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Aliases for NRXN3 Gene

Aliases for NRXN3 Gene

  • Neurexin 3 2 3
  • Neurexin-3-Alpha 3 4
  • C14orf60 3 4
  • Chromosome 14 Open Reading Frame 60 2
  • Neurexin III-Alpha 4
  • Neurexin III-Beta 4
  • Neurexin III 3
  • KIAA0743 4

External Ids for NRXN3 Gene

Previous Symbols for NRXN3 Gene

  • C14orf60

Summaries for NRXN3 Gene

Entrez Gene Summary for NRXN3 Gene

  • This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants and protein isoforms for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. Genetic variation at this locus has been associated with a range of behavioral phenotypes, including alcohol dependence and autism spectrum disorder. [provided by RefSeq, Dec 2012]

GeneCards Summary for NRXN3 Gene

NRXN3 (Neurexin 3) is a Protein Coding gene. Diseases associated with NRXN3 include autism spectrum disorder and alcohol dependence. Among its related pathways are Muscular Dystrophies and Dystrophin-Glycoprotein Complex and Cell adhesion molecules (CAMs). GO annotations related to this gene include receptor activity and calcium channel regulator activity. An important paralog of this gene is CNTNAP1.

UniProtKB/Swiss-Prot for NRXN3 Gene

  • Neuronal cell surface protein that may be involved in cell recognition and cell adhesion. May mediate intracellular signaling

  • Neuronal cell surface protein that may be involved in cell recognition and cell adhesion. May play a role in angiogenesis (By similarity).

Gene Wiki entry for NRXN3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NRXN3 Gene

Genomics for NRXN3 Gene

Genomic Location for NRXN3 Gene

78,170,373 bp from pter
79,868,290 bp from pter
1,697,918 bases
Plus strand

Genomic View for NRXN3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for NRXN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NRXN3 Gene

Regulatory Elements for NRXN3 Gene

Proteins for NRXN3 Gene

  • Protein details for NRXN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A5PKW8
    • A8MPU5
    • B3KPM7
    • Q6NUR0
    • Q8IUD8

    Protein attributes for NRXN3 Gene

    637 amino acids
    Molecular mass:
    69305 Da
    Quaternary structure:
    • The cytoplasmic C-terminal region binds to CASK (By similarity). Binds to neuroligins NLGN1, NLGN2 and NLGN3 (By similarity). Weakly interacts with CBLN1 and CBLN2. Very weak binding, if any, with CBLN4 (By similarity).

    Alternative splice isoforms for NRXN3 Gene

  • Protein details for NRXN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A6NGR4
    • A7MD34
    • O95378
    • Q8IUE3
    • Q9NS47
    • Q9P1V3
    • Q9P1V6
    • Q9UIE2
    • Q9UIE3
    • Q9ULA5
    • Q9Y486

    Protein attributes for NRXN3 Gene

    1643 amino acids
    Molecular mass:
    180599 Da
    Quaternary structure:
    • The laminin G-like domain 2 binds to NXPH1. Specific isoforms bind to alpha-dystroglycan. The cytoplasmic C-terminal region binds to CASK (By similarity).
    • Sequence=BAA34463.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for NRXN3 Gene

neXtProt entry for NRXN3 Gene

Proteomics data for NRXN3 Gene at MOPED

Post-translational modifications for NRXN3 Gene

  • Proccessed by alpha-secretase leading to the formation of an extracellular soluble protein as well as a C-terminal membrane-embedded fragment (CTF). Proteolysis of these CTFs by gamma-secretase releases intracellular domains (ICDs) and extracellular peptides
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn184, Asn252, and Asn296
  • Glycosylation at Asn58, Asn105, Asn757, Asn1189, Asn1257, and Asn1301

No data available for DME Specific Peptides for NRXN3 Gene

Domains for NRXN3 Gene

Suggested Antigen Peptide Sequences for NRXN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 3 EGF-like domains.:
    • Q9Y4C0
  • Contains 6 laminin G-like domains.:
    • Q9Y4C0
  • Contains 1 laminin G-like domain.:
    • Q9HDB5
  • Belongs to the neurexin family.:
    • Q9Y4C0
    • Q9HDB5
genes like me logo Genes that share domains with NRXN3: view

No data available for Gene Families for NRXN3 Gene

Function for NRXN3 Gene

Molecular function for NRXN3 Gene

GENATLAS Biochemistry: rat neurexin III alpha homolog longer form,also coding for the shorter beta neurexin III form,both with multiple alternatively spliced isoforms,potentially involved in neuronal cell adhesion and intercellular signaling,(see also CASPR)
UniProtKB/Swiss-Prot Function: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion. May mediate intracellular signaling
UniProtKB/Swiss-Prot Function: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion. May play a role in angiogenesis (By similarity).

