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Cntn6 contactin 6 [ Mus musculus (house mouse) ]

Gene ID: 53870, updated on 28-Oct-2024

Summary

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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, Oct 2024]
Expression
Biased expression in cerebellum adult (RPKM 7.8), CNS E18 (RPKM 5.0) and 7 other tissues See more
Orthologs
human all
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data 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

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Related articles in PubMed

  1. 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
  2. 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
  3. Expression and regulation of a gene encoding neural recognition molecule NB-3 of the contactin/F3 subgroup in mouse brain. Lee S, et al. Gene, 2000 Mar 21. PMID 10717476
  4. Time origin and structural analysis of the induced CRISPR/cas9 megabase-sized deletions and duplications involving the Cntn6 gene in mice. Pristyazhnyuk IE, et al. Sci Rep, 2019 Oct 2. PMID 31578377, Free PMC Article
  5. Induced NB-3 Limits Regenerative Potential of Serotonergic Axons after Complete Spinal Transection. Huang Z, et al. J Neurotrauma, 2019 Feb 1. PMID 30156464

See all (46) 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

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Alleles

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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

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

NCBI Reference Sequences (RefSeq)

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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

  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

  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

  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

  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

  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
    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

  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

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

    Status: VALIDATED

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

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

    Status: VALIDATED

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

  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

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