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CNTN6 contactin 6 [ Homo sapiens (human) ]

Gene ID: 27255, updated on 13-Mar-2020

Summary

Official Symbol
CNTN6provided by HGNC
Official Full Name
contactin 6provided by HGNC
Primary source
HGNC:HGNC:2176
See related
Ensembl:ENSG00000134115 MIM:607220
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
NB3
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. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Expression
Biased expression in thyroid (RPKM 3.8), lung (RPKM 1.4) and 3 other tissues See more
Orthologs

Genomic context

See CNTN6 in Genome Data Viewer
Location:
3p26.3
Exon count:
32
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (978021..1404217)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (1134342..1445278)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986058 Neighboring gene uncharacterized LOC107986059 Neighboring gene RNA, 7SL, cytoplasmic 120, pseudogene Neighboring gene uncharacterized LOC105376924 Neighboring gene uncharacterized LOC105376923 Neighboring gene crumbs cell polarity complex component 3 pseudogene 1 Neighboring gene ribosomal protein L23a pseudogene 38 Neighboring gene meiotic recombination hotspot S

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

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 for venous thromboembolism: the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
NHGRI GWA Catalog
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
NHGRI GWA Catalog
Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
NHGRI GWA Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog
Genome-wide association of lipid-lowering response to statins in combined study populations.
NHGRI GWA Catalog
GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC133256, AC087430.1

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Notch binding IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion mediator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
central nervous system development TAS
Traceable Author Statement
more info
PubMed 
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 
positive regulation of Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
anchored component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
parallel fiber to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
contactin-6
Names
neural adhesion molecule
neural recognition molecule NB-3

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_047144.1 RefSeqGene

    Range
    89890..401083
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001289080.2NP_001276009.1  contactin-6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001276009.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 4-9 all encode the same isoform (1).
    Source sequence(s)
    AB003592, AC026214, AC034192, BC113118, CN364480, DB170583
    Consensus CDS
    CCDS2557.1
    UniProtKB/Swiss-Prot
    Q9UQ52
    UniProtKB/TrEMBL
    A0A024R2C7, B4DGV0
    Related
    ENSP00000407822.2, ENST00000446702.7
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  2. NM_001289081.2NP_001276010.1  contactin-6 isoform 2

