ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for AP4M1

Gene summary

Gene information	Gene symbol	AP4M1
	Gene ID	9179
	Gene name	adaptor related protein complex 4 subunit mu 1
	Synonyms	CPSQ3\|MU-4\|MU-ARP2\|SPG50
	Cytomap	7q22.1
	Type of gene	protein-coding
	Description	AP-4 complex subunit mu-1AP-4 adaptor complex mu subunitadapter-related protein complex 4 mu-1 subunitadapter-related protein complex 4 subunit mu-1adaptor related protein complex 4 mu 1 subunitadaptor-related protein complex AP-4 mu4 subunitmu subu
	Modification date	20200313
	UniProtAcc	C9IZL5, C9JC87, C9JMG3, C9JWL4, F8WCC5, F8WCR6, F8WDR3, H0Y6K1, H7BZV3, H7C0A0, O00189,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
AP4M1	GO:0006605	protein targeting	20230749
AP4M1	GO:0006622	protein targeting to lysosome	11139587
AP4M1	GO:0090160	Golgi to lysosome transport	11139587

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Gene structures and expression levels for AP4M1

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000221838

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	DOWN	ENST00000445295.1	AP4M1-210:protein_coding:AP4M1	1.444671e+01	-1.383832e+00	6.494515e-07	1.038783e-05
TC	DOWN	ENST00000445295.1	AP4M1-210:protein_coding:AP4M1	1.739751e+01	-8.757919e-01	1.216862e-04	1.892017e-03

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for AP4M1

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_180429	chr7	100102675:100102781:100102864:100102960:100103409:100103519	100102864:100102960
exon_skip_21519	chr7	100106413:100106514:100106658:100106912:100110191:100110319	100106658:100106912
exon_skip_215372	chr7	100104094:100104154:100105045:100105098:100105240:100105346	100105045:100105098
exon_skip_251093	chr7	100104092:100104154:100105045:100105098:100105240:100105346	100105045:100105098
exon_skip_28871	chr7	100104092:100104154:100104874:100104940:100105045:100105098	100104874:100104940
exon_skip_295438	chr7	100101880:100101968:100102675:100102781:100103409:100103519	100102675:100102781
exon_skip_31217	chr7	100102675:100102781:100102864:100102960:100103409:100103445	100102864:100102960
exon_skip_3170	chr7	100101880:100101968:100102675:100102781:100103409:100103445	100102675:100102781
exon_skip_64347	chr7	100105959:100106003:100106241:100106291:100106403:100106514	100106241:100106291
exon_skip_73886	chr7	100101880:100101968:100102675:100102746:100103409:100103519	100102675:100102746
exon_skip_90952	chr7	100101880:100101968:100102246:100102393:100102675:100102746	100102246:100102393
exon_skip_92360	chr7	100104094:100104154:100104874:100104940:100105045:100105098	100104874:100104940

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for AP4M1

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000359593	100102864	100102960	Frame-shift
ENST00000421755	100102864	100102960	Frame-shift
ENST00000359593	100104874	100104940	Frame-shift
ENST00000421755	100104874	100104940	Frame-shift
ENST00000359593	100106241	100106291	In-frame
ENST00000421755	100106241	100106291	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000359593	100104874	100104940	Frame-shift
ENST00000421755	100104874	100104940	Frame-shift
ENST00000359593	100106241	100106291	In-frame
ENST00000421755	100106241	100106291	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000421755	100106658	100106912	3UTR-3CDS
ENST00000359593	100102864	100102960	Frame-shift
ENST00000421755	100102864	100102960	Frame-shift
ENST00000359593	100104874	100104940	Frame-shift
ENST00000421755	100104874	100104940	Frame-shift
ENST00000359593	100106241	100106291	In-frame
ENST00000421755	100106241	100106291	In-frame

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Infer the effects of exon skipping event on protein functional features for AP4M1

p-ENSG00000221838_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000359593	1834	453	100106241	100106291	1134	1183	325	341
ENST00000421755	1589	453	100106241	100106291	1027	1076	325	341

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000359593	1834	453	100106241	100106291	1134	1183	325	341
ENST00000421755	1589	453	100106241	100106291	1027	1076	325	341

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000359593	1834	453	100106241	100106291	1134	1183	325	341
ENST00000421755	1589	453	100106241	100106291	1027	1076	325	341

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O00189	325	341	326	335	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	326	335	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	341	349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	341	349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	1	453	Chain	ID=PRO_0000193787;Note=AP-4 complex subunit mu-1
O00189	325	341	1	453	Chain	ID=PRO_0000193787;Note=AP-4 complex subunit mu-1
O00189	325	341	184	452	Domain	Note=MHD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00404
O00189	325	341	184	452	Domain	Note=MHD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00404
O00189	325	341	338	338	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00189	325	341	338	338	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O00189	325	341	326	335	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	326	335	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	341	349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	341	349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	1	453	Chain	ID=PRO_0000193787;Note=AP-4 complex subunit mu-1
O00189	325	341	1	453	Chain	ID=PRO_0000193787;Note=AP-4 complex subunit mu-1
O00189	325	341	184	452	Domain	Note=MHD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00404
O00189	325	341	184	452	Domain	Note=MHD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00404
O00189	325	341	338	338	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00189	325	341	338	338	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
O00189	325	341	326	335	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	326	335	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	341	349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	341	349	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3L81
O00189	325	341	1	453	Chain	ID=PRO_0000193787;Note=AP-4 complex subunit mu-1
O00189	325	341	1	453	Chain	ID=PRO_0000193787;Note=AP-4 complex subunit mu-1
O00189	325	341	184	452	Domain	Note=MHD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00404
O00189	325	341	184	452	Domain	Note=MHD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00404
O00189	325	341	338	338	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
O00189	325	341	338	338	Sequence conflict	Note=R->G;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in AP4M1

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for AP4M1

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for AP4M1

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AP4M1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for AP4M1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for AP4M1

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for AP4M1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for AP4M1

Gene structures and expression levels for AP4M1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for AP4M1

Open reading frame (ORF) annotation in the exon skipping event for AP4M1

Infer the effects of exon skipping event on protein functional features for AP4M1

3'-UTR located exon skipping events that lost miRNA binding sites in AP4M1

SNVs in the skipped exons for AP4M1

AD stage-associated exon skippint events for AP4M1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AP4M1

Correlation with RNA binding proteins (RBPs) for AP4M1

RelatedDrugs for AP4M1

RelatedDiseases for AP4M1