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    NECTIN1 nectin cell adhesion molecule 1 [ Homo sapiens (human) ]

    Gene ID: 5818, updated on 13-Mar-2020

    Summary

    Official Symbol
    NECTIN1provided by HGNC
    Official Full Name
    nectin cell adhesion molecule 1provided by HGNC
    Primary source
    HGNC:HGNC:9706
    See related
    Ensembl:ENSG00000110400 MIM:600644
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ED4; PRR; HIgR; HV1S; HVEC; OFC7; PRR1; PVRR; CD111; PVRL1; PVRR1; SK-12; CLPED1; nectin-1
    Summary
    This gene encodes an adhesion protein that plays a role in the organization of adherens junctions and tight junctions in epithelial and endothelial cells. The protein is a calcium(2+)-independent cell-cell adhesion molecule that belongs to the immunoglobulin superfamily and has 3 extracellular immunoglobulin-like loops, a single transmembrane domain (in some isoforms), and a cytoplasmic region. This protein acts as a receptor for glycoprotein D (gD) of herpes simplex viruses 1 and 2 (HSV-1, HSV-2), and pseudorabies virus (PRV) and mediates viral entry into epithelial and neuronal cells. Mutations in this gene cause cleft lip and palate/ectodermal dysplasia 1 syndrome (CLPED1) as well as non-syndromic cleft lip with or without cleft palate (CL/P). Alternative splicing results in multiple transcript variants encoding proteins with distinct C-termini. [provided by RefSeq, Oct 2009]
    Expression
    Biased expression in skin (RPKM 64.2), esophagus (RPKM 38.3) and 8 other tissues See more
    Orthologs

    Genomic context

    See NECTIN1 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    109.20200228 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (119638098..119729200, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119508808..119599435, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984398 Neighboring gene keratin 8 pseudogene 7 Neighboring gene uncharacterized LOC105369520 Neighboring gene RNA, U6 small nuclear 1123, pseudogene Neighboring gene NECTIN1 antisense RNA 1 Neighboring gene uncharacterized LOC102724301 Neighboring gene DExD-box helicase 39B pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Cleft lip/palate-ectodermal dysplasia syndrome
    MedGen: C2931488 OMIM: 225060 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of NECTIN1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120-mediated disruption of polarized oral epithelial junctions leads to exposure of nectin-1 and facilitate its binding to HSV-1 PubMed
    Tat tat HIV-1 Tat-mediated disruption of polarized oral epithelial junctions leads to exposure of nectin-1 and facilitate its binding to HSV-1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC16207, MGC142031

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion molecule binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell adhesion molecule binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    coreceptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    virion binding IEA
    Inferred from Electronic Annotation
    more info
     
    virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    adherens junction organization TAS
    Traceable Author Statement
    more info
     
    axon guidance IEA
    Inferred from Electronic Annotation
    more info
     
    cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    desmosome organization IEA
    Inferred from Electronic Annotation
    more info
     
    enamel mineralization IEA
    Inferred from Electronic Annotation
    more info
     
    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    immune response NAS
    Non-traceable Author Statement
    more info
    PubMed 
    iron ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    lens morphogenesis in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    protein localization to cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    viral entry into host cell NAS
    Non-traceable Author Statement
    more info
    PubMed 
    virion attachment to host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    adherens junction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    adherens junction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    apical junction complex IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell contact zone IEA
    Inferred from Electronic Annotation
    more info
     
    dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    growth cone membrane IEA
    Inferred from Electronic Annotation
    more info
     
    hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    integral component of presynaptic active zone membrane IEA
    Inferred from Electronic Annotation
    more info
     
    intracellular membrane-bounded organelle IEA
    Inferred from Electronic Annotation
    more info
     
    membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    nectin-1
    Names
    ectodermal dysplasia 4 (Margarita Island type)
    herpes simplex virus type 1 sensitivity
    herpes virus entry mediator C
    herpesvirus Ig-like receptor
    nectin 1
    poliovirus receptor-like 1
    poliovirus receptor-related 1 (herpesvirus entry mediator C)
    poliovirus receptor-related protein 1

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_013083.2 RefSeqGene

      Range
      4526..95628
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002855.5NP_002846.3  nectin-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_002846.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1; also known as isoform Delta, alpha, or HveC).
      Source sequence(s)
      AI819997, AP003390, AP003393, BC021976, BC104948
      Consensus CDS
      CCDS8426.1
      UniProtKB/Swiss-Prot
      Q15223
      Related
      ENSP00000264025.3, ENST00000264025.8
      Conserved Domains (3) summary
      cd05886
      Location:45143
      Ig1_Nectin-1_like; First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
      cd05890
      Location:146243
      Ig2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
      cd00096
      Location:265330
      Ig; Immunoglobulin domain
    2. NM_203285.2NP_976030.1  nectin-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_976030.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses alternate exons for its 3' end, compared to variant 1, resulting in a protein (isoform 2; also known as isoform Alpha, beta, or HIgR) with a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AF110314, AI819997, AP003390
      Consensus CDS
      CCDS8425.1
      UniProtKB/Swiss-Prot
      Q15223
      Related
      ENSP00000344974.2, ENST00000341398.6
      Conserved Domains (4) summary
      cd05886
      Location:45143
      Ig1_Nectin-1_like; First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
      cd05890
      Location:146243
      Ig2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
      smart00408
      Location:264323
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:38142
      IG_like; Immunoglobulin like
    3. NM_203286.2NP_976031.1  nectin-1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_976031.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate exon for its 3' end, compared to variant 1, resulting in a protein (isoform 3; also known as isoform Gamma) with a shorter and distinct C-terminus, compared to isoform 1. In contrast to isoforms 1 and 2, isoform 3 may be a soluble protein since it is predicted to lack a transmembrane domain.
      Source sequence(s)
      AI819997, AP003390, AY029539, BQ188335
      Consensus CDS
      CCDS8427.1
      UniProtKB/Swiss-Prot
      Q15223
      Related
      ENSP00000345289.2, ENST00000340882.2
      Conserved Domains (4) summary
      cd05886
      Location:45143
      Ig1_Nectin-1_like; First immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
      cd05890
      Location:146243
      Ig2_Nectin-1_like; Second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or as CD111) and similar proteins
      smart00408
      Location:264323
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:38142
      IG_like; Immunoglobulin like

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

      Range
      119638098..119729200 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_032767.1: Suppressed sequence

      Description
      NM_032767.1: This RefSeq was permanently suppressed because it was primarily UTR sequence.
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