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    CNTN1 contactin 1 [ Homo sapiens (human) ]

    Gene ID: 1272, updated on 25-Jan-2022

    Summary

    Official Symbol
    CNTN1provided by HGNC
    Official Full Name
    contactin 1provided by HGNC
    Primary source
    HGNC:HGNC:2171
    See related
    Ensembl:ENSG00000018236 MIM:600016; AllianceGenome:HGNC:2171
    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
    F3; GP135; MYPCN
    Summary
    The protein encoded by this gene is a member of the immunoglobulin superfamily. It is a glycosylphosphatidylinositol (GPI)-anchored neuronal membrane protein that functions as a cell adhesion molecule. It may play a role in the formation of axon connections in the developing nervous system. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Biased expression in brain (RPKM 51.8), ovary (RPKM 13.6) and 10 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CNTN1 in Genome Data Viewer
    Location:
    12q12
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    109.20211119 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (40692429..41072415)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (41086241..41466217)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene microtubule associated protein 6 pseudogene Neighboring gene mucin 19, oligomeric Neighboring gene RNA, U6 small nuclear 713, pseudogene Neighboring gene methionyl aminopeptidase 1 pseudogene Neighboring gene uncharacterized LOC107984496 Neighboring gene PDZ domain containing ring finger 4 Neighboring gene uncharacterized LOC107984499 Neighboring gene uncharacterized LOC107984498

    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

    Associated conditions

    Description Tests
    Myopathy, congenital, compton-north
    MedGen: C2675527 OMIM: 612540 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    EBI GWAS Catalog
    A genome-wide association study identifies susceptibility loci of silica related pneumoconiosis in Han Chinese.
    EBI GWAS Catalog
    A genome-wide association study of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS 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
    enables carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables cell-cell adhesion mediator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Notch signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in central nervous system myelin formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cerebellum development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of peptidyl-tyrosine phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of sodium ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in anchored component of postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in anchored component of presynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    contactin-1
    Names
    glycoprotein gP135
    neural cell surface protein F3

    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.

    Genomic

    1. NG_012058.2 RefSeqGene

      Range
      4884..384860
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256063.2NP_001242992.1  contactin-1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001242992.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks several 3' exons and includes an alternate 3' terminal exon, compared to variant 1. The resulting isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3 and 4 encode the same isoform 3.
      Source sequence(s)
      AC015540, AC074030, AK289698, BC036569, DQ442054
      Consensus CDS
      CCDS58225.1
      UniProtKB/Swiss-Prot
      Q12860
      Related
      ENSP00000448004.1, ENST00000547702.5
      Conserved Domains (6) summary
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1
      cd04970
      Location:520602
      Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    2. NM_001256064.2NP_001242993.1  contactin-1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001242993.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks several 3' exons and includes an alternate 3' terminal exon, compared to variant 1. The resulting isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3 and 4 encode the same isoform 3.
      Source sequence(s)
      AC015540, AK289544
      Consensus CDS
      CCDS58225.1
      UniProtKB/Swiss-Prot
      Q12860
      Related
      ENSP00000448653.1, ENST00000547849.5
      Conserved Domains (6) summary
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1
      cd04970
      Location:520602
      Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    3. NM_001843.4NP_001834.2  contactin-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001834.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC024900, AC074030, AI473107, AK289698, BM717031, BX648591, BY799936, DQ442054, U07819, Z21488
      Consensus CDS
      CCDS8737.1
      UniProtKB/Swiss-Prot
      Q12860
      UniProtKB/TrEMBL
      A0A024R104
      Related
      ENSP00000447006.1, ENST00000551295.7
      Conserved Domains (10) summary
      cd04970
      Location:520601
      Ig6_Contactin_like; Sixth Ig domain of contactin
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First Ig domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third Ig domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth Ig domain of contactin-1
      smart00410
      Location:422501
      IG_like; Immunoglobulin like
      cd00063
      Location:610697
      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 ...
      pfam07679
      Location:331408
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:811893
      fn3; Fibronectin type III domain
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    4. NM_175038.2NP_778203.1  contactin-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_778203.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame coding exon, compared to variant 1. The resulting isoform (2) lacks an internal segment in the N-terminal region, compared to isoform 1.
      Source sequence(s)
      AI473107, BC036569, BM717031, BX648591, BY799936, U07820
      Consensus CDS
      CCDS8738.1
      UniProtKB/Swiss-Prot
      Q12860
      Related
      ENSP00000261160.3, ENST00000348761.2
      Conserved Domains (10) summary
      cd04970
      Location:509590
      Ig6_Contactin_like; Sixth Ig domain of contactin
      cd05727
      Location:123219
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:29121
      Ig1_Contactin-1; First Ig domain of contactin-1
      cd05851
      Location:230317
      Ig3_Contactin-1; Third Ig domain of contactin-1
      cd05852
      Location:418490
      Ig5_Contactin-1; Fifth Ig domain of contactin-1
      smart00410
      Location:411490
      IG_like; Immunoglobulin like
      cd00063
      Location:599686
      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 ...
      pfam07679
      Location:320397
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:800882
      fn3; Fibronectin type III domain
      cl11960
      Location:321397
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

