ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NLRC4

Gene summary

Gene information	Gene symbol	NLRC4
	Gene ID	58484
	Gene name	NLR family CARD domain containing 4
	Synonyms	AIFEC\|CARD12\|CLAN\|CLAN1\|CLANA\|CLANB\|CLANC\|CLAND\|CLR2.1\|FCAS4\|IPAF
	Cytomap	2p22.3
	Type of gene	protein-coding
	Description	NLR family CARD domain-containing protein 4CARD, LRR, and NACHT-containing proteinICE-protease activating factorNOD-like receptor C4caspase recruitment domain family, member 12caspase recruitment domain-containing protein 12nucleotide-binding oligom
	Modification date	20180523
	UniProtAcc	Q9NPP4
	Context	PubMed: NLRC4 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene	GO ID	GO term	PubMed ID
NLRC4	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	15030775
NLRC4	GO:0016045	detection of bacterium	15107016
NLRC4	GO:0042742	defense response to bacterium	15107016
NLRC4	GO:0043065	positive regulation of apoptotic process	12646168
NLRC4	GO:0050702	interleukin-1 beta secretion	15882992
NLRC4	GO:0051092	positive regulation of NF-kappaB transcription factor activity	12646168

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Exon skipping events across known transcript of Ensembl for NLRC4 from UCSC genome browser

Skipped 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.

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Gene isoform structures and expression levels for NLRC4

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for NLRC4

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_338240	2	32466101:32466194:32474675:32476670:32477487:32477748	32474675:32476670	ENSG00000091106.14	ENST00000404025.2,ENST00000360906.5,ENST00000402280.1
exon_skip_338243	2	32474675:32476670:32477487:32477748:32481843:32481962	32477487:32477748	ENSG00000091106.14	ENST00000404025.2,ENST00000360906.5,ENST00000402280.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NLRC4

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_338240	2	32466101:32466194:32474675:32476670:32477487:32477748	32474675:32476670	ENSG00000091106.14	ENST00000360906.5,ENST00000402280.1,ENST00000404025.2
exon_skip_338242	2	32466101:32466194:32477487:32477748:32481843:32481962	32477487:32477748	ENSG00000091106.14	ENST00000342905.6
exon_skip_338243	2	32474675:32476670:32477487:32477748:32481843:32481962	32477487:32477748	ENSG00000091106.14	ENST00000360906.5,ENST00000402280.1,ENST00000404025.2

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for NLRC4

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000360906	32474675	32476670	In-frame
ENST00000402280	32474675	32476670	In-frame
ENST00000404025	32474675	32476670	In-frame
ENST00000360906	32477487	32477748	In-frame
ENST00000402280	32477487	32477748	In-frame
ENST00000404025	32477487	32477748	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000360906	32474675	32476670	In-frame
ENST00000402280	32474675	32476670	In-frame
ENST00000404025	32474675	32476670	In-frame
ENST00000360906	32477487	32477748	In-frame
ENST00000402280	32477487	32477748	In-frame
ENST00000404025	32477487	32477748	In-frame

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Infer the effects of exon skipping event on protein functional features for NLRC4

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

Loci of skipped exons in TCGA 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
ENST00000360906	3376	1024	32477487	32477748	266	526	0	87
ENST00000402280	3372	1024	32477487	32477748	263	523	0	87
ENST00000404025	3598	1024	32477487	32477748	491	751	0	87
ENST00000360906	3376	1024	32474675	32476670	527	2521	87	752
ENST00000402280	3372	1024	32474675	32476670	524	2518	87	752
ENST00000404025	3598	1024	32474675	32476670	752	2746	87	752

Loci of skipped exons in GTEx 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
ENST00000360906	3376	1024	32477487	32477748	266	526	0	87
ENST00000402280	3372	1024	32477487	32477748	263	523	0	87
ENST00000404025	3598	1024	32477487	32477748	491	751	0	87
ENST00000360906	3376	1024	32474675	32476670	527	2521	87	752
ENST00000402280	3372	1024	32474675	32476670	524	2518	87	752
ENST00000404025	3598	1024	32474675	32476670	752	2746	87	752

