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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

NLGN4Y Gene

protein-coding   GIFtS: 52
GCID: GC0YP016634

neuroligin 4, Y-linked

(Previous names: neuroligin 4, Y linked )
 Explore 4 diseases affiliated with
NLGN4Y via our new
 Human Malady Compendium 
Biological research products
for NLGN4Y
    

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

Aliases
Neuroligin 4, Y-Linked1 2
KIAA09511 3 5
Neuroligin 4, Y Linked1
Neuroligin-4, Y-Linked2
Neuroligin Y3

External Ids:    HGNC: 155291   Entrez Gene: 228292   Ensembl: ENSG000001652467   OMIM: 4000285   UniProtKB: Q8NFZ33   

Export aliases for NLGN4Y gene to outside databases

Previous GC identifers: GC0YU990048 GC0YM9A0047 GC0XM005269 GC0YP015072 GC0YP015145 GC0YP011242


(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 NLGN4Y:
This gene encodes a type I membrane protein that belongs to the family of neuroligins, which are cell adhesion
molecules present at the postsynaptic side of the synapse, and may be essential for the formation of functional
synapses. Alternatively spliced transcript variants have been found for this gene.(provided by RefSeq, Mar 2011)

UniProtKB/Swiss-Prot: NLGNY_HUMAN, Q8NFZ3
Function: Putative neuronal cell surface protein involved in cell-cell-interactions




(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_000024.9  NT_011875.12  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for NLGN4Y
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNLGN4Y promoter sequence
   Search SABiosciences Chromatin IP Primers for NLGN4Y

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NLGN4Y


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

Entrez Gene cytogenetic band: Yq11.221   Ensembl cytogenetic band:  Yq11.221   HGNC chromosome: Y

NLGN4Y Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NLGN4Y gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP016634:  view genomic region     (about GC identifiers)

Start:
16,634,488 bp from pter      End:
16,957,530 bp from pter
Size:
323,043 bases      Orientation:
plus 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: NLGNY_HUMAN, Q8NFZ3 (See protein sequence)
Recommended Name: Neuroligin-4, Y-linked precursor  
Size: 816 amino acids; 92021 Da
Subunit: Homodimer. Interacts with NRXN1 in a calcium-dependent manner. Interacts through its C-terminus with
DLG4/PSD-95 third PDZ domain (By similarity)
Subcellular location: Cell membrane; Single-pass type I membrane protein. Cell junction, synapse, postsynaptic cell
membrane, postsynaptic density (By similarity)
Sequence caution: Sequence=BAA76795.2; Type=Erroneous initiation;
Secondary accessions: F5H6W0 Q14D08 Q7Z3T5 Q8N5B6 Q9Y2F8
Alternative splicing: 3 isoforms:  Q8NFZ3-1   Q8NFZ3-2   Q8NFZ3-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for NLGN4Y: NX_Q8NFZ3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8NFZ3

  • NLGN4Y Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001157710.1  NP_001193779.1  NP_055708.3  

    ENSEMBL proteins: 
     ENSP00000372325   ENSP00000348169   ENSP00000372320   ENSP00000342535   ENSP00000412638  
     ENSP00000407960   ENSP00000297967  

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    Uscn Proteins for NLGN4Y

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral to plasma membrane IBA--
    GO:0009986cell surface IBA--
    GO:0014069postsynaptic density IEA--
    GO:0016020membrane ----
    GO:0030054cell junction IEA--


    NLGN4Y 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

    NLGN4Y for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR000460 Neuroligin
     IPR019819 Carboxylesterase_B_CS
     IPR002018 CarbesteraseB

    Graphical View of Domain Structure for InterPro Entry Q8NFZ3

    ProtoNet protein and cluster: Q8NFZ3

    1 Blocks protein family: IPB000460 Neuroligin signature

    UniProtKB/Swiss-Prot: NLGNY_HUMAN, Q8NFZ3
    Similarity: Belongs to the type-B carboxylesterase/lipase family


    (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

    Function Summary:

         UniProtKB/Swiss-Prot: NLGNY_HUMAN, Q8NFZ3
    Function: Putative neuronal cell surface protein involved in cell-cell-interactions

    miRNA
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004091NOT carboxylesterase activity IKR--
    GO:0004872receptor activity IBA--
    GO:0005515protein binding IPI17292328
    GO:0042043neurexin family protein binding IBA--


