Format

Send to:

Choose Destination

CNTN1 contactin 1 [ Homo sapiens (human) ]

Gene ID: 1272, updated on 13-Mar-2020

Summary

Official Symbol
CNTN1provided by HGNC
Official Full Name
contactin 1provided by HGNC
Primary source
HGNC:HGNC:2171
See related
Ensembl:ENSG00000018236 MIM:600016
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

Genomic context

See CNTN1 in Genome Data Viewer
Location:
12q12
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (40692429..41072415)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (41086244..41466214)

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

NHGRI GWAS Catalog

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

General protein information

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

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.

Genomic

  1. NG_012058.2 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001256063.1NP_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, 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_001256064.1NP_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, DA215712
    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.

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

Support Center