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

Gene ID: 253559, updated on 7-Apr-2024

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; AllianceGenome:HGNC:29849
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
NECL3; IGSF4D; Necl-3; synCAM2; SynCAM 2; 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
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Genomic context

Location:
3p12.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (84958989..86074429)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (85024005..86146272)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (85008140..86123579)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:84954381-84954880 Neighboring gene uncharacterized LOC105377193 Neighboring gene long intergenic non-protein coding RNA 2025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:85010305-85010847 Neighboring gene NANOG hESC enhancer GRCh37_chr3:85079080-85079638 Neighboring gene uncharacterized LOC124906200 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:85169693-85170523 Neighboring gene small nucleolar RNA, H/ACA box 95 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:85443162-85443393 Neighboring gene microRNA 5688 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:85625238-85625814 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:85794578-85794816 Neighboring gene CADM2 antisense RNA 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:86132353-86132853 Neighboring gene THAP domain containing 12 pseudogene 2 Neighboring gene small nucleolar RNA Z40 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:86224689-86225518 Neighboring gene uncharacterized LOC102723364 Neighboring gene RNA, U6 small nuclear 1129, 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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC104534, MGC138341, MGC138343

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in axon IEA
Inferred from Electronic Annotation
more info
 
is_active_in neuronal cell body membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in 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)

NEW Try the new Transcript table

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_001167674.2NP_001161146.1  cell adhesion molecule 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001161146.1

    Status: REVIEWED

    Source sequence(s)
    AC107024, BC105999, BC112138
    Consensus CDS
    CCDS54614.1
    UniProtKB/Swiss-Prot
    G3XHN7, G3XHN8, Q3KQY9, Q658Q7, Q8IZP8, Q8N3J6
    Related
    ENSP00000384575.2, ENST00000407528.6
    Conserved Domains (5) summary
    smart00294
    Location:388406
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:240303
    IGc2; Immunoglobulin C-2 Type
    cd00096
    Location:242251
    Ig; Ig strand B [structural motif]
    cd05884
    Location:120223
    IgI_2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains
    cd07701
    Location:26121
    IgV_1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains
  2. NM_001167675.2NP_001161147.1  cell adhesion molecule 2 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001161147.1

    Status: REVIEWED

    Source sequence(s)
    AC107024, BC105999
    Consensus CDS
    CCDS54613.1
    UniProtKB/TrEMBL
    B4DJ19, G3XHN4
    Related
    ENSP00000373200.3, ENST00000383699.8
    Conserved Domains (5) summary
    smart00294
    Location:357375
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:249312
    IGc2; Immunoglobulin C-2 Type
    cd00096
    Location:251260
    Ig; Ig strand B [structural motif]
    cd05884
    Location:129232
    IgI_2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains
    cd07701
    Location:35130
    IgV_1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains
  3. NM_001256502.2NP_001243431.1  cell adhesion molecule 2 isoform 4

    See identical proteins and their annotated locations for NP_001243431.1

    Status: REVIEWED

    Source sequence(s)
    AC018361, AC107024, AC117452, AC119726
    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_001256503.2NP_001243432.1  cell adhesion molecule 2 isoform 4

    See identical proteins and their annotated locations for NP_001243432.1

    Status: REVIEWED

    Source sequence(s)
    AC018361, AC107024, AC117452, AC119726
    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_001256504.2NP_001243433.1  cell adhesion molecule 2 isoform 5

    See identical proteins and their annotated locations for NP_001243433.1

    Status: REVIEWED

    Source sequence(s)
    AC018361, AC107024, AC117452, AC119726, AC119729
    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (3) summary
    smart00294
    Location:240258
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:132195
    IGc2; Immunoglobulin C-2 Type
    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))
  6. NM_001256505.2NP_001243434.1  cell adhesion molecule 2 isoform 5

    See identical proteins and their annotated locations for NP_001243434.1

    Status: REVIEWED

    Source sequence(s)
    AC018361, AC107024, AC117452, AC119726
    UniProtKB/Swiss-Prot
    Q8N3J6
    Conserved Domains (3) summary
    smart00294
    Location:240258
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:132195
    IGc2; Immunoglobulin C-2 Type
    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))
  7. NM_001375960.1NP_001362889.1  cell adhesion molecule 2 isoform 6 precursor