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 feature	Description of feature
Q9NPP4	0	87	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	0	87	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	0	87	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	0	87	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	0	87	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	0	87	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	0	87	39	39	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	0	87	39	39	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	0	87	39	39	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	89	753	Alternative sequence	ID=VSP_000784;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	89	753	Alternative sequence	ID=VSP_000784;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	89	753	Alternative sequence	ID=VSP_000784;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	90	92	Alternative sequence	ID=VSP_000787;Note=In isoform 4. FHQ->LTA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	90	92	Alternative sequence	ID=VSP_000787;Note=In isoform 4. FHQ->LTA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	90	92	Alternative sequence	ID=VSP_000787;Note=In isoform 4. FHQ->LTA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	93	1024	Alternative sequence	ID=VSP_000788;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	93	1024	Alternative sequence	ID=VSP_000788;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	93	1024	Alternative sequence	ID=VSP_000788;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	155	156	Alternative sequence	ID=VSP_000785;Note=In isoform 3. NG->VL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	155	156	Alternative sequence	ID=VSP_000785;Note=In isoform 3. NG->VL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	155	156	Alternative sequence	ID=VSP_000785;Note=In isoform 3. NG->VL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	157	1024	Alternative sequence	ID=VSP_000786;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	157	1024	Alternative sequence	ID=VSP_000786;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	157	1024	Alternative sequence	ID=VSP_000786;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	87	752	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	87	752	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	87	752	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	87	752	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	87	752	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	87	752	163	476	Domain	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	163	476	Domain	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	163	476	Domain	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	533	533	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3UP24
Q9NPP4	87	752	533	533	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3UP24
Q9NPP4	87	752	533	533	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3UP24
Q9NPP4	87	752	337	337	Natural variant	ID=VAR_072484;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. T->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217959;Dbxref=dbSNP:rs587777840,PMID:25217959
Q9NPP4	87	752	337	337	Natural variant	ID=VAR_072484;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. T->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217959;Dbxref=dbSNP:rs587777840,PMID:25217959
Q9NPP4	87	752	337	337	Natural variant	ID=VAR_072484;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. T->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217959;Dbxref=dbSNP:rs587777840,PMID:25217959
Q9NPP4	87	752	341	341	Natural variant	ID=VAR_072485;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217960;Dbxref=dbSNP:rs587781260,PMID:25217960
Q9NPP4	87	752	341	341	Natural variant	ID=VAR_072485;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217960;Dbxref=dbSNP:rs587781260,PMID:25217960
Q9NPP4	87	752	341	341	Natural variant	ID=VAR_072485;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217960;Dbxref=dbSNP:rs587781260,PMID:25217960
Q9NPP4	87	752	443	443	Natural variant	ID=VAR_072645;Note=In FCAS4%3B the mutation increases oligomerization of the NLRC4 protein%3B results in hyperactivation of caspase-1 with an increase in IL1B protein secretion. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25385754;Dbxref=db
Q9NPP4	87	752	443	443	Natural variant	ID=VAR_072645;Note=In FCAS4%3B the mutation increases oligomerization of the NLRC4 protein%3B results in hyperactivation of caspase-1 with an increase in IL1B protein secretion. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25385754;Dbxref=db
Q9NPP4	87	752	443	443	Natural variant	ID=VAR_072645;Note=In FCAS4%3B the mutation increases oligomerization of the NLRC4 protein%3B results in hyperactivation of caspase-1 with an increase in IL1B protein secretion. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25385754;Dbxref=db
Q9NPP4	87	752	169	176	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	169	176	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	169	176	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	95	298	Region	Note=Nucleotide-binding domain (NBD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	95	298	Region	Note=Nucleotide-binding domain (NBD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	95	298	Region	Note=Nucleotide-binding domain (NBD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	356	463	Region	Note=Winged-helix domain (WHD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	356	463	Region	Note=Winged-helix domain (WHD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	356	463	Region	Note=Winged-helix domain (WHD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	578	598	Repeat	Note=LRR 1
Q9NPP4	87	752	578	598	Repeat	Note=LRR 1
Q9NPP4	87	752	578	598	Repeat	Note=LRR 1
Q9NPP4	87	752	656	679	Repeat	Note=LRR 2
Q9NPP4	87	752	656	679	Repeat	Note=LRR 2
Q9NPP4	87	752	656	679	Repeat	Note=LRR 2
Q9NPP4	87	752	735	758	Repeat	Note=LRR 3
Q9NPP4	87	752	735	758	Repeat	Note=LRR 3
Q9NPP4	87	752	735	758	Repeat	Note=LRR 3
Q9NPP4	87	752	138	138	Sequence conflict	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	138	138	Sequence conflict	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	138	138	Sequence conflict	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	393	393	Sequence conflict	Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	393	393	Sequence conflict	Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	393	393	Sequence conflict	Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	420	420	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	420	420	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	420	420	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	678	678	Sequence conflict	Note=R->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	678	678	Sequence conflict	Note=R->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	678	678	Sequence conflict	Note=R->T;Ontology_term=ECO:0000305;evidence=ECO:0000305

