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NECTIN3 nectin cell adhesion molecule 3 [ Homo sapiens (human) ]

Gene ID: 25945, updated on 7-Sep-2023

Summary

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Official Symbol
NECTIN3provided by HGNC
Official Full Name
nectin cell adhesion molecule 3provided by HGNC
Primary source
HGNC:HGNC:17664
See related
Ensembl:ENSG00000177707 MIM:607147; AllianceGenome:HGNC:17664
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
PPR3; PRR3; CD113; PVRL3; PVRR3; CDW113; NECTIN-3
Summary
This gene encodes a member of the nectin family of proteins, which function as adhesion molecules at adherens junctions. This family member interacts with other nectin-like proteins and with afadin, a filamentous actin-binding protein involved in the regulation of directional motility, cell proliferation and survival. This gene plays a role in ocular development involving the ciliary body. Mutations in this gene are believed to result in congenital ocular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression
Broad expression in thyroid (RPKM 7.4), testis (RPKM 7.4) and 22 other tissues See more
Orthologs
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Genomic context

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See NECTIN3 in Genome Data Viewer
Location:
3q13.13
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (111071816..111194170)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (113792242..113914605)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (110790663..110913017)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:110404170-110404746 Neighboring gene ribosomal protein SA pseudogene 29 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:110607916-110608531 Neighboring gene putative uncharacterized protein LOC151760 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:110683374-110684573 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:110764172-110765371 Neighboring gene NECTIN3 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:110929660-110930290 Neighboring gene uncharacterized LOC124909493 Neighboring gene uncharacterized LOC105374038

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Loss of nectin-3 expression as a marker of tumor aggressiveness in pancreatic neuroendocrine tumor. Hirabayashi K, et al. Pathol Int, 2020 Feb. PMID 31855317
  2. Nectin-3 is a new biomarker that mediates the upregulation of MMP2 and MMP9 in ovarian cancer cells. Xu F, et al. Biomed Pharmacother, 2019 Feb. PMID 30469078
  3. Binding and entry of Clostridium difficile toxin B is mediated by multiple domains. Manse JS, et al. FEBS Lett, 2015 Dec 21. PMID 26602083
  4. Identification of an epithelial cell receptor responsible for Clostridium difficile TcdB-induced cytotoxicity. LaFrance ME, et al. Proc Natl Acad Sci U S A, 2015 Jun 2. PMID 26038560, Free PMC Article
  5. Nectin expression in pancreatic adenocarcinoma: nectin-3 is associated with a poor prognosis. Izumi H, et al. Surg Today, 2015 Apr. PMID 25690753, Free PMC Article

See all (53) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Loss of nectin-3 expression as a marker of tumor aggressiveness in pancreatic neuroendocrine tumor.
    Title: Loss of nectin-3 expression as a marker of tumor aggressiveness in pancreatic neuroendocrine tumor.
  2. Nectin-3 expression was associated with ovarian cancer, and a greater expression level of nectin-3 was related to poor overall survival.
    Title: Nectin-3 is a new biomarker that mediates the upregulation of MMP2 and MMP9 in ovarian cancer cells.
  3. Nectin-3 mutation in men with severe teratospermia
    Title: Detection of candidate nectin gene mutations in infertile men with severe teratospermia.
  4. Data suggest that 3 independent regions of TcdB (Clostridium difficile toxin B; 1372-1493, 1493-1848, 1851-2366) contribute to binding and entry of TcdB into mammalian cells; residues 1372-1493 are sufficient for interaction with PVRL3.
    Title: Binding and entry of Clostridium difficile toxin B is mediated by multiple domains.
  5. Expression of nectin-3 in pancreatic cancer can be a prognostic factor.
    Title: Nectin expression in pancreatic adenocarcinoma: nectin-3 is associated with a poor prognosis.
  6. PVRL3 is a physiologically relevant binding partner that can serve as a target for the prevention of TcdB-induced cytotoxicity in C. difficile infection.
    Title: Identification of an epithelial cell receptor responsible for Clostridium difficile TcdB-induced cytotoxicity.
  7. Nectin-3 is associated with the formation of cell junctions and be a putative suppressor molecule to the invasion of breast cancer cells.
    Title: The expression of the Nectin complex in human breast cancer and the role of Nectin-3 in the control of tight junctions during metastasis.
  8. Nectin-3 trans-interacts with Nectin-2 to promote lymphocyte and monocyte extravasation.
    Title: Nectin-3 (CD113) interacts with Nectin-2 (CD112) to promote lymphocyte transendothelial migration.
  9. Data suggest that expression of nectin-3 is up-regulated in eutopic endometrium of patients with endometriosis as compared with control subjects and up-regulated in all endometriotic lesions investigated compared with eutopic endometrium.
    Title: Eutopic endometrium and peritoneal, ovarian and colorectal endometriotic tissues express a different profile of nectin-1, -3, -4 and nectin-like molecule 2.
  10. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of NECTIN3 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat downregulates the expression of poliovirus receptor-related 3 (PVRL3) in human primary T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ90624, DKFZp566B0846

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule 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
  
