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CADM2 cell adhesion molecule 2 [ Homo sapiens (human) ]

Gene ID: 253559, updated on 14-Oct-2018

Summary

Official Symbol
CADM2provided by HGNC
Official Full Name
cell adhesion molecule 2provided by HGNC
Primary source
HGNC:HGNC:29849
See related
Ensembl:ENSG00000175161 MIM:609938; Vega:OTTHUMG00000158990
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
NECL3; IGSF4D; Necl-3; synCAM2; SynCAM 2
Summary
This gene encodes a member of the synaptic cell adhesion molecule 1 (SynCAM) family which belongs to the immunoglobulin (Ig) superfamily. The encoded protein has three Ig-like domains and a cytosolic protein 4.1 binding site near the C-terminus. Proteins belonging to the protein 4.1 family crosslink spectrin and interact with other cytoskeletal proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
Expression
Biased expression in brain (RPKM 29.4), fat (RPKM 2.4) and 1 other tissue See more
Orthologs

Genomic context

See CADM2 in Genome Data Viewer
Location:
3p12.1
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (84958982..86074429)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (85008133..86123579)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377193 Neighboring gene long intergenic non-protein coding RNA 2025 Neighboring gene small nucleolar RNA, H/ACA box 95 Neighboring gene microRNA 5688 Neighboring gene CADM2 antisense RNA 2 Neighboring gene THAP domain containing 12 pseudogene 2 Neighboring gene uncharacterized LOC102723364 Neighboring gene RNA, U6 small nuclear 1129, pseudogene Neighboring gene RNA, 7SK small nuclear pseudogene 284

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide meta-analysis of association studies of Cloninger's Temperament Scales.
NHGRI GWA Catalog
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
NHGRI GWA Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
NHGRI GWA Catalog
GWAS of Longevity in CHARGE Consortium Confirms APOE and FOXO3 Candidacy.
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 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC104534, MGC138341, MGC138343

Gene Ontology Provided by GOA

Process Evidence Code Pubs
adherens junction organization TAS
Traceable Author Statement
more info
 
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
axon IEA
Inferred from Electronic Annotation
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
cell adhesion molecule 2
Names
immunoglobulin superfamily member 4D
nectin-like 3
nectin-like protein 3
synaptic cell adhesion molecule 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.

mRNA and Protein(s)

  1. NM_001167674.1NP_001161146.1  cell adhesion molecule 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001161146.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AC107024, BC105999, BC112138
    Consensus CDS
    CCDS54614.1
    UniProtKB/Swiss-Prot
    Q8N3J6
    Related
    ENSP00000384575.2, OTTHUMP00000213816, ENST00000407528.6, OTTHUMT00000352822
    Conserved Domains (4) summary
    smart00294
    Location:388406
    4.1m; putative band 4.1 homologues' binding motif
    pfam13927
    Location:227300
    Ig_3; Immunoglobulin domain
    cd05884
    Location:141223
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cd07701
    Location:26120
    Ig1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
  2. NM_001167675.1NP_001161147.1  cell adhesion molecule 2 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001161147.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes an alternate in-frame exon in the 5' coding region and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (2) differs in two regions, compared to isoform 1.
    Source sequence(s)
    AC107024, BC105999
    Consensus CDS
    CCDS54613.1
    UniProtKB/Swiss-Prot
    Q8N3J6
    UniProtKB/TrEMBL
    G3XHN4
    Related
    ENSP00000373200.3, OTTHUMP00000213815, ENST00000383699.7, OTTHUMT00000352818
    Conserved Domains (4) summary
    smart00294
    Location:357375
    4.1m; putative band 4.1 homologues' binding motif
    pfam13927
    Location:236309
    Ig_3; Immunoglobulin domain
    cd05884
    Location:150232
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cd07701
    Location:35129
    Ig1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
  3. NM_001256502.1NP_001243431.1  cell adhesion molecule 2 isoform 4

    See identical proteins and their annotated locations for NP_001243431.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding region and uses a downstream start codon compared to variant 1. The resulting protein (isoform 4) is shorter and has a shorter N-terminus compared to isoform 1. Variants 4 and 5 encode the same protein.
    Source sequence(s)
    AB646741, AC107024
    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (4) summary
    smart00294
    Location:280298
    4.1m; putative band 4.1 homologues' binding motif
    cd05884
    Location:33115
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    smart00408
    Location:132195
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:131205
    IG_like; Immunoglobulin like
  4. NM_001256503.1NP_001243432.1  cell adhesion molecule 2 isoform 4