    See identical proteins and their annotated locations for NP_001276010.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC026214, AC034192, AK294786, BC113118, CN364480, DA094373
    UniProtKB/Swiss-Prot
    Q9UQ52
    UniProtKB/TrEMBL
    B4DGV0
    Conserved Domains (5) summary
    cd04969
    Location:352424
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:434522
    IG_like; Immunoglobulin like
    cd00063
    Location:526619
    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:336424
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:247331
    Ig; Immunoglobulin domain
  3. NM_001349350.2NP_001336279.1  contactin-6 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 1, 2, and 5-9, encodes isoform 1.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Consensus CDS
    CCDS2557.1
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  4. NM_001349351.2NP_001336280.1  contactin-6 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variants 1, 2, 4, and 6-9, encodes isoform 1.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Consensus CDS
    CCDS2557.1
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  5. NM_001349352.2NP_001336281.1  contactin-6 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variants 1, 2, 4, 5, and 7-9, encodes isoform 1.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Consensus CDS
    CCDS2557.1
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  6. NM_001349353.2NP_001336282.1  contactin-6 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), as well as variants 1, 2, 4-6, 8 and 9, encodes isoform 1.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Consensus CDS
    CCDS2557.1
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  7. NM_001349354.2NP_001336283.1  contactin-6 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variants 1, 2, 4-7, and 9, encodes isoform 1.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Consensus CDS
    CCDS2557.1
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  8. NM_001349355.2NP_001336284.1  contactin-6 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9), as well as variants 1, 2, and 4-8, encodes isoform 1.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Consensus CDS
    CCDS2557.1
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  9. NM_001349356.2NP_001336285.1  contactin-6 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) encodes isoform 3.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (2) summary
    cd00063
    Location:562655
    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:283367
    Ig; Immunoglobulin domain
  10. NM_001349357.2NP_001336286.1  contactin-6 isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) encodes isoform 4.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (2) summary
    cd00063
    Location:494587
    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:215299
    Ig; Immunoglobulin domain
  11. NM_001349358.2NP_001336287.1  contactin-6 isoform 5 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) encodes isoform 5.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (3) summary
    smart00060
    Location:718798
    FN3; Fibronectin type 3 domain
    cd00063
    Location:413506
    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:330413
    Ig; Immunoglobulin domain
  12. NM_001349359.2NP_001336288.1  contactin-6 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13), as well as variants 14-16, encodes isoform 6.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (3) summary
    smart00060
    Location:529609
    FN3; Fibronectin type 3 domain
    cd00063
    Location:224317
    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:141224
    Ig; Immunoglobulin domain
  13. NM_001349360.2NP_001336289.1  contactin-6 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14), as well as variants 13, 15, and 16, encodes isoform 6.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (3) summary
    smart00060
    Location:529609
    FN3; Fibronectin type 3 domain
    cd00063
    Location:224317
    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:141224
    Ig; Immunoglobulin domain
  14. NM_001349361.2NP_001336290.1  contactin-6 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (15), as well as variants 13, 14, and 16, encodes isoform 6.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (3) summary
    smart00060
    Location:529609
    FN3; Fibronectin type 3 domain
    cd00063
    Location:224317
    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:141224
    Ig; Immunoglobulin domain
  15. NM_001349362.2NP_001336291.1  contactin-6 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16), as well as variants 13-15, encodes isoform 6.
    Source sequence(s)
    AC026214, AC027123, AC034192
    Conserved Domains (3) summary
    smart00060
    Location:529609
    FN3; Fibronectin type 3 domain
    cd00063
    Location:224317
    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:141224
    Ig; Immunoglobulin domain
  16. NM_014461.4NP_055276.1  contactin-6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_055276.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 2, and 4-9 all encode the same isoform (1).
    Source sequence(s)
    AB003592, AC026214, AC034192, BC036338, CN364480
    Consensus CDS
    CCDS2557.1
    UniProtKB/Swiss-Prot
    Q9UQ52
    UniProtKB/TrEMBL
    A0A024R2C7, B4DGV0
    Related
    ENSP00000341882.2, ENST00000350110.2
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    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_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    978021..1404217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006171.1XP_016861660.1  contactin-6 isoform X1

    UniProtKB/Swiss-Prot
    Q9UQ52
    UniProtKB/TrEMBL
    A0A024R2C7
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  2. XM_017006177.2XP_016861666.1  contactin-6 isoform X3

  3. XM_011533590.2XP_011531892.1  contactin-6 isoform X1

    See identical proteins and their annotated locations for XP_011531892.1

    UniProtKB/Swiss-Prot
    Q9UQ52
    UniProtKB/TrEMBL
    A0A024R2C7
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  4. XM_017006172.2XP_016861661.1  contactin-6 isoform X1

    UniProtKB/Swiss-Prot
    Q9UQ52
    UniProtKB/TrEMBL
    A0A024R2C7
    Conserved Domains (2) summary
    cd00063
    Location:598691
    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:319403
    Ig; Immunoglobulin domain
  5. XM_011533591.3XP_011531893.1  contactin-6 isoform X2

    See identical proteins and their annotated locations for XP_011531893.1

    Conserved Domains (5) summary
    cd04969
    Location:352424
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:434522
    IG_like; Immunoglobulin like
    cd00063
    Location:526619
    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:336424
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:247331
    Ig; Immunoglobulin domain
  6. XM_017006174.1XP_016861663.1  contactin-6 isoform X2

    Conserved Domains (5) summary
    cd04969
    Location:352424
    Ig5_Contactin_like; Fifth Ig domain of contactin
    smart00410
    Location:434522
    IG_like; Immunoglobulin like
    cd00063
    Location:526619
    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:336424
    I-set; Immunoglobulin I-set domain
    cl11960
    Location:247331
    Ig; Immunoglobulin domain

RNA

  1. XR_940415.2 RNA Sequence

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