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Cntn6 contactin 6 [ Mus musculus (house mouse) ]

Gene ID: 53870, updated on 6-Jun-2024

Summary

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 parallel fiber to Purkinje cell synapse and plasma membrane. Is anchored component of presynaptic membrane. Is expressed in brain; spinal cord; and tooth. Orthologous to human CNTN6 (contactin 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in cerebellum adult (RPKM 7.8), CNS E18 (RPKM 5.0) and 7 other tissues See more
Orthologs
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
acts_upstream_of_or_within Notch signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within 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
 
located_in membrane IEA
Inferred from Electronic Annotation
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

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

NCBI Reference Sequences (RefSeq)

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_001411154.1NP_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_001411155.1NP_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_001411156.1NP_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_001411157.1NP_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_001411158.1NP_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_001411159.1NP_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_001411160.1NP_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_001411161.1NP_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_001411162.1NP_001398091.1  contactin-6 isoform b precursor

    Status: VALIDATED

    Source sequence(s)
    AC116110, AC117728, AC153023, AC153990
    UniProtKB/TrEMBL
    E0CXE3
  10. NM_001411163.1NP_001398092.1  contactin-6 isoform b precursor

    Status: VALIDATED

    Source sequence(s)
    AC116110, AC117728, AC153023, AC153990
    UniProtKB/TrEMBL
    E0CXE3
  11. NM_001411164.1NP_001398093.1  contactin-6 isoform c precursor

    Status: VALIDATED

    Source sequence(s)
    AC116110, AC117728, AC153990
  12. NM_001411165.1NP_001398094.1  contactin-6 isoform c precursor

    Status: VALIDATED

    Source sequence(s)
    AC116110, AC117728, AC153990
  13. NM_001411166.1NP_001398095.1  contactin-6 isoform c precursor

    Status: VALIDATED

    Source sequence(s)
    AC116110, AC117728, AC153990
  14. NM_001411167.1NP_001398096.1  contactin-6 isoform c precursor

    Status: VALIDATED

    Source sequence(s)
    AC116110, AC117728, AC153990
  15. NM_017383.4NP_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:903983
    FN3; Fibronectin type 3 domain
    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 ...
    cd00096
    Location:319322
    Ig; Ig strand A [structural motif]
    cd04969
    Location:408496
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:319403
    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_011241409.4XP_011239711.1  contactin-6 isoform X3

    Conserved Domains (3) summary
    smart00060
    Location:702782
    FN3; Fibronectin type 3 domain
    cd00063
    Location:397490
    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:314397
    Ig; Immunoglobulin domain
  2. XM_036166292.1XP_036022185.1  contactin-6 isoform X4

    Conserved Domains (4) summary
    smart00060
    Location:685765
    FN3; Fibronectin type 3 domain
    cd00063
    Location:380473
    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:289294
    Ig; Ig strand A' [structural motif]
    cl11960
    Location:282380
    Ig; Immunoglobulin domain
  3. XM_036166287.1XP_036022180.1  contactin-6 isoform X2

    UniProtKB/TrEMBL
    E0CXE3
    Conserved Domains (5) summary
    smart00060
    Location:886966
    FN3; Fibronectin type 3 domain
    cd00063
    Location:581674
    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:302305
    Ig; Ig strand A [structural motif]
    cd04969
    Location:391479
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:302386
    Ig; Immunoglobulin domain
  4. XM_036166288.1XP_036022181.1  contactin-6 isoform X2

    UniProtKB/TrEMBL
    E0CXE3
    Conserved Domains (5) summary
    smart00060
    Location:886966
    FN3; Fibronectin type 3 domain
    cd00063
    Location:581674
    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:302305
    Ig; Ig strand A [structural motif]
    cd04969
    Location:391479
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:302386
    Ig; Immunoglobulin domain
  5. XM_036166285.1XP_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:903983
    FN3; Fibronectin type 3 domain
    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 ...
    cd00096
    Location:319322
    Ig; Ig strand A [structural motif]
    cd04969
    Location:408496
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:319403
    Ig; Immunoglobulin domain
  6. XM_036166289.1XP_036022182.1  contactin-6 isoform X2

    UniProtKB/TrEMBL
    E0CXE3
    Conserved Domains (5) summary
    smart00060
    Location:886966
    FN3; Fibronectin type 3 domain
    cd00063
    Location:581674
    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:302305
    Ig; Ig strand A [structural motif]
    cd04969
    Location:391479
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:302386
    Ig; Immunoglobulin domain
  7. XM_036166290.1XP_036022183.1  contactin-6 isoform X2

    UniProtKB/TrEMBL
    E0CXE3
    Conserved Domains (5) summary
    smart00060
    Location:886966
    FN3; Fibronectin type 3 domain
    cd00063
    Location:581674
    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:302305
    Ig; Ig strand A [structural motif]
    cd04969
    Location:391479
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:302386
    Ig; Immunoglobulin domain
  8. XM_006506381.5XP_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:903983
    FN3; Fibronectin type 3 domain
    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 ...
    cd00096
    Location:319322
    Ig; Ig strand A [structural motif]
    cd04969
    Location:408496
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:319403
    Ig; Immunoglobulin domain
  9. XM_036166286.1XP_036022179.1  contactin-6 isoform X1

    UniProtKB/Swiss-Prot
    Q8C6X1, Q9JMB8
    UniProtKB/TrEMBL
    E0CXE3
    Conserved Domains (5) summary
    smart00060
    Location:903983
    FN3; Fibronectin type 3 domain
    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 ...
    cd00096
    Location:319322
    Ig; Ig strand A [structural motif]
    cd04969
    Location:408496
    Ig5_Contactin; Fifth immunoglobulin (Ig) domain of contactin
    cl11960
    Location:319403
    Ig; Immunoglobulin domain

RNA

  1. XR_003956233.2 RNA Sequence

  2. XR_004942984.1 RNA Sequence