    NLGN4Y 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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1GABA A receptor activation
    GABA signaling in brain0.26

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    1 EMD Millipore Pathway for NLGN4Y
        GABA signaling in brain




    NLGN4Y for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for NLGN4Y

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

    2 Interacting proteins for NLGN4Y (ENSP000003425354) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NRXN1ENSP000003851424STRING: ENSP00000385142
    NRXN2ENSP000002654594STRING: ENSP00000265459
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IEA--
    GO:0007416synapse assembly IBA--


    NLGN4Y 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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for NLGN4Y
    Search CenterWatch for drugs/clinical trials and news about NLGN4Y / NLGNY 

    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for NLGN4Y gene (3 alternative transcripts): 
    NM_001164238.1  NM_001206850.1  NM_014893.4  

    Unigene Cluster for NLGN4Y:

    Neuroligin 4, Y-linked
    Hs.439199  [show with all ESTs]
    Unigene Representative Sequence: NR_028319
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000382872(uc004fte.2) ENST00000355905(uc004ftg.2) ENST00000382868(uc011nas.1)
    ENST00000476359(uc004ftf.2) ENST00000339174(uc004fth.2) ENST00000413217
    ENST00000471252 ENST00000481089 ENST00000434873 ENST00000297967(uc004fti.4)


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    hsa-miR-607 hsa-miR-16-1* hsa-miR-3653 hsa-miR-570 hsa-miR-124 hsa-miR-9 hsa-miR-3658 hsa-miR-155*
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    Additional cDNA sequence: 

    AB023168.1 AF376804.1 AK295117.1 BC032567.1 BC113525.1 BC113551.1 BX537428.1 NR_028319.1 
    NR_046355.1 

    5 DOTS entries:

    DT.75189473  DT.92424999  DT.100021787  DT.100779335  DT.120654855 

    24/39 AceView cDNA sequences (see all 39):

    BE465446 BQ002163 BE857978 BU727218 NM_014893 BQ924832 AL120487 AF376804 
    AX773941 AI807783 AX773943 CD108831 BX537428 BF060948 AB023168 BM722570 
    BM972838 BX105854 AA578623 AI597685 AW304721 AA187847 BI834043 CD654789 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for NLGN4Y    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8 ^ 9
    SP1:                                                                                          
    SP2:                                                                                          
    SP3:        -     -     -     -     -     -                                                   
    SP4:                                                                                          
    SP5:                                -     -                                                   


    ECgene alternative splicing isoforms for NLGN4Y

    (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

    NLGN4Y expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAACTGCAAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See NLGN4Y Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for NLGN4Y

    SOURCE GeneReport for Unigene cluster: Hs.439199

    UniProtKB/Swiss-Prot: NLGNY_HUMAN, Q8NFZ3
    Tissue specificity: Expressed in fetal and adult brain, prostate and testis

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    In Situ
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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 animals.

    Orthologs for NLGN4Y gene from 5/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves D2X2H2_CHICK6
    Neuroligin 4Uncharacterized protein
    92(a)
    1 → many
    1(130855539-131025943)
    lizard
    (Anolis carolinensis)
    Reptilia D2X2I0_ANOCA6
    Neuroligin 4
    92(a)
    1 → many
    3(116270616-116421197)
    zebrafish
    (Danio rerio)
    Actinopterygii nlgn4b1 neuroligin 4b 71.2(n)
    78.82(a)
      100147967  NM_001166337.1  NP_001159809.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG341391 CG34139 51.73(n)
    43.92(a)
      42402  NM_001043265.2  NP_001036730.2 
    worm
    (Caenorhabditis elegans)
    Secernentea nlg-16
    Neuroligin-1
    24(a)
    1 → many
    X(13625340-13631047)


    ENSEMBL Gene Tree for NLGN4Y (if available)
    TreeFam Gene Tree for NLGN4Y (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for NLGN4Y gene
    NLGN12  CES22  ACHE2  CES4A2  NLGN4X2  CES32  NLGN32  NLGN22  
    CES12  CEL2  BCHE2  CES5A2  
    9 SIMAP similar genes for NLGN4Y using alignment to 4 protein entries:     NLGNY_HUMAN (see all proteins):
    NLGN4X    DKFZp686F02202    NLGN3    nlgn1    NLGN1    NLGN2
    CES1P1    BCHE    CES2