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC119729, AC132660
    Conserved Domains (5) summary
    smart00294
    Location:397415
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:249312
    IGc2; Immunoglobulin C-2 Type
    cd00096
    Location:251260
    Ig; Ig strand B [structural motif]
    cd05884
    Location:129232
    IgI_2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains
    cd07701
    Location:35130
    IgV_1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains
  8. NM_001375961.1NP_001362890.1  cell adhesion molecule 2 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC119729, AC132660
    UniProtKB/TrEMBL
    B4DJ19
    Conserved Domains (4) summary
    smart00294
    Location:341359
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:233296
    IGc2; Immunoglobulin C-2 Type
    cd05884
    Location:134216
    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:19113
    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))
  9. NM_001375964.1NP_001362893.1  cell adhesion molecule 2 isoform 8 precursor

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC119729, AC132660
    UniProtKB/TrEMBL
    B4DJ19
    Conserved Domains (4) summary
    smart00294
    Location:311329
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:203266
    IGc2; Immunoglobulin C-2 Type
    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))
    cl11960
    Location:129186
    Ig; Immunoglobulin domain
  10. NM_001375967.1NP_001362896.1  cell adhesion molecule 2 isoform 9 precursor

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC119729, AC132660
    UniProtKB/TrEMBL
    B4DJ19
    Conserved Domains (4) summary
    smart00294
    Location:307325
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:199262
    IGc2; Immunoglobulin C-2 Type
    cd05884
    Location:100182
    Ig2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2))
    cl11960
    Location:2979
    Ig; Immunoglobulin domain
  11. NM_001375968.1NP_001362897.1  cell adhesion molecule 2 isoform 10 precursor

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC119729, AC132660
    Conserved Domains (3) summary
    smart00294
    Location:260278
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:152215
    IGc2; Immunoglobulin C-2 Type
    cl11960
    Location:66135
    Ig; Immunoglobulin domain
  12. NM_001381963.1NP_001368892.1  cell adhesion molecule 2 isoform 11 precursor

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC132660
    UniProtKB/TrEMBL
    B4DJ19
    Conserved Domains (5) summary
    smart00294
    Location:348366
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:240303
    IGc2; Immunoglobulin C-2 Type
    cd00096
    Location:242251
    Ig; Ig strand B [structural motif]
    cd05884
    Location:120223
    IgI_2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains
    cd07701
    Location:26121
    IgV_1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains
  13. NM_001381964.1NP_001368893.1  cell adhesion molecule 2 isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC132660
    Consensus CDS
    CCDS54614.1
    UniProtKB/Swiss-Prot
    G3XHN7, G3XHN8, Q3KQY9, Q658Q7, Q8IZP8, Q8N3J6
    Conserved Domains (5) summary
    smart00294
    Location:388406
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:240303
    IGc2; Immunoglobulin C-2 Type
    cd00096
    Location:242251
    Ig; Ig strand B [structural motif]
    cd05884
    Location:120223
    IgI_2_Necl-3; Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains
    cd07701
    Location:26121
    IgV_1_Necl-3; First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains
  14. NM_153184.4NP_694854.2  cell adhesion molecule 2 isoform 3 precursor

    See identical proteins and their annotated locations for NP_694854.2

    Status: REVIEWED

    Source sequence(s)
    AC107024, AC117452, AC119726, AC119729
    Consensus CDS
    CCDS33792.1
    UniProtKB/Swiss-Prot
    Q8N3J6
    Related
    ENSP00000384193.2, ENST00000405615.2
    Conserved Domains (4) summary
    smart00294
    Location:390408
    4.1m; putative band 4.1 homologues' binding motif
    smart00408
    Location:242305
    IGc2; Immunoglobulin C-2 Type
    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: GCF_000001405.40-RS_2023_10

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
    84958989..86074429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006062.3XP_016861551.1  cell adhesion molecule 2 isoform X1

  2. XM_047447872.1XP_047303828.1  cell adhesion molecule 2 isoform X3

  3. XM_017006063.3XP_016861552.1  cell adhesion molecule 2 isoform X2

    UniProtKB/TrEMBL
    B4DJ19
    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.p14 PATCHES

Genomic

  1. NW_018654711.1 Reference GRCh38.p14 PATCHES

    Range
    174212..174894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    85024005..86146272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345952.1XP_054201927.1  cell adhesion molecule 2 isoform X1

  2. XM_054345954.1XP_054201929.1  cell adhesion molecule 2 isoform X3

  3. XM_054345953.1XP_054201928.1  cell adhesion molecule 2 isoform X2