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

    Gene ID: 5818, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:9706
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NECTIN1 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119638098..119729200, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119660108..119752026, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119508808..119599910, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902770 Neighboring gene uncharacterized LOC107984398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119456019-119456834 Neighboring gene NANOG hESC enhancer GRCh37_chr11:119484842-119485365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119486841-119487430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119488611-119489198 Neighboring gene keratin 8 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119493452-119494328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119494329-119495203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119498707-119499582 Neighboring gene uncharacterized LOC105369520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119507935-119508436 Neighboring gene uncharacterized LOC124900303 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:119520624-119521191 Neighboring gene RNA, U6 small nuclear 1123, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119535306-119535844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119535845-119536381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5633 Neighboring gene Sharpr-MPRA regulatory region 6199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119560233-119560733 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119562395-119563120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119563121-119563847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119564585-119565134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119565135-119565682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119566971-119567596 Neighboring gene NECTIN1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119584957-119585597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119588639-119589412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119594703-119595203 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:119597492-119598434 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:119599234-119600095 and GRCh37_chr11:119600096-119600956 Neighboring gene NECTIN1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119618498-119618998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119656890-119657713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119657714-119658536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119658954-119659491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119666350-119666971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119680838-119681338 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
    not available

    EBI GWAS Catalog

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

    Clone Names

    • MGC16207, MGC142031

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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..72734
      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
      O75465, Q15223, Q2M3D3, Q9HBE6, Q9HBW2
      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
      UniProtKB/TrEMBL
      A0A8V8TKI1
      Related
      ENSP00000513010.1, ENST00000531468.2
      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
    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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      119660108..119752026 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.