Gene Ontology (GO) - Molecular Function for NRXN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity TAS 1621094
GO:0004888 transmembrane signaling receptor activity NAS 18923512
GO:0005246 calcium channel regulator activity IEA --
GO:0005515 protein binding --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with NRXN3: view
genes like me logo Genes that share phenotypes with NRXN3: view

Animal Models for NRXN3 Gene

MGI Knock Outs for NRXN3:

miRNA for NRXN3 Gene

miRTarBase miRNAs that target NRXN3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for NRXN3 Gene

Localization for NRXN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NRXN3 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for NRXN3 Gene COMPARTMENTS Subcellular localization image for NRXN3 gene
Compartment Confidence
plasma membrane 4
cytosol 1
endoplasmic reticulum 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for NRXN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane TAS 1621094
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NRXN3: view

Pathways for NRXN3 Gene

genes like me logo Genes that share pathways with NRXN3: view

Pathways by source for NRXN3 Gene

1 KEGG pathway for NRXN3 Gene

Interacting Proteins for NRXN3 Gene

Gene Ontology (GO) - Biological Process for NRXN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis ISS --
GO:0007158 neuron cell-cell adhesion TAS 18923512
GO:0007165 signal transduction NAS 18923512
GO:0007268 synaptic transmission IEA --
GO:0007269 neurotransmitter secretion IEA --
genes like me logo Genes that share ontologies with NRXN3: view

Transcripts for NRXN3 Gene

Unigene Clusters for NRXN3 Gene

Neurexin 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for NRXN3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b
SP1: - - - - - - - -
SP2: - - - - -
SP4: - - -
SP5: - - -

Relevant External Links for NRXN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for NRXN3 Gene

mRNA expression in normal human tissues for NRXN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NRXN3 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (9.8) and Brain - Cerebellum (7.3).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for NRXN3 Gene

SOURCE GeneReport for Unigene cluster for NRXN3 Gene Hs.368307

mRNA Expression by UniProt/SwissProt for NRXN3 Gene

Tissue specificity: Expressed in the blood vessel walls (at protein level). Highly expressed in brain, lung, and pancreas; a lower level of expression is detectable in heart, placenta, liver, and kidney, whereas no expression can be observed in skeletal muscle. Isoform 4a is heart-specific.
genes like me logo Genes that share expressions with NRXN3: view

Orthologs for NRXN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NRXN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia NRXN3 36
  • 65 (a)
(Bos Taurus)
Mammalia NRXN3 36
  • 72 (a)
(Canis familiaris)
Mammalia -- 36
  • 98 (a)
-- 36
  • 45 (a)
(Mus musculus)
Mammalia Nrxn3 16
Nrxn3 36
  • 67 (a)
(Monodelphis domestica)
Mammalia NRXN3 36
  • 68 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 44 (a)
-- 36
  • 61 (a)
-- 36
  • 18 (a)
-- 36
  • 79 (a)
-- 36
  • 36 (a)
(Gallus gallus)
Aves NRXN3 36
  • 81 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 51 (a)
-- 36
  • 63 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.609 35
(Danio rerio)
Actinopterygii nrxn3a 36
  • 53 (a)
nrxn3b 36
  • 51 (a)
fruit fly
(Drosophila melanogaster)
Insecta Nrx-1 36
  • 22 (a)
Nrx-1 37
  • 38 (a)
(Caenorhabditis elegans)
Secernentea nrx-1 36
  • 17 (a)
Species with no ortholog for NRXN3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for NRXN3 Gene

Gene Tree for NRXN3 (if available)
Gene Tree for NRXN3 (if available)

Paralogs for NRXN3 Gene

Paralogs for NRXN3 Gene

Selected SIMAP similar genes for NRXN3 Gene using alignment to 5 proteins: Pseudogenes for NRXN3 Gene

genes like me logo Genes that share paralogs with NRXN3: view

Variants for NRXN3 Gene

Sequence variations from dbSNP and Humsavar for NRXN3 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type MAF
rs3356 -- 79,673,569(-) GGGAA(C/T)ACTTC intron-variant
rs17188 -- 78,330,154(+) TTTAA(A/G)GAAGC intron-variant
rs31349 -- 78,922,088(+) CAAAT(A/C)ACTTC intron-variant
rs31350 -- 78,923,214(+) ATTGA(A/T)TATCC intron-variant
rs31351 -- 78,923,369(+) ATGTT(A/C)GATGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for NRXN3 Gene