    See identical proteins and their annotated locations for NP_001243432.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding region and uses a downstream start codon compared to variant 1. The resulting protein (isoform 4) is shorter and has a shorter N-terminus compared to isoform 1. Variants 4 and 5 encode the same protein.
    Source sequence(s)
    AB646743, AC107024
    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (4) summary
    smart00294
    Location:280298
    4.1m; putative band 4.1 homologues' binding motif
    cd05884
    Location:33115
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    smart00408
    Location:132195
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:131205
    IG_like; Immunoglobulin like
  5. NM_001256504.1NP_001243433.1  cell adhesion molecule 2 isoform 5

    See identical proteins and their annotated locations for NP_001243433.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding region, lacks an alternate in-frame exon in the 3' CDS and uses a downstream start codon compared to variant 1. The resulting protein (isoform 5) is shorter and has a shorter N-terminus compared to isoform 1. Variants 6 and 7 encode the same protein.
    Source sequence(s)
    AB646742, AC107024
    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (4) summary
    smart00294
    Location:240258
    4.1m; putative band 4.1 homologues' binding motif
    cd05884
    Location:33115
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    smart00408
    Location:132195
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:131205
    IG_like; Immunoglobulin like
  6. NM_001256505.1NP_001243434.1  cell adhesion molecule 2 isoform 5

    See identical proteins and their annotated locations for NP_001243434.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and coding region, lacks an alternate in-frame exon in the 3' CDS and uses a downstream start codon compared to variant 1. The resulting protein (isoform 5) is shorter and has a shorter N-terminus compared to isoform 1. Variants 6 and 7 encode the same protein.
    Source sequence(s)
    AB646740, AC107024
    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (4) summary
    smart00294
    Location:240258
    4.1m; putative band 4.1 homologues' binding motif
    cd05884
    Location:33115
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    smart00408
    Location:132195
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:131205
    IG_like; Immunoglobulin like
  7. NM_153184.3NP_694854.2  cell adhesion molecule 2 isoform 3 precursor

    See identical proteins and their annotated locations for NP_694854.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) represents a distinct 5' coding region, compared to variant 1. The resulting isoform (3) has a longer and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC107024, AF538973, AL834270, BC105999
    Consensus CDS
    CCDS33792.1
    UniProtKB/Swiss-Prot
    Q8N3J6
    Related
    ENSP00000384193.2, OTTHUMP00000213814, ENST00000405615.2, OTTHUMT00000352817
    Conserved Domains (4) summary
    smart00294
    Location:390408
    4.1m; putative band 4.1 homologues' binding motif
    pfam13927
    Location:229302
    Ig_3; Immunoglobulin domain
    cd05884
    Location:143225
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cd07701
    Location:28122
    Ig1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))

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.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    84958982..86074429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713082.3XP_006713145.1  cell adhesion molecule 2 isoform X4

    See identical proteins and their annotated locations for XP_006713145.1

    Conserved Domains (4) summary
    smart00294
    Location:348366
    4.1m; putative band 4.1 homologues' binding motif
    pfam13927
    Location:227300
    Ig_3; Immunoglobulin domain
    cd05884
    Location:141223
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cd07701
    Location:26120
    Ig1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
  2. XM_017006062.2XP_016861551.1  cell adhesion molecule 2 isoform X1

  3. XM_006713081.4XP_006713144.1  cell adhesion molecule 2 isoform X2

    See identical proteins and their annotated locations for XP_006713144.1

    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (4) summary
    smart00294
    Location:388406
    4.1m; putative band 4.1 homologues' binding motif
    pfam13927
    Location:227300
    Ig_3; Immunoglobulin domain
    cd05884
    Location:141223
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cd07701
    Location:26120
    Ig1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
  4. XM_017006063.2XP_016861552.1  cell adhesion molecule 2 isoform X3

    Conserved Domains (5) summary
    smart00294
    Location:350368
    4.1m; putative band 4.1 homologues' binding motif
    cd05884
    Location:143225
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cd07701
    Location:28122
    Ig1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    smart00408
    Location:242305
    IGc2; Immunoglobulin C-2 Type
    smart00410
    Location:241315
    IG_like; Immunoglobulin like

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_018654711.1 Reference GRCh38.p12 PATCHES

    Range
    174205..174894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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