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CADM1 cell adhesion molecule 1 [ Homo sapiens (human) ]

Gene ID: 23705, updated on 11-Sep-2019

Summary

Official Symbol
CADM1provided by HGNC
Official Full Name
cell adhesion molecule 1provided by HGNC
Primary source
HGNC:HGNC:5951
See related
Ensembl:ENSG00000182985 MIM:605686
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BL2; ST17; IGSF4; NECL2; RA175; TSLC1; IGSF4A; Necl-2; SYNCAM; sgIGSF; sTSLC-1; synCAM1
Expression
Broad expression in lung (RPKM 23.7), thyroid (RPKM 19.5) and 23 other tissues See more
Orthologs

Genomic context

See CADM1 in Genome Data Viewer
Location:
11q23.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (115169236..115504428, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (115039933..115375241, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene neurexophilin and PC-esterase domain family member 2 Neighboring gene uncharacterized LOC105369504 Neighboring gene uncharacterized LOC105369506 Neighboring gene uncharacterized LOC105369505 Neighboring gene uncharacterized LOC105369509 Neighboring gene uncharacterized LOC105369507 Neighboring gene uncharacterized LOC105369511 Neighboring gene ferritin light chain pseudogene 7

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
Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
NHGRI GWA Catalog
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
NHGRI GWA Catalog
Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog

Pathways from BioSystems

  • 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...
  • 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

  • MGC51880, MGC149785, DKFZp686F1789

Gene Ontology Provided by GOA

Function Evidence Code Pubs
PDZ domain binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Process Evidence Code Pubs
NOT T cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
PubMed 
NOT activated T cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
adherens junction organization TAS
Traceable Author Statement
more info
 
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cell recognition IDA
Inferred from Direct Assay
more info
PubMed 
cell recognition ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
detection of stimulus IDA
Inferred from Direct Assay
more info
PubMed 
detection of stimulus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cytokine secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of natural killer cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of natural killer cell mediated cytotoxicity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
susceptibility to natural killer cell mediated cytotoxicity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
susceptibility to natural killer cell mediated cytotoxicity IDA
Inferred from Direct Assay
more info
PubMed 
susceptibility to natural killer cell mediated cytotoxicity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basolateral plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cell-cell junction ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
cell adhesion molecule 1
Names
TSLC-1
TSLC1/Nectin-like 2/IGSF4
immunoglobulin superfamily member 4
immunoglobulin superfamily, member 4D variant 1
immunoglobulin superfamily, member 4D variant 2
nectin-like 2
nectin-like protein 2
spermatogenic immunoglobulin superfamily
synaptic cell adhesion molecule
truncated CADM1 protein
tumor suppressor in lung cancer 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.

mRNA and Protein(s)

  1. NM_001098517.2NP_001091987.1  cell adhesion molecule 1 isoform E precursor

    See identical proteins and their annotated locations for NP_001091987.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks three alternate in-frame exons compared to variant 3. The resulting isoform (2, also known as E) has the same N- and C-termini but is shorter compared to isoform A.
    Source sequence(s)
    AF132811, AP003179, BC125103, BI915307, BM309987, CA447277, CA777709
    Consensus CDS
    CCDS53711.1
    UniProtKB/Swiss-Prot
    Q9BY67
    Related
    ENSP00000439176.1, ENST00000542447.6
    Conserved Domains (3) summary
    cd05881
    Location:46140
    Ig1_Necl-2; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2
    cd05883
    Location:161242
    Ig2_Necl-2; Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    smart00409
    Location:252330
    IG; Immunoglobulin
  2. NM_001301043.2NP_001287972.1  cell adhesion molecule 1 isoform A precursor

    See identical proteins and their annotated locations for NP_001287972.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (A).
    Source sequence(s)
    AP003179, BC047021, CA447277, HE586498
    Consensus CDS
    CCDS73399.1
    UniProtKB/Swiss-Prot
    Q9BY67
    UniProtKB/TrEMBL
    A0A4Z1, X5D7A8
    Related
    ENSP00000329797.6, ENST00000331581.10
    Conserved Domains (4) summary
    cd05881
    Location:46140
    Ig1_Necl-2; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    cd05883
    Location:161242
    Ig2_Necl-2; Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    smart00408
    Location:259320
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:252330
    IG_like; Immunoglobulin like
  3. NM_001301044.2NP_001287973.1  cell adhesion molecule 1 isoform B precursor

    See identical proteins and their annotated locations for NP_001287973.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (B) has the same N- and C-termini but is shorter compared to isoform A.
    Source sequence(s)
    AP003179, BC047021, CA447277, HE586497
    Consensus CDS
    CCDS73398.1
    UniProtKB/Swiss-Prot
    Q9BY67
    UniProtKB/TrEMBL
    A0A4Z1, X5DQR8
    Related
    ENSP00000439817.1, ENST00000537058.5
    Conserved Domains (4) summary
    cd05881
    Location:46140
    Ig1_Necl-2; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    cd05883
    Location:161242
    Ig2_Necl-2; Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    smart00408
    Location:259320
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:252330
    IG_like; Immunoglobulin like
  4. NM_001301045.2NP_001287974.1  cell adhesion molecule 1 isoform C precursor

    See identical proteins and their annotated locations for NP_001287974.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon compared to variant 3. The resulting isoform (C) has the same N- and C-termini but is shorter compared to isoform A.
    Source sequence(s)
    AP003179, BC047021, CA447277, KJ534797
    Consensus CDS
    CCDS73397.1
    UniProtKB/Swiss-Prot
    Q9BY67
    UniProtKB/TrEMBL
    A0A4Z1, X5DQS5
    Related
    ENSP00000440322.1, ENST00000536727.5
    Conserved Domains (3) summary
    cd05881
    Location:46140
    Ig1_Necl-2; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2
    cd05883
    Location:161242
    Ig2_Necl-2; Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    smart00409
    Location:252330
    IG; Immunoglobulin
  5. NM_014333.4NP_055148.3  cell adhesion molecule 1 isoform D precursor

    See identical proteins and their annotated locations for NP_055148.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks two alternate in-frame exons compared to variant 3. The resulting isoform (1, also known as D) has the same N- and C-termini but is shorter compared to isoform A.
    Source sequence(s)
    AF132811, AP003179, BC035930, BC125103, BM309987, CA447277, CA777709
    Consensus CDS
    CCDS8373.1
    UniProtKB/Swiss-Prot
    Q9BY67
    UniProtKB/TrEMBL
    X5D8W0
    Related
    ENSP00000395359.2, ENST00000452722.7
    Conserved Domains (3) summary
    cd05881
    Location:46140
    Ig1_Necl-2; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2
    cd05883
    Location:161242
    Ig2_Necl-2; Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    smart00409
    Location:252330
    IG; Immunoglobulin

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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
    115169236..115504428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005271494.3XP_005271551.1  cell adhesion molecule 1 isoform X2

    See identical proteins and their annotated locations for XP_005271551.1

    Conserved Domains (4) summary
    cd05881
    Location:46140
    Ig1_Necl-2; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    cd05883
    Location:161242
    Ig2_Necl-2; Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1))
    smart00408
    Location:259320
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:252330
    IG_like; Immunoglobulin like
  2. XM_017017457.2XP_016872946.1  cell adhesion molecule 1 isoform X1

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