Format

Send to:

Choose Destination

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

Gene ID: 5818, updated on 15-Jun-2019

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 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (119638098..119728725, 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 FunctionsWhat'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 BioSystems

  • Adherens junction, organism-specific biosystem (from KEGG)
    Adherens junction, organism-specific biosystemCell-cell adherens junctions (AJs), the most common type of intercellular adhesions, are important for maintaining tissue architecture and cell polarity and can limit cell movement and proliferation....
  • Adherens junction, conserved biosystem (from KEGG)
    Adherens junction, conserved biosystemCell-cell adherens junctions (AJs), the most common type of intercellular adhesions, are important for maintaining tissue architecture and cell polarity and can limit cell movement and proliferation....
  • Adherens junctions interactions, organism-specific biosystem (from REACTOME)
    Adherens junctions interactions, organism-specific biosystemThe adherens junctions (AJ) are multiprotein complexes that promote homotypic cell adhesion in nearly all types of tissue by linking membrane and cytoskeletal components at discrete contact regions (...
  • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
    Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
    Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
  • Cell junction organization, organism-specific biosystem (from REACTOME)
    Cell junction organization, organism-specific biosystem
    Cell junction organization
  • Cell-Cell communication, organism-specific biosystem (from REACTOME)
    Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
  • Cell-cell junction organization, organism-specific biosystem (from REACTOME)
    Cell-cell junction organization, organism-specific biosystemEpithelial cell-cell contacts consist of three major adhesion systems: adherens junctions (AJs), tight junctions (TJs), and desmosomes. These adhesion systems differ in their function and compositio...
  • Herpes simplex infection, organism-specific biosystem (from KEGG)
    Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Herpes simplex infection, conserved biosystem (from KEGG)
    Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Nectin adhesion pathway, organism-specific biosystem (from Pathway Interaction Database)
    Nectin adhesion pathway, organism-specific biosystem
    Nectin adhesion pathway
  • Nectin/Necl trans heterodimerization, organism-specific biosystem (from REACTOME)
    Nectin/Necl trans heterodimerization, organism-specific biosystemNectins and Nectin-like molecules (Necls) also undergo trans-heterophilic interactions to interact with other nectin or Necl family members. Besides these trans interactions among nectins and nectin-...

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 heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
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
 
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 NAS
Non-traceable Author Statement
more info
PubMed 
apical junction complex IEA
Inferred from Electronic Annotation
more info
 
cell-cell adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell adherens junction IDA
Inferred from Direct Assay
more info
PubMed 
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
    5001..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 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.
Support Center