCTp.A104T
HCC2157_BREAST38175443381755003817546838175468Missense_MutationTCp.M100V
OSC20_UPPER_AERODIGESTIVE_TRACT38175443381755003817546238175462Nonsense_MutationGAp.R102*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ACAA1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_382442338167316:38167372:38167652:38168191:38169276:3816935738167652:38168191ENST00000480865.1,ENST00000411549.1COADrs61095322chr3:38168125A/C1.91e-06
exon_skip_382442338167316:38167372:38167652:38168191:38169276:3816935738167652:38168191ENST00000480865.1,ENST00000411549.1LGGrs61095322chr3:38168125A/C2.02e-14
exon_skip_382446338167316:38167372:38168000:38168191:38169276:3816935738168000:38168191ENST00000452171.1,ENST00000301810.7COADrs61095322chr3:38168125A/C1.91e-06
exon_skip_382446338167316:38167372:38168000:38168191:38169276:3816935738168000:38168191ENST00000452171.1,ENST00000301810.7LGGrs61095322chr3:38168125A/C2.02e-14

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ACAA1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ACAA1


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RelatedDrugs for ACAA1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P09110DB09069Trimetazidine3-ketoacyl-CoA thiolase, peroxisomalsmall moleculeapproved|investigational

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RelatedDiseases for ACAA1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource