ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for COMMD1

Gene summary

Gene information	Gene symbol	COMMD1
	Gene ID	150684
	Gene name	copper metabolism domain containing 1
	Synonyms	C2orf5\|MURR1
	Cytomap	2p15
	Type of gene	protein-coding
	Description	COMM domain-containing protein 1copper metabolism (Murr1) domain containing 1copper metabolism gene MURR1protein Murr1
	Modification date	20200313
	UniProtAcc	A0A2Z4SWX4, E9PE85, H0Y7J4, H7C169, H7C377, Q8N668,
	Context

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

Gene	GO ID	GO term	PubMed ID
COMMD1	GO:0031398	positive regulation of protein ubiquitination	17183367\|21741370
COMMD1	GO:0032088	negative regulation of NF-kappaB transcription factor activity	15799966\|16573520
COMMD1	GO:0048227	plasma membrane to endosome transport	21741370
COMMD1	GO:0055070	copper ion homeostasis	14685266
COMMD1	GO:1902306	negative regulation of sodium ion transmembrane transport	14645214
COMMD1	GO:2000009	negative regulation of protein localization to cell surface	21741370

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Gene structures and expression levels for COMMD1

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.

ENSG00000173163

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

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 COMMD1

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_142126	chr2	61905758:61905858:62000701:62000982:62135831:62135979	62000701:62000982
exon_skip_158707	chr2	61905758:61905858:61968969:61969130:62000701:62000875	61968969:61969130
exon_skip_59616	chr2	61905758:61905858:61968969:61969130:62000701:62000847	61968969:61969130
exon_skip_72123	chr2	61905798:61905858:61968969:61969130:62000701:62000847	61968969:61969130

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 COMMD1

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
ENST00000311832	62000701	62000982	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

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
ENST00000311832	62000701	62000982	In-frame

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Infer the effects of exon skipping event on protein functional features for COMMD1

p-ENSG00000173163_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
ENST00000311832	928	190	62000701	62000982	214	494	60	154

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

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
ENST00000311832	928	190	62000701	62000982	214	494	60	154

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
Q8N668	60	154	82	84	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	102	106	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	2	190	Chain	ID=PRO_0000077384;Note=COMM domain-containing protein 1
Q8N668	60	154	118	186	Domain	Note=COMM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00602
Q8N668	60	154	59	62	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	76	79	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	88	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	101	101	Metal binding	Note=Copper;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N668	60	154	110	110	Metal binding	Note=Copper;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N668	60	154	134	134	Metal binding	Note=Copper;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N668	60	154	110	110	Mutagenesis	Note=Reduces copper-induced fluorescence change. M->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17309234;Dbxref=PMID:17309234
Q8N668	60	154	134	134	Mutagenesis	Note=Reduces copper-induced fluorescence change. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17309234;Dbxref=PMID:17309234
Q8N668	60	154	2	123	Region	Note=Sufficient for interaction with SLC12A2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23515529;Dbxref=PMID:23515529
Q8N668	60	154	125	190	Region	Note=Required for binding to PtdIns(4%2C5)P2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18940794;Dbxref=PMID:18940794
Q8N668	60	154	63	65	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	69	71	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	73	75	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	95	101	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M

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

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
Q8N668	60	154	82	84	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	102	106	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	2	190	Chain	ID=PRO_0000077384;Note=COMM domain-containing protein 1
Q8N668	60	154	118	186	Domain	Note=COMM;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00602
Q8N668	60	154	59	62	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	76	79	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	88	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	101	101	Metal binding	Note=Copper;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N668	60	154	110	110	Metal binding	Note=Copper;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N668	60	154	134	134	Metal binding	Note=Copper;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N668	60	154	110	110	Mutagenesis	Note=Reduces copper-induced fluorescence change. M->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17309234;Dbxref=PMID:17309234
Q8N668	60	154	134	134	Mutagenesis	Note=Reduces copper-induced fluorescence change. H->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17309234;Dbxref=PMID:17309234
Q8N668	60	154	2	123	Region	Note=Sufficient for interaction with SLC12A2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23515529;Dbxref=PMID:23515529
Q8N668	60	154	125	190	Region	Note=Required for binding to PtdIns(4%2C5)P2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18940794;Dbxref=PMID:18940794
Q8N668	60	154	63	65	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	69	71	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	73	75	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M
Q8N668	60	154	95	101	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2H2M

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3'-UTR located exon skipping events that lost miRNA binding sites in COMMD1

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 COMMD1

- 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 COMMD1

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 COMMD1

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 COMMD1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for COMMD1

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 COMMD1

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 COMMD1

Gene structures and expression levels for COMMD1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for COMMD1

Open reading frame (ORF) annotation in the exon skipping event for COMMD1

Infer the effects of exon skipping event on protein functional features for COMMD1

3'-UTR located exon skipping events that lost miRNA binding sites in COMMD1

SNVs in the skipped exons for COMMD1

AD stage-associated exon skippint events for COMMD1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COMMD1

Correlation with RNA binding proteins (RBPs) for COMMD1

RelatedDrugs for COMMD1

RelatedDiseases for COMMD1