    NLGN4Y for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for NLGN4Y
    PGOHUM00000241175


    (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

    10/730 NCBI SNPs in NLGN4Y are shown (see all 730    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr Y posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs97861031,2
    C--16633829(+) AAATAT/CAGGGG 3 -- us2k11Minor allele frequency- C:0.00WA 2
    rs97866981,2
    C,F--16636022(+) AAAAGC/TTGGAA 4 -- int1 us2k12Minor allele frequency- T:0.50WA NA 4
    rs173072941,2
    C,F--16638804(+) ATGGTA/GAGCAT 4 -- int13Minor allele frequency- G:0.09NA 66
    rs558231511,2
    C--16641085(+) TATTTC/TGCTAA 4 -- int10--------
    rs169804671,2
    C,F--16641386(+) TGGGAC/TGGGCA 4 -- int15Minor allele frequency- T:0.26NA WA 70
    rs561007301,2
    C--16641774(+) GTTTTC/TCTCAG 4 -- int10--------
    rs560672621,2
    C--16642381(+) TTTTTC/TTAAAT 4 -- int10--------
    rs773464071,2
    C--16642946(+) ACAGGC/TTCTTT 4 -- int10--------
    rs341658111,2
    C--16643296(+) AGCTGT/GTTAAT 4 -- int11Minor allele frequency- G:0.00NA 2
    rs752344711,2
    C--16645096(+) GATTCA/GACAAA 4 -- int10--------

    HapMap Linkage Disequilibrium report for NLGN4Y (16634488 - 16884488 bp, first 250kb of NLGN4Y)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for NLGN4Y: --
    Human Gene Mutation Database (HGMD): NLGN4Y

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NLGN4Y
    DNA2.0 Custom Variant and Variant Library Synthesis for NLGN4Y

    (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

    NLGN4Y for disorders           About GeneDecksing

    OMIM gene information: 400028    OMIM disorders: --

    4 diseases for NLGN4Y:    About MalaCards
    tuberculosis    prostatitis    neuronitis    mycobacterium tuberculosis

    2 diseases from the University of Copenhagen DISEASES database for NLGN4Y:
    Asperger syndrome     Autistic disorder
    Human Genome Epidemiology (HuGE) Navigator: NLGN4Y (2 documents)

    Export disorders for NLGN4Y 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 NLGN4Y gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with NLGN4Y)
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    1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10231032)1, 2, 3 Nagase T.... Ohara O. (1999)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2 Skaletsky H.... Page D.C. (2003)
    4. Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. (PubMed id 12669065)1, 2 Jamain S.... Van Maldergem L. (2003)
    5. Analysis of the neuroligin 4Y gene in patients with autism. (PubMed id 18628683)1, 9 Yan J....Sommer S.S. (2008)
    6. Analysis of four neuroligin genes as candidates for autism. (PubMed id 16077734)1, 9 Ylisaukko-oja T....Jarvela I. (2005)
    7. Association of Y chromosome haplotypes with autism. (PubMed id 19605777)1 Serajee F.J. and Mahbubul Huq A.H. (2009)
    8. Reduced social interaction and ultrasonic communicati on in a mouse model of monogenic heritable autism. (PubMed id 18227507)1 Jamain S....Brose N. (2008)
    9. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    10. Neuroligins 3 and 4X interact with syntrophin-gamma2, and the interactions are affected by autism-related mutations. (PubMed id 17292328)1 Yamakawa H....Ishiura S. (2007)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 22829 HGNC: 15529 AceView: NLGN4Y Ensembl:ENSG00000165246 euGenes: HUgn22829
    ECgene: NLGN4Y H-InvDB: NLGN4Y

    (According to HUGE)
    About This Section
    HUGE: KIAA0951

    (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
    NameDescription
    PharmGKB entry for NLGN4Y Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for NLGN4Y gene:
    Search GeneIP for patents involving NLGN4Y

    GeneCards and IP:
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