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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CNTNAP3 Gene

protein-coding GIFtS: 48
GCID: GC09M039064

contactin associated protein-like 3

Explore 2 diseases affiliated with
CNTNAP3 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Contactin Associated Protein-Like 3¹ ²		FLJ14195¹
CASPR3¹ ² ³		RP11-138L21.1²
CNTNAP3A¹ ²		RP11-290L7.1²
KIAA1714¹ ³		Contactin-Associated Protein-Like 3²
Cell Recognition Molecule Caspr3² ³

External Ids:	HGNC: 13834¹	Entrez Gene: 79937²	Ensembl: ENSG00000106714⁷	OMIM: 610517⁵	UniProtKB: Q9BZ76³

Export aliases for CNTNAP3 gene to outside databases

Previous GC identifers: GC09M039063 GC09M038813

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for CNTNAP3:

The protein encoded by this gene belongs to the NCP family of cell-recognition molecules. This family represents a

distinct subgroup of the neurexins. NCP proteins mediate neuron-glial interactions in vertebrates and glial-glial

contact in invertebrates. The protein encoded by this gene may play a role in cell recognition within the nervous

system. Alternatively spliced transcript variants encoding different isoforms have been described but their biological

nature has not been determined. (provided by RefSeq, Jul 2008)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000009.11 NC_018920.1 NT_008413.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the CNTNAP3 gene promoter:
LHX3b/Lhx3b ATF-2 XBP-1 FOXJ2 (long isoform) LHX3a/Lhx3a Cart-1 FOXO1a FOXJ2 RSRFC4 FOXO1
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search SABiosciences Chromatin IP Primers for CNTNAP3

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CNTNAP3

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9p13.1 Ensembl cytogenetic band: 9p13.1 HGNC cytogenetic band: 9q12

CNTNAP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CNTNAP3 gene location

GeneLoc information about chromosome 9 GeneLoc Exon Structure

GeneLoc location for GC09M039064: view genomic region (about GC identifiers)

Start:	39,072,764 bp from pter	End:	39,288,456 bp from pter
Size:	215,693 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CNTP3_HUMAN, Q9BZ76 (See protein sequence)

Recommended Name: Contactin-associated protein-like 3 precursor

Size: 1288 amino acids; 140690 Da

Subcellular location: Isoform 1: Cell membrane; Single-pass type I membrane protein (Potential)

Subcellular location: Isoform 2: Secreted (Probable)

Sequence caution: Sequence=BAB21805.2; Type=Erroneous initiation;

Secondary accessions: B1AMA0 Q9C0E9

Alternative splicing: 2 isoforms: Q9BZ76-1 Q9BZ76-2 (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CNTNAP3: NX_Q9BZ76

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9BZ76

CNTNAP3 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_387504.2

ENSEMBL proteins:

ENSP00000297668 ENSP00000350863 ENSP00000432863 ENSP00000366887 ENSP00000366881

ENSP00000366884 ENSP00000320728

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Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	IEA	--
GO:0005886	plasma membrane	IEA	--
GO:0016021	integral to membrane	NAS	12093160

CNTNAP3 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

CNTNAP3 for domains About GeneDecksing

5/8 InterPro domains/families (see all 8):

IPR000742 EG-like_dom

IPR013320 ConA-like_subgrp

IPR001791 Laminin_G

IPR014716 Fibrinogen_a/b/g_C_1

IPR008979 Galactose-bd-like

Graphical View of Domain Structure for InterPro Entry Q9BZ76

ProtoNet protein and cluster: Q9BZ76

3 Blocks protein families:

IPB000421 Coagulation factor 5/8 type C domain (FA58C)

IPB001791 Laminin G

IPB006210 Type I EGF

UniProtKB/Swiss-Prot: CNTP3_HUMAN, Q9BZ76

Similarity: Belongs to the neurexin family

Similarity: Contains 2 EGF-like domains

Similarity: Contains 1 F5/8 type C domain

Similarity: Contains 1 fibrinogen C-terminal domain

Similarity: Contains 4 laminin G-like domains

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005102	receptor binding	IEA	--
GO:0005488	binding	--	--