      Range
      40692429..41072415
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011537926.3XP_011536228.1  contactin-1 isoform X1

      See identical proteins and their annotated locations for XP_011536228.1

      UniProtKB/Swiss-Prot
      Q12860
      UniProtKB/TrEMBL
      A0A024R104
      Conserved Domains (10) summary
      cd04970
      Location:520601
      Ig6_Contactin_like; Sixth Ig domain of contactin
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First Ig domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third Ig domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth Ig domain of contactin-1
      smart00410
      Location:422501
      IG_like; Immunoglobulin like
      cd00063
      Location:610697
      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 ...
      pfam07679
      Location:331408
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:811893
      fn3; Fibronectin type III domain
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    2. XM_024448843.1XP_024304611.1  contactin-1 isoform X2

      Conserved Domains (6) summary
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1
      cd04970
      Location:520602
      Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    3. XM_005268651.2XP_005268708.1  contactin-1 isoform X1

      See identical proteins and their annotated locations for XP_005268708.1

      UniProtKB/Swiss-Prot
      Q12860
      UniProtKB/TrEMBL
      A0A024R104
      Conserved Domains (10) summary
      cd04970
      Location:520601
      Ig6_Contactin_like; Sixth Ig domain of contactin
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First Ig domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third Ig domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth Ig domain of contactin-1
      smart00410
      Location:422501
      IG_like; Immunoglobulin like
      cd00063
      Location:610697
      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 ...
      pfam07679
      Location:331408
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:811893
      fn3; Fibronectin type III domain
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    4. XM_011537927.2XP_011536229.1  contactin-1 isoform X1

      See identical proteins and their annotated locations for XP_011536229.1

      UniProtKB/Swiss-Prot
      Q12860
      UniProtKB/TrEMBL
      A0A024R104
      Conserved Domains (10) summary
      cd04970
      Location:520601
      Ig6_Contactin_like; Sixth Ig domain of contactin
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First Ig domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third Ig domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth Ig domain of contactin-1
      smart00410
      Location:422501
      IG_like; Immunoglobulin like
      cd00063
      Location:610697
      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 ...
      pfam07679
      Location:331408
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:811893
      fn3; Fibronectin type III domain
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    5. XM_006719241.2XP_006719304.1  contactin-1 isoform X1

      See identical proteins and their annotated locations for XP_006719304.1

      UniProtKB/Swiss-Prot
      Q12860
      UniProtKB/TrEMBL
      A0A024R104
      Related
      ENSP00000325660.3, ENST00000347616.5
      Conserved Domains (10) summary
      cd04970
      Location:520601
      Ig6_Contactin_like; Sixth Ig domain of contactin
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First Ig domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third Ig domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth Ig domain of contactin-1
      smart00410
      Location:422501
      IG_like; Immunoglobulin like
      cd00063
      Location:610697
      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 ...
      pfam07679
      Location:331408
      I-set; Immunoglobulin I-set domain
      pfam00041
      Location:811893
      fn3; Fibronectin type III domain
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    6. XM_017018827.2XP_016874316.1  contactin-1 isoform X2

      UniProtKB/Swiss-Prot
      Q12860
      Conserved Domains (6) summary
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1
      cd04970
      Location:520602
      Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:332408
      Ig; Immunoglobulin domain
    7. XM_017018826.2XP_016874315.1  contactin-1 isoform X2

      UniProtKB/Swiss-Prot
      Q12860
      Conserved Domains (6) summary
      cd05727
      Location:134230
      Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins
      cd05849
      Location:40132
      Ig1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1
      cd05851
      Location:241328
      Ig3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1
      cd05852
      Location:429501
      Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1
      cd04970
      Location:520602
      Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:332408
      Ig; Immunoglobulin domain

    RNA

    1. XR_002957289.1 RNA Sequence

    2. XR_002957288.1 RNA Sequence

    3. XR_002957290.1 RNA Sequence

    4. XR_002957291.1 RNA Sequence

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