U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Cntn6 contactin 6 [ Mus musculus (house mouse) ]

    Gene ID: 53870, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Cntn6provided by MGI
    Official Full Name
    contactin 6provided by MGI
    Primary source
    MGI:MGI:1858223
    See related
    Ensembl:ENSMUSG00000030092 AllianceGenome:MGI:1858223
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    NB-3
    Summary
    Predicted to enable cell-cell adhesion mediator activity. Acts upstream of or within positive regulation of Notch signaling pathway. Located in plasma membrane. Is active in parallel fiber to Purkinje cell synapse and presynaptic membrane. Is expressed in brain; spinal cord; and tooth. Orthologous to human CNTN6 (contactin 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in cerebellum adult (RPKM 7.8), CNS E18 (RPKM 5.0) and 7 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Cntn6 in Genome Data Viewer
    Location:
    6 E1; 6 48.93 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (104469566..104840367)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (104492662..104863406)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_16918 Neighboring gene STARR-seq mESC enhancer starr_16919 Neighboring gene STARR-seq mESC enhancer starr_16920 Neighboring gene POU domain, class 5, transcription factor 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_16921 Neighboring gene STARR-seq mESC enhancer starr_16922 Neighboring gene ribosomal protein L17 pseudogene Neighboring gene STARR-seq mESC enhancer starr_16923 Neighboring gene predicted gene, 38871 Neighboring gene STARR-seq mESC enhancer starr_16925 Neighboring gene SURP and G patch domain containing 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_16926 Neighboring gene predicted gene, 23339

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Developmental role of the cell adhesion molecule Contactin-6 in the cerebral cortex and hippocampus. Zuko A, et al. Cell Adh Migr, 2016 Jul 3. PMID 26939565, Free PMC Article
    2. NB-3 signaling mediates the cross-talk between post-traumatic spinal axons and scar-forming cells. Huang Z, et al. EMBO J, 2016 Aug 15. PMID 27192985, Free PMC Article
    3. Contactin-6-deficient male mice exhibit the abnormal function of the accessory olfactory system and impaired reproductive behavior. Zhang W, et al. Brain Behav, 2023 Apr. PMID 36860170, Free PMC Article
    4. NB-3 expression in endothelial cells contributes to the maintenance of blood brain barrier integrity in a mouse high-altitude cerebral edema model. Zhou Y, et al. Exp Neurol, 2022 Aug. PMID 35584741
    5. Synaptic formation in subsets of glutamatergic terminals in the mouse hippocampal formation is affected by a deficiency in the neural cell recognition molecule NB-3. Sakurai K, et al. Neurosci Lett, 2010 Apr 5. PMID 20176085

    See all (47) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Contactin 6, A Novel Causative Gene for Congenital Hypothyroidism, Mediates Thyroid Hormone Biosynthesis Through Notch Signaling.
      Title: Contactin 6, A Novel Causative Gene for Congenital Hypothyroidism, Mediates Thyroid Hormone Biosynthesis Through Notch Signaling.
    2. Contactin-6-deficient male mice exhibit the abnormal function of the accessory olfactory system and impaired reproductive behavior.
      Title: Contactin-6-deficient male mice exhibit the abnormal function of the accessory olfactory system and impaired reproductive behavior.
    3. NB-3 expression in endothelial cells contributes to the maintenance of blood brain barrier integrity in a mouse high-altitude cerebral edema model.
      Title: NB-3 expression in endothelial cells contributes to the maintenance of blood brain barrier integrity in a mouse high-altitude cerebral edema model.
    4. Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice.
      Title: Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice.
    5. NB-3 deficiency promoted synapse reformation between sRST regenerative axons and motor neurons and enhanced the potential for electrical activity of muscle contraction and motor coordination.
      Title: Induced NB-3 Limits Regenerative Potential of Serotonergic Axons after Complete Spinal Transection.
    6. decrease of vermian SYP1 and CNTN6 in reln(+/-) mice displayed patterns compatible with the structural modifications of the autistic cerebellum.
      Title: Decreased Expression of Synaptophysin 1 (SYP1 Major Synaptic Vesicle Protein p38) and Contactin 6 (CNTN6/NB3) in the Cerebellar Vermis of reln Haplodeficient Mice.
    7. Cntn6 is expressed during postnatal hippocampal development. The absence of Cntn6 affects hippocampal Spatial Learning and memory, and affects allocentric navigation of the animals.
      Title: Cntn6 deficiency impairs allocentric navigation in mice.
    8. The common phenotypic features of 40 patients with microdeletions and microduplications of CNTN6 appeared to be the autism spectrum disorders, developmental delay, intellectual disability, seizures, cognitive impairment, cardiological defects, and behavioral problems.
      Title: [Estimation of association of CNTN6 copy number variation with idiopathic intellectual disability].
    9. Cntn6 engages in both trans- and cis-interactions and may be involved in larger protein interaction networks.
      Title: Developmental role of the cell adhesion molecule Contactin-6 in the cerebral cortex and hippocampus.
    10. These findings demonstrate that NB-3 trans-homophilic interactions mediate the cross-talk between post-traumatic axons and scar-forming cells and impair the intrinsic growth ability of injured axons.
      Title: NB-3 signaling mediates the cross-talk between post-traumatic spinal axons and scar-forming cells.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Targeted (1)  1 citation

