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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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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