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NCAM1 neural cell adhesion molecule 1 [ Homo sapiens (human) ]

Gene ID: 4684, updated on 7-Jun-2020

Summary

Official Symbol
NCAM1provided by HGNC
Official Full Name
neural cell adhesion molecule 1provided by HGNC
Primary source
HGNC:HGNC:7656
See related
Ensembl:ENSG00000149294 MIM:116930
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
CD56; NCAM; MSK39
Summary
This gene encodes a cell adhesion protein which is a member of the immunoglobulin superfamily. The encoded protein is involved in cell-to-cell interactions as well as cell-matrix interactions during development and differentiation. The encoded protein has been shown to be involved in development of the nervous system, and for cells involved in the expansion of T cells and dendritic cells which play an important role in immune surveillance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2011]
Expression
Biased expression in brain (RPKM 90.3), adrenal (RPKM 31.4) and 6 other tissues See more
Orthologs

Genomic context

See NCAM1 in Genome Data Viewer
Location:
11q23.2
Exon count:
25
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (112961420..113278436)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (112831969..113149158)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369496 Neighboring gene uncharacterized LOC105369498 Neighboring gene uncharacterized LOC101928847 Neighboring gene RNA, U7 small nuclear 187 pseudogene Neighboring gene NCAM1 antisense RNA1 Neighboring gene tetratricopeptide repeat domain 12 Neighboring gene ankyrin repeat and kinase domain containing 1

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

NHGRI GWAS Catalog

Description
Genetic relationships between suicide attempts, suicidal ideation and major psychiatric disorders: a genome-wide association and polygenic scoring study.
NHGRI GWA Catalog
Genetic variation in NCAM1 contributes to left ventricular wall thickness in hypertensive families.
NHGRI GWA Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
virus receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
MAPK cascade TAS
Traceable Author Statement
more info
 
axon guidance TAS
Traceable Author Statement
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
commissural neuron axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
interferon-gamma-mediated signaling pathway TAS
Traceable Author Statement
more info
 
regulation of semaphorin-plexin signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
viral entry into host cell IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
collagen-containing extracellular matrix HDA PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
neural cell adhesion molecule 1
Names
antigen recognized by monoclonal antibody 5.1H11
neural cell adhesion molecule, NCAM
NP_000606.3
NP_001070150.1
NP_001229536.1
NP_001229537.1
NP_851996.2

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_032036.1 RefSeqGene

    Range
    5174..322190
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000615.7NP_000606.3  neural cell adhesion molecule 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_000606.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks two alternate in-frame exons in the 3' coding region compared to variant 5. The resulting protein (isoform 1) is shorter compared to isoform 5.
    Source sequence(s)
    AK054570, AW131780, BC014205, BC047244, DA337649, S71824
    Consensus CDS
    CCDS73388.1
    UniProtKB/Swiss-Prot
    P13591
    Related
    ENSP00000484943.1, ENST00000531044.5
    Conserved Domains (8) summary
    cd05865
    Location:20115
    Ig1_NCAM-1; First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1
    cd05869
    Location:306402
    Ig_NCAM-1; Immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-1 (NCAM)
    smart00409
    Location:124190
    IG; Immunoglobulin
    cd00063
    Location:498595
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:603684
    fn3; Fibronectin type III domain
    pfam13927
    Location:411483
    Ig_3; Immunoglobulin domain
    cl11960
    Location:211307
    Ig; Immunoglobulin domain
    cl25865
    Location:756828
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)
  2. NM_001076682.4NP_001070150.1  neural cell adhesion molecule 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001070150.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region and uses an alternate splice site in the 3' coding region compared to variant 5. The resulting protein (isoform 3) is shorter and has a distinct C-terminus compared to isoform 5.
    Source sequence(s)
    AB209443, BC019845, BC047244, DA337649, S71824, X16841
    Consensus CDS
    CCDS73386.1
    UniProtKB/Swiss-Prot
    P13591
    Related
    ENSP00000480774.1, ENST00000621850.4
    Conserved Domains (7) summary
    cd05865
    Location:20115
    Ig1_NCAM-1; First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1
    cd05869
    Location:306402
    Ig_NCAM-1; Immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-1 (NCAM)
    smart00410
    Location:124190
    IG_like; Immunoglobulin like
    cd00063
    Location:498595
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:638719
    fn3; Fibronectin type III domain
    pfam13927
    Location:411483
    Ig_3; Immunoglobulin domain
    cl11960
    Location:211307
    Ig; Immunoglobulin domain
  3. NM_001242607.2NP_001229536.1  neural cell adhesion molecule 1 isoform 5 precursor

    See identical proteins and their annotated locations for NP_001229536.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents the longest transcript and encodes the longest protein (isoform 5).
    Source sequence(s)
    AK314589, AP000880, AP002853
    Consensus CDS
    CCDS73384.1
    UniProtKB/TrEMBL
    A0A087WWD4
    Related
    ENSP00000480132.1, ENST00000619839.4
    Conserved Domains (7) summary
    cd05865
    Location:20115
    Ig1_NCAM-1; First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1
    smart00409
    Location:124190
    IG; Immunoglobulin
    cd00063
    Location:534631
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:639720
    fn3; Fibronectin type III domain
    pfam13927
    Location:447519
    Ig_3; Immunoglobulin domain
    cl11960
    Location:306438
    Ig; Immunoglobulin domain
    cl25865
    Location:792864
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)
  4. NM_001242608.2NP_001229537.1  neural cell adhesion molecule 1 isoform 4 precursor

    See identical proteins and their annotated locations for NP_001229537.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks 2 alternate in-frame exons and uses an alternate splice site in the 3' coding region compared to variant 5. The resulting protein (isoform 4) is shorter and has a distinct C-terminus compared to isoform 5.
    Source sequence(s)
    AA029449, AB209443
    Consensus CDS
    CCDS73387.1
    UniProtKB/Swiss-Prot
    P13591
    Related
    ENSP00000481083.1, ENST00000621128.4
    Conserved Domains (7) summary
    cd05865
    Location:20115
    Ig1_NCAM-1; First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1
    cd05869
    Location:306402
    Ig_NCAM-1; Immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-1 (NCAM)
    smart00409
    Location:124190
    IG; Immunoglobulin
    cd00063
    Location:498595
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:603684
    fn3; Fibronectin type III domain
    pfam13927
    Location:411483
    Ig_3; Immunoglobulin domain
    cl11960
    Location:211307
    Ig; Immunoglobulin domain
  5. NM_181351.5NP_851996.2  neural cell adhesion molecule 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_851996.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 5. The resulting protein (isoform 2) is shorter compared to isoform 5.
    Source sequence(s)
    AK054570, AW131780, BC014205, BC047244, DA337649, S71824
    Consensus CDS
    CCDS73385.1
    UniProtKB/Swiss-Prot
    P13591
    Related
    ENSP00000318472.8, ENST00000316851.11
    Conserved Domains (8) summary
    cd05865
    Location:20115
    Ig1_NCAM-1; First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1
    cd05869
    Location:306412
    Ig_NCAM-1; Immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-1 (NCAM)
    smart00409
    Location:124190
    IG; Immunoglobulin
    cd00063
    Location:508605
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:613694
    fn3; Fibronectin type III domain
    pfam13927
    Location:421493
    Ig_3; Immunoglobulin domain
    cl11960
    Location:211307
    Ig; Immunoglobulin domain
    cl25865
    Location:766838
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)

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
    112961420..113278436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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