Process Evidence Code Pubs
involved_in establishment of protein localization to plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in fertilization 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
 PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lens morphogenesis in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in protein localization to cell junction IEA
Inferred from Electronic Annotation
more info
  
involved_in retina morphogenesis in camera-type eye IEA
Inferred from Electronic Annotation
more info
  
involved_in viral entry into host cell IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
is_active_in apical junction complex IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in axon IEA
Inferred from Electronic Annotation
more info
  
located_in cell-cell contact zone IEA
Inferred from Electronic Annotation
more info
  
located_in cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nectin-3
Names
nectin 3
poliovirus receptor-related 3
poliovirus receptor-related protein 3

NCBI Reference Sequences (RefSeq)

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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_029835.1 RefSeqGene

    Range
    5058..70802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001243286.2 → NP_001230215.1  nectin-3 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AA555086, AC133477, AC137833, BC067808, BI464010
    Consensus CDS
    CCDS58842.1
    UniProtKB/Swiss-Prot
    Q9NQS3
    Related
    ENSP00000321514.3, ENST00000319792.7
    Conserved Domains (4) summary
    cd00096
    Location:269 → 275
    Ig; Ig strand A [structural motif]
    cd05887
    Location:58 → 167
    IgV_1_Nectin-3_like; First immunoglobulin variable (IgV) domain of nectin-3 (also known as poliovirus receptor related protein 3), and similar domains
    cd07704
    Location:170 → 265
    IgC1_2_Nectin-3-4_like; Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains
    cl11960
    Location:269 → 355
    Ig; Immunoglobulin domain

  2. NM_001243288.2 → NP_001230217.1  nectin-3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, uses a distinct start codon, and has alternate exon structure in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has distinct N- and C-termini and is shorter than isoform 1.
    Source sequence(s)
    AC133436, AC133477, AK075105, BQ025085
    Consensus CDS
    CCDS58843.1
    UniProtKB/Swiss-Prot
    Q9NQS3
    Related
    ENSP00000420579.1, ENST00000493615.5
    Conserved Domains (4) summary
    cd05887
    Location:49 → 144
    Ig1_Nectin-3_like; First immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3) and similar proteins
    smart00410
    Location:41 → 143
    IG_like; Immunoglobulin like
    pfam13927
    Location:264 → 319
    Ig_3; Immunoglobulin domain
    cl11960
    Location:147 → 242
    Ig; Immunoglobulin domain

  3. NM_015480.3 → NP_056295.1  nectin-3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_056295.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA555086, AC137833, AF282874, BI464010
    Consensus CDS
    CCDS2957.1
    UniProtKB/Swiss-Prot
    E9PFR0, Q6NVZ3, Q8NC05, Q8WVU4, Q9BVA9, Q9NQS3, Q9Y412
    Related
    ENSP00000418070.1, ENST00000485303.6
    Conserved Domains (5) summary
    cd12087
    Location:404 → 432
    TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases
    cd00096
    Location:269 → 275
    Ig; Ig strand A [structural motif]
    cd05887
    Location:58 → 167
    IgV_1_Nectin-3_like; First immunoglobulin variable (IgV) domain of nectin-3 (also known as poliovirus receptor related protein 3), and similar domains
    cd07704
    Location:170 → 265
    IgC1_2_Nectin-3-4_like; Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains
    cl11960
    Location:269 → 355
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    111071816..111194170
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006123.2 → XP_016861612.1  nectin-3 isoform X2

  2. XM_017006126.2 → XP_016861615.1  nectin-3 isoform X5

  3. XM_017006125.2 → XP_016861614.1  nectin-3 isoform X4

  4. XM_011512663.2 → XP_011510965.1  nectin-3 isoform X1

    Conserved Domains (5) summary
    cd05887
    Location:103 → 198
    Ig1_Nectin-3_like; First immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3) and similar proteins
    cd12087
    Location:435 → 463
    TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases
    smart00410
    Location:95 → 197
    IG_like; Immunoglobulin like
    pfam13927
    Location:318 → 373
    Ig_3; Immunoglobulin domain
    cl11960
    Location:201 → 296
    Ig; Immunoglobulin domain

  5. XM_047447934.1 → XP_047303890.1  nectin-3 isoform X6

  6. XM_017006127.3 → XP_016861616.1  nectin-3 isoform X6

    Conserved Domains (4) summary
    cd12087
    Location:192 → 220
    TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases
    smart00410
    Location:75 → 136
    IG_like; Immunoglobulin like
    pfam13927
    Location:75 → 130
    Ig_3; Immunoglobulin domain
    cl11960
    Location:1 → 53
    Ig; Immunoglobulin domain

  7. XM_017006124.2 → XP_016861613.1  nectin-3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    113792242..113914605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346112.1 → XP_054202087.1  nectin-3 isoform X2

  2. XM_054346115.1 → XP_054202090.1  nectin-3 isoform X5

  3. XM_054346114.1 → XP_054202089.1  nectin-3 isoform X4

  4. XM_054346111.1 → XP_054202086.1  nectin-3 isoform X1

  5. XM_054346116.1 → XP_054202091.1  nectin-3 isoform X6

  6. XM_054346113.1 → XP_054202088.1  nectin-3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQS3.1 GenPept UniProtKB/Swiss-Prot:Q9NQS3

Gene LinkOut

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