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables cell-cell adhesion mediator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dendrite self-avoidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of Notch signaling pathway IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in parallel fiber to Purkinje cell synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in parallel fiber to Purkinje cell synapse IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in presynapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in presynapse IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    is_active_in presynaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in presynaptic membrane IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    contactin-6
    Names
    mNB-3
    neural recognition molecule NB-3

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001411154.1 → NP_001398083.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    2. NM_001411155.1 → NP_001398084.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    3. NM_001411156.1 → NP_001398085.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    4. NM_001411157.1 → NP_001398086.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    5. NM_001411158.1 → NP_001398087.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    6. NM_001411159.1 → NP_001398088.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3
      Related
      ENSMUSP00000124025.2, ENSMUST00000162872.2

    7. NM_001411160.1 → NP_001398089.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    8. NM_001411161.1 → NP_001398090.1  contactin-6 isoform a precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3

    9. NM_001411162.1 → NP_001398091.1  contactin-6 isoform b precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/TrEMBL
      E0CXE3

    10. NM_001411163.1 → NP_001398092.1  contactin-6 isoform b precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      UniProtKB/TrEMBL
      E0CXE3

    11. NM_001411164.1 → NP_001398093.1  contactin-6 isoform c precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153990

    12. NM_001411165.1 → NP_001398094.1  contactin-6 isoform c precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153990

    13. NM_001411166.1 → NP_001398095.1  contactin-6 isoform c precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153990

    14. NM_001411167.1 → NP_001398096.1  contactin-6 isoform c precursor

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153990

    15. NM_017383.4 → NP_059079.2  contactin-6 isoform a precursor

      See identical proteins and their annotated locations for NP_059079.2

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990
      Consensus CDS
      CCDS20394.1
      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3
      Related
      ENSMUSP00000086623.6, ENSMUST00000089215.12
      Conserved Domains (5) summary
      smart00060
      Location:903 → 983
      FN3; Fibronectin type 3 domain
      cd00063
      Location:598 → 691
      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 ...
      cd00096
      Location:319 → 322
      Ig; Ig strand A [structural motif]
      cd04969
      Location:408 → 496
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:319 → 403
      Ig; Immunoglobulin domain

    RNA

    1. NR_177191.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990

    2. NR_177192.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC116110, AC117728, AC153023, AC153990

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      104469566..104840367
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011241409.4 → XP_011239711.1  contactin-6 isoform X3

      Conserved Domains (3) summary
      smart00060
      Location:702 → 782
      FN3; Fibronectin type 3 domain
      cd00063
      Location:397 → 490
      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:314 → 397
      Ig; Immunoglobulin domain

    2. XM_036166292.1 → XP_036022185.1  contactin-6 isoform X4

      Conserved Domains (4) summary
      smart00060
      Location:685 → 765
      FN3; Fibronectin type 3 domain
      cd00063
      Location:380 → 473
      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 ...
      cd00096
      Location:289 → 294
      Ig; Ig strand A' [structural motif]
      cl11960
      Location:282 → 380
      Ig; Immunoglobulin domain