Variant ID Type Subtype PubMed ID
nsv832837 CNV Gain 17160897
essv8004 CNV CNV 17122850
dgv645e1 CNV Complex 17122850
esv25836 CNV Loss 19812545
esv270066 CNV Insertion 20981092
esv274035 CNV Insertion 20981092
nsv9157 CNV Gain 18304495
esv34435 CNV Loss 17911159
essv23163 CNV CNV 17122850
nsv1367 CNV Loss 18451855
esv2675515 CNV Deletion 23128226
esv28584 CNV Loss 19812545
esv2421742 CNV Deletion 20811451
nsv442348 CNV CNV 18776908
nsv517018 CNV Loss 19592680
nsv524797 CNV Loss 19592680
nsv514753 CNV Complex 21397061
nsv819821 CNV Gain 19587683
nsv1368 CNV Insertion 18451855
nsv832838 CNV Gain 17160897
esv2546858 CNV Deletion 19546169
esv6644 CNV Gain 19470904
esv2674347 CNV Deletion 23128226
esv2661212 CNV Deletion 23128226
esv28416 CNV Loss 19812545
nsv902110 CNV Loss 21882294
esv2748912 CNV Deletion 23290073
esv1996512 CNV Deletion 18987734
esv4655 CNV Deletion 18987735
dgv37n6 CNV Loss 16902084
esv990720 CNV Deletion 20482838
esv2748913 CNV Deletion 23290073
esv1465114 CNV Deletion 17803354
nsv827002 CNV Loss 20364138
dgv646e1 CNV Complex 17122850
nsv526245 CNV Loss 19592680
nsv528346 CNV Loss 19592680
nsv513413 CNV Insertion 21212237
esv2471037 CNV Insertion 19546169
esv2666928 CNV Deletion 23128226
nsv902111 CNV Loss 21882294
nsv902112 CNV Gain 21882294
esv2748914 CNV Deletion 23290073
nsv521160 CNV Gain 19592680
esv2666514 CNV Deletion 23128226
esv28866 CNV Loss 19812545
nsv518333 CNV Loss 19592680
nsv1369 CNV Insertion 18451855
nsv827003 CNV Loss 20364138
esv2674009 CNV Deletion 23128226
esv2404426 CNV Deletion 18987734
nsv511536 CNV Loss 21212237
esv2675415 CNV Deletion 23128226
nsv1370 CNV Loss 18451855
dgv46e180 CNV Deletion 20482838
nsv820296 CNV Gain 19587683
nsv514754 CNV Loss 21397061
nsv512366 CNV Loss 21212237
dgv378n67 CNV Loss 20364138
nsv820615 CNV Deletion 20802225
esv22035 CNV Gain+Loss 19812545
esv2673043 CNV Deletion 23128226
nsv498833 CNV Loss 21111241
nsv84516 CNV Loss 16902084
esv2748915 CNV Deletion 23290073
esv32903 CNV Loss 17666407
esv33123 CNV Gain 17666407
nsv902113 CNV Gain 21882294
esv2748916 CNV Deletion 23290073
esv7301 CNV Gain 19470904
dgv405e199 CNV Deletion 23128226
esv22714 CNV Loss 19812545
esv2669148 CNV Deletion 23128226
esv2748917 CNV Deletion 23290073
esv2748920 CNV Deletion 23290073
esv2748921 CNV Deletion 23290073
esv2748922 CNV Deletion 23290073
esv1541911 CNV Deletion 17803354
nsv819807 CNV Gain 19587683

Relevant External Links for NRXN3 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NRXN3 Gene

Disorders for NRXN3 Gene

(2) University of Copenhagen DISEASES for NRXN3 Gene

Relevant External Links for NRXN3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with NRXN3: view

No data available for UniProtKB/Swiss-Prot for NRXN3 Gene

Publications for NRXN3 Gene

  1. Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. (PMID: 11944992) Rowen L. … Graveley B.R. (Genomics 2002) 2 3 4 23
  2. Identification and characterization of heart-specific splicing of human neurexin 3 mRNA (NRXN3). (PMID: 12379233) Occhi G. … Antonio Danieli G. (Biochem. Biophys. Res. Commun. 2002) 2 3 4 23
  3. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira A.R. … Marazita M.L. (Genet. Med. 2008) 3 23 48
  4. NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. (PMID: 19557197) Heard-Costa N.L. … North K.E. (PLoS Genet. 2009) 3 23 48
  5. Association of a polymorphism in the NRXN3 gene with the degree of smoking in schizophrenia: a preliminary study. (PMID: 19658047) Novak G. … Le Foll B. (World J. Biol. Psychiatry 2009) 3 23 48

Products for NRXN3 Gene

Sources for NRXN3 Gene

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