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 feature	Description of feature
Q9NPP4	0	87	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	0	87	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	0	87	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	0	87	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	0	87	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	0	87	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	0	87	39	39	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	0	87	39	39	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	0	87	39	39	Sequence conflict	Note=N->D;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	89	753	Alternative sequence	ID=VSP_000784;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	89	753	Alternative sequence	ID=VSP_000784;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	89	753	Alternative sequence	ID=VSP_000784;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	90	92	Alternative sequence	ID=VSP_000787;Note=In isoform 4. FHQ->LTA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	90	92	Alternative sequence	ID=VSP_000787;Note=In isoform 4. FHQ->LTA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	90	92	Alternative sequence	ID=VSP_000787;Note=In isoform 4. FHQ->LTA;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	93	1024	Alternative sequence	ID=VSP_000788;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	93	1024	Alternative sequence	ID=VSP_000788;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	93	1024	Alternative sequence	ID=VSP_000788;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	155	156	Alternative sequence	ID=VSP_000785;Note=In isoform 3. NG->VL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	155	156	Alternative sequence	ID=VSP_000785;Note=In isoform 3. NG->VL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	155	156	Alternative sequence	ID=VSP_000785;Note=In isoform 3. NG->VL;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	157	1024	Alternative sequence	ID=VSP_000786;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	157	1024	Alternative sequence	ID=VSP_000786;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	157	1024	Alternative sequence	ID=VSP_000786;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11472070;Dbxref=PMID:11472070
Q9NPP4	87	752	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	87	752	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	87	752	1	1024	Chain	ID=PRO_0000144087;Note=NLR family CARD domain-containing protein 4
Q9NPP4	87	752	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	87	752	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	87	752	1	88	Domain	Note=CARD;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00046
Q9NPP4	87	752	163	476	Domain	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	163	476	Domain	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	163	476	Domain	Note=NACHT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	533	533	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3UP24
Q9NPP4	87	752	533	533	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3UP24
Q9NPP4	87	752	533	533	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q3UP24
Q9NPP4	87	752	337	337	Natural variant	ID=VAR_072484;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. T->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217959;Dbxref=dbSNP:rs587777840,PMID:25217959
Q9NPP4	87	752	337	337	Natural variant	ID=VAR_072484;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. T->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217959;Dbxref=dbSNP:rs587777840,PMID:25217959
Q9NPP4	87	752	337	337	Natural variant	ID=VAR_072484;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. T->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217959;Dbxref=dbSNP:rs587777840,PMID:25217959
Q9NPP4	87	752	341	341	Natural variant	ID=VAR_072485;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217960;Dbxref=dbSNP:rs587781260,PMID:25217960
Q9NPP4	87	752	341	341	Natural variant	ID=VAR_072485;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217960;Dbxref=dbSNP:rs587781260,PMID:25217960
Q9NPP4	87	752	341	341	Natural variant	ID=VAR_072485;Note=In AIFEC%3B results in a gain of function mutation with constitutive activation of caspase-1. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25217960;Dbxref=dbSNP:rs587781260,PMID:25217960
Q9NPP4	87	752	443	443	Natural variant	ID=VAR_072645;Note=In FCAS4%3B the mutation increases oligomerization of the NLRC4 protein%3B results in hyperactivation of caspase-1 with an increase in IL1B protein secretion. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25385754;Dbxref=db
Q9NPP4	87	752	443	443	Natural variant	ID=VAR_072645;Note=In FCAS4%3B the mutation increases oligomerization of the NLRC4 protein%3B results in hyperactivation of caspase-1 with an increase in IL1B protein secretion. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25385754;Dbxref=db
Q9NPP4	87	752	443	443	Natural variant	ID=VAR_072645;Note=In FCAS4%3B the mutation increases oligomerization of the NLRC4 protein%3B results in hyperactivation of caspase-1 with an increase in IL1B protein secretion. H->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25385754;Dbxref=db
Q9NPP4	87	752	169	176	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	169	176	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	169	176	Nucleotide binding	Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00136
Q9NPP4	87	752	95	298	Region	Note=Nucleotide-binding domain (NBD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	95	298	Region	Note=Nucleotide-binding domain (NBD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	95	298	Region	Note=Nucleotide-binding domain (NBD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	356	463	Region	Note=Winged-helix domain (WHD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	356	463	Region	Note=Winged-helix domain (WHD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	356	463	Region	Note=Winged-helix domain (WHD);Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9NPP4	87	752	578	598	Repeat	Note=LRR 1
Q9NPP4	87	752	578	598	Repeat	Note=LRR 1
Q9NPP4	87	752	578	598	Repeat	Note=LRR 1
Q9NPP4	87	752	656	679	Repeat	Note=LRR 2
Q9NPP4	87	752	656	679	Repeat	Note=LRR 2
Q9NPP4	87	752	656	679	Repeat	Note=LRR 2
Q9NPP4	87	752	735	758	Repeat	Note=LRR 3
Q9NPP4	87	752	735	758	Repeat	Note=LRR 3
Q9NPP4	87	752	735	758	Repeat	Note=LRR 3
Q9NPP4	87	752	138	138	Sequence conflict	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	138	138	Sequence conflict	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	138	138	Sequence conflict	Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	393	393	Sequence conflict	Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	393	393	Sequence conflict	Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	393	393	Sequence conflict	Note=C->R;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	420	420	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	420	420	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	420	420	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	678	678	Sequence conflict	Note=R->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	678	678	Sequence conflict	Note=R->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9NPP4	87	752	678	678	Sequence conflict	Note=R->T;Ontology_term=ECO:0000305;evidence=ECO:0000305

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SNVs in the skipped exons for NLRC4

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

- Differential PSIs between mutated versus non-mutated samples.

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

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A39Y-01	exon_skip_338240	32474676	32476670	32474849	32474849	Frame_Shift_Del	T	-	p.K695fs
HNSC	TCGA-CV-7101-01	exon_skip_338240	32474676	32476670	32475056	32475056	Frame_Shift_Del	T	-	p.K626fs
LIHC	TCGA-DD-A1EG-01	exon_skip_338240	32474676	32476670	32475077	32475077	Frame_Shift_Del	C	-	p.G619fs
SKCM	TCGA-EE-A29T-06	exon_skip_338240	32474676	32476670	32475300	32475300	Frame_Shift_Del	T	-	p.I545fs
COAD	TCGA-G4-6588-01	exon_skip_338240	32474676	32476670	32475317	32475317	Frame_Shift_Del	T	-	p.N539fs
LIHC	TCGA-DD-A39Y-01	exon_skip_338240	32474676	32476670	32475812	32475812	Frame_Shift_Del	T	-	p.N374fs
LIHC	TCGA-DD-A1EG-01	exon_skip_338240	32474676	32476670	32475855	32475855	Frame_Shift_Del	T	-	p.T361fs
LIHC	TCGA-DD-A39Y-01	exon_skip_338240	32474676	32476670	32476339	32476339	Frame_Shift_Del	T	-	p.K198fs
UCEC	TCGA-BS-A0UL-01	exon_skip_338240	32474676	32476670	32476663	32476663	Frame_Shift_Del	A	-	p.F90fs
LIHC	TCGA-BC-A112-01	exon_skip_338240	32474676	32476670	32476338	32476339	Frame_Shift_Ins	-	T	p.NR198fs
PAAD	TCGA-IB-7651-01	exon_skip_338240	32474676	32476670	32475213	32475213	Nonsense_Mutation	C	A	p.E574*
PAAD	TCGA-IB-7651-01	exon_skip_338240	32474676	32476670	32475213	32475213	Nonsense_Mutation	C	A	p.E574X
UCEC	TCGA-D1-A16X-01	exon_skip_338240	32474676	32476670	32475303	32475303	Nonsense_Mutation	C	A	p.E544*
BLCA	TCGA-KQ-A41R-01	exon_skip_338240	32474676	32476670	32475393	32475393	Nonsense_Mutation	G	A	p.Q514*
THCA	TCGA-EL-A3T0-01	exon_skip_338240	32474676	32476670	32475708	32475708	Nonsense_Mutation	C	A	p.E409*
SKCM	TCGA-EB-A4IS-01	exon_skip_338240	32474676	32476670	32476005	32476005	Nonsense_Mutation	G	A	p.R310*
SKCM	TCGA-EB-A4IS-01	exon_skip_338240	32474676	32476670	32476005	32476005	Nonsense_Mutation	G	A	p.R310X
PAAD	TCGA-IB-7651-01	exon_skip_338240	32474676	32476670	32476155	32476155	Nonsense_Mutation	C	A	p.E260*
PAAD	TCGA-IB-7651-01	exon_skip_338240	32474676	32476670	32476155	32476155	Nonsense_Mutation	C	A	p.E260X
BRCA	TCGA-E2-A155-01	exon_skip_338240	32474676	32476670	32476278	32476278	Nonsense_Mutation	G	A	p.Q219*
UCS	TCGA-ND-A4WC-01	exon_skip_338240	32474676	32476670	32476392	32476392	Nonsense_Mutation	G	A	p.R181*
UCS	TCGA-ND-A4WC-01	exon_skip_338240	32474676	32476670	32476392	32476392	Nonsense_Mutation	G	A	p.R181X
UCEC	TCGA-AP-A059-01	exon_skip_338240	32474676	32476670	32476527	32476527	Nonsense_Mutation	C	A	p.E136*
ACC	TCGA-OR-A5KB-01	exon_skip_338243	32477488	32477748	32477523	32477523	Nonsense_Mutation	C	T	p.W76*
ACC	TCGA-OR-A5KB-01	exon_skip_338243	32477488	32477748	32477523	32477523	Nonsense_Mutation	C	T	p.W76X
UCEC	TCGA-D1-A176-01	exon_skip_338243	32477488	32477748	32477560	32477560	Nonsense_Mutation	C	A	p.E64*
LUSC	TCGA-63-6202-01	exon_skip_338243	32477488	32477748	32477621	32477621	Nonsense_Mutation	G	T	p.C43*
LGG	TCGA-DU-7013-01	exon_skip_338240	32474676	32476670	32476671	32476671	Splice_Site	C	T	.

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
NCIH1781_LUNG	32474676	32476670	32475168	32475169	Frame_Shift_Del	CT	-	p.G589fs
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	32474676	32476670	32476663	32476663	Frame_Shift_Del	A	-	p.F90fs
NCIH1435_LUNG	32474676	32476670	32474678	32474678	Missense_Mutation	G	T	p.P752Q
SNUC5_LARGE_INTESTINE	32474676	32476670	32474724	32474724	Missense_Mutation	T	C	p.N737D
GP2D_LARGE_INTESTINE	32474676	32476670	32474741	32474741	Missense_Mutation	T	C	p.H731R
HEC59_ENDOMETRIUM	32474676	32476670	32474897	32474897	Missense_Mutation	T	C	p.Y679C
PECAPJ15_UPPER_AERODIGESTIVE_TRACT	32474676	32476670	32474928	32474928	Missense_Mutation	A	T	p.F669I
CPCN_LUNG	32474676	32476670	32475068	32475068	Missense_Mutation	G	A	p.A622V
HEC251_ENDOMETRIUM	32474676	32476670	32475105	32475105	Missense_Mutation	C	A	p.D610Y
JHUEM1_ENDOMETRIUM	32474676	32476670	32475131	32475131	Missense_Mutation	T	C	p.H601R
MM415_SKIN	32474676	32476670	32475203	32475203	Missense_Mutation	G	A	p.A577V
SNU81_LARGE_INTESTINE	32474676	32476670	32475335	32475335	Missense_Mutation	G	T	p.S533Y
ONCODG1_OVARY	32474676	32476670	32475363	32475363	Missense_Mutation	C	T	p.A524T
NIHOVCAR3_OVARY	32474676	32476670	32475363	32475363	Missense_Mutation	C	T	p.A524T
SUM159PT_BREAST	32474676	32476670	32475381	32475381	Missense_Mutation	G	C	p.L518V
DOV13_OVARY	32474676	32476670	32475470	32475470	Missense_Mutation	C	A	p.S488I
HS294T_SKIN	32474676	32476670	32475470	32475470	Missense_Mutation	C	A	p.S488I
HCC2450_LUNG	32474676	32476670	32475489	32475489	Missense_Mutation	C	G	p.D482H
M14_SKIN	32474676	32476670	32475528	32475528	Missense_Mutation	T	C	p.K469E
NCIH69_LUNG	32474676	32476670	32475529	32475530	Missense_Mutation	GG	CT	p.T468K
NCIH69_LUNG	32474676	32476670	32475530	32475530	Missense_Mutation	G	T	p.T468N
LNCAPCLONEFGC_PROSTATE	32474676	32476670	32475613	32475613	Missense_Mutation	T	A	p.K440N
SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	32474676	32476670	32475780	32475780	Missense_Mutation	C	T	p.D385N
NCIH835_LUNG	32474676	32476670	32475886	32475886	Missense_Mutation	C	A	p.M349I
SKPNDW_BONE	32474676	32476670	32475933	32475933	Missense_Mutation	G	T	p.L334I
BICR6_UPPER_AERODIGESTIVE_TRACT	32474676	32476670	32476017	32476017	Missense_Mutation	G	T	p.Q306K
CW2_LARGE_INTESTINE	32474676	32476670	32476052	32476052	Missense_Mutation	G	A	p.T294I
SW684_SOFT_TISSUE	32474676	32476670	32476069	32476070	Missense_Mutation	CC	TT	p.R288Q
EFO27_OVARY	32474676	32476670	32476103	32476103	Missense_Mutation	A	G	p.V277A
JHUEM1_ENDOMETRIUM	32474676	32476670	32476124	32476124	Missense_Mutation	C	T	p.R270H
HCT15_LARGE_INTESTINE	32474676	32476670	32476241	32476241	Missense_Mutation	G	A	p.T231I
MEWO_SKIN	32474676	32476670	32476277	32476277	Missense_Mutation	T	C	p.Q219R
COLO792_SKIN	32474676	32476670	32476302	32476302	Missense_Mutation	C	T	p.G211R
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	32474676	32476670	32476394	32476394	Missense_Mutation	T	C	p.Q180R
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	32474676	32476670	32476421	32476421	Missense_Mutation	G	T	p.S171Y
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	32474676	32476670	32476457	32476457	Missense_Mutation	T	G	p.Q159P
MDST8_LARGE_INTESTINE	32474676	32476670	32476553	32476553	Missense_Mutation	A	G	p.I127T
NB5_AUTONOMIC_GANGLIA	32474676	32476670	32476575	32476575	Missense_Mutation	G	A	p.L120F
HEC108_ENDOMETRIUM	32474676	32476670	32476608	32476608	Missense_Mutation	A	G	p.Y109H
C32_SKIN	32474676	32476670	32476609	32476609	Missense_Mutation	C	G	p.L108F
MPP89_PLEURA	32474676	32476670	32476629	32476629	Missense_Mutation	C	G	p.A102P
CHSA8926_BONE	32474676	32476670	32476637	32476637	Missense_Mutation	T	C	p.D99G
MEWO_SKIN	32477488	32477748	32477494	32477494	Missense_Mutation	C	G	p.G86R
HCC38_BREAST	32477488	32477748	32477496	32477496	Missense_Mutation	T	C	p.N85S
TE11_OESOPHAGUS	32477488	32477748	32477512	32477512	Missense_Mutation	G	C	p.L80V
SW954_VULVA	32477488	32477748	32477579	32477579	Missense_Mutation	C	G	p.M57I
SARC9371_BONE	32477488	32477748	32477644	32477644	Missense_Mutation	C	T	p.E36K
HCC2450_LUNG	32474676	32476670	32475012	32475012	Nonsense_Mutation	C	A	p.E641*
786O_KIDNEY	32477488	32477748	32477506	32477506	Nonsense_Mutation	G	A	p.Q82*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NLRC4

sQTL information located at the skipped exons.

Exon skip ID

Chromosome

Three exons

Skippped exon

ENST

Cancer type

SNP id

Location

DNA change (ref/var)

P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NLRC4

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NLRC4

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RelatedDrugs for NLRC4

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for NLRC4

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
NLRC4	C0751422	Hereditary Autoinflammatory Diseases	2	CTD_human
NLRC4	C4015067	AUTOINFLAMMATION WITH INFANTILE ENTEROCOLITIS	2	ORPHANET;UNIPROT
NLRC4	C0014356	Enterocolitis	1	CTD_human
NLRC4	C1096155	Macrophage Activation Syndrome	1	CTD_human
NLRC4	C4015276	FAMILIAL COLD AUTOINFLAMMATORY SYNDROME 4	1	UNIPROT

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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