    3. XM_036166287.1 → XP_036022180.1  contactin-6 isoform X2

      UniProtKB/TrEMBL
      E0CXE3
      Conserved Domains (5) summary
      smart00060
      Location:886 → 966
      FN3; Fibronectin type 3 domain
      cd00063
      Location:581 → 674
      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 ...
      cd00096
      Location:302 → 305
      Ig; Ig strand A [structural motif]
      cd04969
      Location:391 → 479
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:302 → 386
      Ig; Immunoglobulin domain

    4. XM_036166288.1 → XP_036022181.1  contactin-6 isoform X2

      UniProtKB/TrEMBL
      E0CXE3
      Conserved Domains (5) summary
      smart00060
      Location:886 → 966
      FN3; Fibronectin type 3 domain
      cd00063
      Location:581 → 674
      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 ...
      cd00096
      Location:302 → 305
      Ig; Ig strand A [structural motif]
      cd04969
      Location:391 → 479
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:302 → 386
      Ig; Immunoglobulin domain

    5. XM_036166285.1 → XP_036022178.1  contactin-6 isoform X1

      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3
      Related
      ENSMUSP00000124714.2, ENSMUST00000161070.8
      Conserved Domains (5) summary
      smart00060
      Location:903 → 983
      FN3; Fibronectin type 3 domain
      cd00063
      Location:598 → 691
      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 ...
      cd00096
      Location:319 → 322
      Ig; Ig strand A [structural motif]
      cd04969
      Location:408 → 496
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:319 → 403
      Ig; Immunoglobulin domain

    6. XM_036166289.1 → XP_036022182.1  contactin-6 isoform X2

      UniProtKB/TrEMBL
      E0CXE3
      Conserved Domains (5) summary
      smart00060
      Location:886 → 966
      FN3; Fibronectin type 3 domain
      cd00063
      Location:581 → 674
      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 ...
      cd00096
      Location:302 → 305
      Ig; Ig strand A [structural motif]
      cd04969
      Location:391 → 479
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:302 → 386
      Ig; Immunoglobulin domain

    7. XM_036166290.1 → XP_036022183.1  contactin-6 isoform X2

      UniProtKB/TrEMBL
      E0CXE3
      Conserved Domains (5) summary
      smart00060
      Location:886 → 966
      FN3; Fibronectin type 3 domain
      cd00063
      Location:581 → 674
      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 ...
      cd00096
      Location:302 → 305
      Ig; Ig strand A [structural motif]
      cd04969
      Location:391 → 479
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:302 → 386
      Ig; Immunoglobulin domain

    8. XM_006506381.5 → XP_006506444.1  contactin-6 isoform X1

      See identical proteins and their annotated locations for XP_006506444.1

      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3
      Conserved Domains (5) summary
      smart00060
      Location:903 → 983
      FN3; Fibronectin type 3 domain
      cd00063
      Location:598 → 691
      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 ...
      cd00096
      Location:319 → 322
      Ig; Ig strand A [structural motif]
      cd04969
      Location:408 → 496
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:319 → 403
      Ig; Immunoglobulin domain

    9. XM_036166286.1 → XP_036022179.1  contactin-6 isoform X1

      UniProtKB/Swiss-Prot
      Q8C6X1, Q9JMB8
      UniProtKB/TrEMBL
      E0CXE3
      Conserved Domains (5) summary
      smart00060
      Location:903 → 983
      FN3; Fibronectin type 3 domain
      cd00063
      Location:598 → 691
      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 ...
      cd00096
      Location:319 → 322
      Ig; Ig strand A [structural motif]
      cd04969
      Location:408 → 496
      Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
      cl11960
      Location:319 → 403
      Ig; Immunoglobulin domain

    RNA

    1. XR_003956233.2 RNA Sequence

    2. XR_004942984.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JMB8.2 GenPept UniProtKB/Swiss-Prot:Q9JMB8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools