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CNTN4 contactin 4 [ Homo sapiens (human) ]

Gene ID: 152330, updated on 27-Dec-2018

Summary

Official Symbol
CNTN4provided by HGNC
Official Full Name
contactin 4provided by HGNC
Primary source
HGNC:HGNC:2174
See related
Ensembl:ENSG00000144619 MIM:607280
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
AXCAM; BIG-2
Summary
This gene encodes a member of the contactin family of immunoglobulins. Contactins are axon-associated cell adhesion molecules that function in neuronal network formation and plasticity. The encoded protein is a glycosylphosphatidylinositol-anchored neuronal membrane protein that may play a role in the formation of axon connections in the developing nervous system. Deletion or mutation of this gene may play a role in 3p deletion syndrome and autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
Expression
Broad expression in endometrium (RPKM 2.7), thyroid (RPKM 2.4) and 21 other tissues See more
Orthologs

Genomic context

See CNTN4 in Genome Data Viewer
Location:
3p26.3-p26.2
Exon count:
34
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (2098803..3059080)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (2140550..3099645)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene 17 Neighboring gene RNA, 7SK small nuclear pseudogene 144 Neighboring gene CNTN4 antisense RNA 2 Neighboring gene meiotic recombination hotspot T Neighboring gene histidine triad nucleotide binding protein 2 pseudogene 1 Neighboring gene uncharacterized LOC105376926 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 4 Neighboring gene CNTN4 antisense RNA 1 Neighboring gene uncharacterized LOC107986006 Neighboring gene interleukin 5 receptor subunit alpha Neighboring gene tRNA nucleotidyl transferase 1

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 FunctionsWhat's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2017-10-18)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated (2017-10-18)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study identifies SNP in DCC is associated with gallbladder cancer in the Japanese population.
NHGRI GWA Catalog
A genome-wide association study of acenocoumarol maintenance dosage.
NHGRI GWA Catalog
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness.
NHGRI GWA Catalog
Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
NHGRI GWA Catalog
Genome-wide association analysis confirms and extends the association of SLC2A9 with serum uric acid levels to Mexican Americans.
NHGRI GWA Catalog
Genome-wide association study of intelligence: additive effects of novel brain expressed genes.
NHGRI GWA Catalog
Genome-Wide Association Study of Primary Dentition Pit-and-Fissure and Smooth Surface Caries.
NHGRI GWA Catalog
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
NHGRI GWA Catalog
Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity.
NHGRI GWA Catalog
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC33615

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cell-cell adhesion mediator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon guidance TAS
Traceable Author Statement
more info
PubMed 
axonal fasciculation TAS
Traceable Author Statement
more info
PubMed 
axonogenesis TAS
Traceable Author Statement
more info
PubMed 
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
dendrite self-avoidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of neuron differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neuron cell-cell adhesion TAS
Traceable Author Statement
more info
PubMed 
neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of synaptic plasticity TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon NAS
Non-traceable Author Statement
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
contactin-4
Names
axonal-associated cell adhesion molecule
brain-derived immunoglobulin superfamily protein 2
neural cell adhesion protein BIG-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.

Genomic

  1. NG_012827.2 RefSeqGene

    Range
    3304..962399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206955.1NP_001193884.1  contactin-4 isoform a precursor

    See identical proteins and their annotated locations for NP_001193884.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1, 4 and 6 encode the same isoform (a).
    Source sequence(s)
    AC022002, AC024057, AF549455, R42166
    Consensus CDS
    CCDS43041.1
    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Related
    ENSP00000380602.1, ENST00000397461.5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  2. NM_001206956.1NP_001193885.1  contactin-4 isoform d

    See identical proteins and their annotated locations for NP_001193885.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon, and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC022002, BC026119, DB457029, R42166
    UniProtKB/Swiss-Prot
    Q8IWV2
    Conserved Domains (2) summary
    cd00063
    Location:268361
    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 ...
    cl11960
    Location:185268
    Ig; Immunoglobulin domain
  3. NM_001350095.1NP_001337024.1  contactin-4 isoform a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1, 4 and 6 encode the same isoform (a).
    Source sequence(s)
    AC022002, AK125460, AY090737, BM718335, CD697898, CN282428, DN991363, HY130029, R42166
    Consensus CDS
    CCDS43041.1
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  4. NM_175607.3NP_783200.1  contactin-4 isoform a precursor

    See identical proteins and their annotated locations for NP_783200.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 4 and 6 encode the same isoform (a).
    Source sequence(s)
    AC022002, AF464063, AF549455, AY090737, DA063654, DA796385, R42166
    Consensus CDS
    CCDS43041.1
    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Related
    ENSP00000396010.1, ENST00000418658.5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  5. NM_175613.2NP_783302.1  contactin-4 isoform c

    See identical proteins and their annotated locations for NP_783302.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AC022002, AK314396, DB457029, R42166
    Consensus CDS
    CCDS2558.1
    UniProtKB/Swiss-Prot
    Q8IWV2
    Related
    ENSP00000380600.2, ENST00000397459.6
    Conserved Domains (5) summary
    cd04969
    Location:94166
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05853
    Location:185269
    Ig6_Contactin-4; Sixth Ig domain of contactin-4
    smart00410
    Location:87166
    IG_like; Immunoglobulin like
    cd00063
    Location:269362
    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 ...
    cl11960
    Location:473
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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
    2098803..3059080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533425.3XP_011531727.1  contactin-4 isoform X1

    See identical proteins and their annotated locations for XP_011531727.1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  2. XM_006713004.4XP_006713067.1  contactin-4 isoform X2

    Conserved Domains (5) summary
    cd04969
    Location:422494
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:415494
    IG_like; Immunoglobulin like
    cd00063
    Location:596689
    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:26117
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:513596
    Ig; Immunoglobulin domain
  3. XM_017005785.1XP_016861274.1  contactin-4 isoform X2

    Conserved Domains (5) summary
    cd04969
    Location:422494
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:415494
    IG_like; Immunoglobulin like
    cd00063
    Location:596689
    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:26117
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:513596
    Ig; Immunoglobulin domain
  4. XM_017005783.1XP_016861272.1  contactin-4 isoform X1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  5. XM_011533427.2XP_011531729.1  contactin-4 isoform X1

    See identical proteins and their annotated locations for XP_011531729.1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  6. XM_017005784.2XP_016861273.1  contactin-4 isoform X1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  7. XM_017005782.1XP_016861271.1  contactin-4 isoform X1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  8. XM_011533428.2XP_011531730.1  contactin-4 isoform X1

    See identical proteins and their annotated locations for XP_011531730.1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  9. XM_017005786.1XP_016861275.1  contactin-4 isoform X2

    Conserved Domains (5) summary
    cd04969
    Location:422494
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:415494
    IG_like; Immunoglobulin like
    cd00063
    Location:596689
    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:26117
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:513596
    Ig; Immunoglobulin domain
  10. XM_011533430.2XP_011531732.1  contactin-4 isoform X1

    See identical proteins and their annotated locations for XP_011531732.1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  11. XM_017005787.1XP_016861276.1  contactin-4 isoform X2

    Conserved Domains (5) summary
    cd04969
    Location:422494
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:415494
    IG_like; Immunoglobulin like
    cd00063
    Location:596689
    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:26117
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:513596
    Ig; Immunoglobulin domain
  12. XM_011533429.2XP_011531731.1  contactin-4 isoform X1

    See identical proteins and their annotated locations for XP_011531731.1

    UniProtKB/Swiss-Prot
    Q8IWV2
    UniProtKB/TrEMBL
    A0A024R2E5
    Conserved Domains (4) summary
    cd05853
    Location:513597
    Ig6_Contactin-4; Sixth immunoglobulin (Ig) domain of contactin-4
    cd00063
    Location:597690
    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 ...
    cd04969
    Location:422494
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:225313
    Ig; Immunoglobulin domain
  13. XM_011533431.2XP_011531733.1  contactin-4 isoform X3

    Conserved Domains (6) summary
    cd04969
    Location:411483
    Ig5_Contactin_like; Fifth Ig domain of contactin
    cd05853
    Location:502586
    Ig6_Contactin-4; Sixth Ig domain of contactin-4
    smart00410
    Location:404483
    IG_like; Immunoglobulin like
    cd00063
    Location:586679
    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:15106
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:214302
    Ig; Immunoglobulin domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_175612.1: Suppressed sequence

    Description
    NM_175612.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
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