CNTNAP3 for ontologies About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for CNTNAP3

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for CNTNAP3 (Q9BZ76³ ENSP00000297668⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
APBA1	Q02410³, ENSP00000265381⁴	I2D: score=2 STRING: ENSP00000265381
UBC	ENSP00000344818⁴	STRING: ENSP00000344818

About this table

Gene Ontology (GO): 3 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007155	cell adhesion	IEA	--
GO:0007165	signal transduction	IEA	--
GO:0008037	cell recognition	NAS	12093160

CNTNAP3 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

REFSEQ mRNAs for CNTNAP3 gene:

NM_033655.3

Unigene Cluster for CNTNAP3:

Contactin associated protein-like 3

Hs.128474 [show with all ESTs]

Unigene Representative Sequence: AB051501

13 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000297668(uc004abi.3 uc004abj.3 uc011lqr.2) ENST00000493965

ENST00000477002 ENST00000358144(uc004abk.1) ENST00000483502 ENST00000448573

ENST00000443583 ENST00000495573 ENST00000377659(uc011lqs.1) ENST00000469061

ENST00000377653 ENST00000377656 ENST00000323947

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		hsa-miR-520d-5p hsa-miR-524-5p hsa-miR-4282 hsa-miR-507 hsa-miR-3670
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Additional cDNA sequence:

AB051501.2 AF333769.2 AK056833.1 AK294281.1 BC132737.1 BC144130.1

11 DOTS entries:

DT.121148273 DT.100780860 DT.121148258 DT.95262953 DT.91906049 DT.101979763 DT.121186712 DT.121190421

DT.121203798 DT.121154825 DT.121169679

24/37 AceView cDNA sequences (see all 37):

AV726871 CA397290 BF196181 CR614145 CB121131 C01420 NM_033655 BF197858

BG169871 AI439093 BI670343 AI299744 AK056833 D60823 BF327494 BV183628

BI668345 AF333769 BF904677 AB051501 BV190384 AW271943 AI796942 BI038903

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

CNTNAP3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AAAACCAGAA

About this image

CNTNAP3 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 3 LifeMap Cells

Name

Category

PureStem™ mesenchymal progenitor E15 (Embryonic Progenitor Cell)

Adipose, Bone, Cartilage

PureStem™ progenitor U31 (Embryonic Progenitor Cell)

Line H7 (WA07) (Embryonic Stem Cell)

Early Embryo, Inner Cell Mass

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See CNTNAP3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CNTNAP3

SOURCE GeneReport for Unigene cluster: Hs.128474

SABiosciences Custom PCR Arrays for CNTNAP3

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for CNTNAP3 gene from 1/10 species (see all 10) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
zebrafish (Danio rerio)	Actinopterygii	si:ch211-122m3.1⁶ cntnap5b⁶ (see all 4)	contactin associated protein-like 5b (see all 4)	51(a) 49(a) (see all 4)	many ↔ many many ↔ many (see all 4)	10(2201990-2420674) 22(13602277-13734557)

ENSEMBL Gene Tree for CNTNAP3 (if available)
TreeFam Gene Tree for CNTNAP3 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for CNTNAP3 gene

CNTNAP1² NRXN3² CNTNAP5² CNTNAP3B² NRXN2² LOC643792² CNTNAP2² CNTNAP4²

NRXN1²

7 SIMAP similar genes for CNTNAP3 using alignment to 8 protein entries: CNTP3_HUMAN (see all proteins):

CNTNAP3B CASPR4 CNTNAP4 CNTNAP2 DKFZp686I15204 CNTNAP5

CNTNAP1

CNTNAP3 for paralogs About GeneDecksing

5/16 Pseudogenes.org Pseudogenes for CNTNAP3 (see all 16)
PGOHUM00000236932 PGOHUM00000236971 PGOHUM00000236061 PGOHUM00000236064 PGOHUM00000236071

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Clinical significance	Chr 9 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
rs16925199^1,2	--	39072296(+)	`ATATTC/TTCAGC`	1	--	ds500¹		0	--	--	--	--
rs142604574^1,2	--	39072361(+)	`TATCTA/GGAATA`	1	--	ds500¹		0	--	--	--	--
rs191666014^1,2	--	39072384(+)	`CATCAC/TTGCTT`	1	--	ds500¹		0	--	--	--	--
rs201141828^1,2	--	39072664(+)	`TGAAC-/AGTCTTC`	1	--	ds500¹		0	--	--	--	--
rs145110819^1,2	--	39072666(+)	`AACAGC/TCTTCA`	1	--	ds500¹		0	--	--	--	--
rs140619312^1,2	--	39073535(+)	`TTTTCC/TCATCT`	1	--	ut3¹		0	--	--	--	--
rs150491839^1,2	--	39074292(+)	`AATTGC/TTGGGA`	1	--	int¹		0	--	--	--	--
rs185321727^1,2	--	39074414(+)	`ACCAAA/CCACCT`	1	--	int¹		0	--	--	--	--
rs149045082^1,2	--	39074617(+)	`GACCGC/TGTACA`	1	--	int¹		0	--	--	--	--
rs62568848^1,2	--	39074739(+)	`TGAAAA/TTGTTT`	1	--	int¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for CNTNAP3 (39072764 - 39288456 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 19 variations for CNTNAP3
15/17 CNVs (see all 17): 70560 2128 52817 82950 7745 9616 95973 52818 70559 33096 3769 59530 95972 2817 4620
2 Indels: 13169 33470

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

CNTNAP3 for disorders           About GeneDecksing

OMIM gene information: 610517    OMIM disorders: --

2 diseases for CNTNAP3:    About MalaCards

bipolar disorder neuronitis

Export disorders for CNTNAP3 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for CNTNAP3 gene integrated from 9 sources:
(articles sorted by number of sources associating them with CNTNAP3)

Utopia: connect your pdf to the dynamic
world of online information

Caspr3 and Caspr4, two novel members of the Caspr family are expressed in the nervous system and interact with PDZ domains. (PubMed id 12093160)^{1, 2, 3} Spiegel I.... Peles E. (2002)
Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 11214970)^{1, 2} Nagase T.... Ohara O. (2000)
Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)¹ Kim W....Gygi S.P. (2011)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (2006)
DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)² Humphray S.J.... Dunham I. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)¹ Ota T.... Sugano S. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
Identification of susceptibility loci at 7q31 and 9p1 3 for bipolar disorder in an isolated population. (PubMed id 19851985)⁹ Palo O.M....Peltonen L. (2010)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 79937	HGNC: 13834	AceView: CNTNAP3	Ensembl:ENSG00000106714	euGenes: HUgn79937
ECgene: CNTNAP3	H-InvDB: CNTNAP3

(According to HUGE)
About This Section

HUGE: KIAA1714

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for CNTNAP3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for CNTNAP3 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for CNTNAP3 gene:
Search GeneIP for patents involving CNTNAP3

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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About This Section


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	Browse OriGene Antibodies		OriGene shRNA RFP for CNTNAP3
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat CNTNAP3
	QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CNTNAP3
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CNTNAP3
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat CNTNAP3
	QIAGEN QuantiFast Probe-based Assays in human, mouse, rat CNTNAP3
	QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat CNTNAP3

	GenScript Custom Purified and Recombinant Proteins Services for CNTNAP3		GenScript cDNA clones with any tag delivered in your preferred vector for CNTNAP3
	GenScript Custom Assay Services for CNTNAP3		GenScript Custom Superior Antibodies Services for CNTNAP3
	GenScript Custom overexpressing Cell Line Services for CNTNAP3		CloneReady with Over 120,000 Genes
	Gene Synthesis: Any Gene in Any Vector		Vector-based siRNA and miRNA, Ready for Transfection
	Gene Mutant Library, Variants up to 10^11		Plasmid Preparation
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CNTNAP3

GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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CNTNAP3 Gene

contactin associated protein-like 3

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CNTNAP3 Gene

contactin associated protein-like 3

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