Cntn6 MGI Mouse Gene Detail - MGI:1858223

Symbol

Cntn6
Name

contactin 6
Synonyms

NB-3

Feature Type

protein coding gene
IDs

MGI:1858223
NCBI Gene: 53870
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr6:104469751-104840367 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 48.93 cM, cytoband E2
Mapping Data

2 experiments

SNPs within 2kb

11568 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1858223	protein coding gene	Chr6:104469566-104840367 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031092	protein coding gene	Chr6:106650280-107035364 (+)
A/J	MGP_AJ_G0031061	protein coding gene	Chr6:102576731-102963009 (+)
AKR/J	MGP_AKRJ_G0030992	protein coding gene	Chr6:105367048-105752522 (+)
BALB/cJ	MGP_BALBcJ_G0031072	protein coding gene	Chr6:102526324-102912451 (+)
C3H/HeJ	MGP_C3HHeJ_G0030636	protein coding gene	Chr6:78603282-78983476 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0031531	protein coding gene	Chr6:109360336-109767351 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028695	protein coding gene	Chr6:100148451-100503636 (+)
CAST/EiJ	MGP_CASTEiJ_G0030179	protein coding gene	Chr6:105717363-106109226 (+)
CBA/J	MGP_CBAJ_G0030758	protein coding gene	Chr6:113628895-114050493 (+)
DBA/2J	MGP_DBA2J_G0030911	protein coding gene	Chr6:101707298-102085618 (+)
FVB/NJ	MGP_FVBNJ_G0030865	protein coding gene	Chr6:100819177-101194412 (+)
LP/J	MGP_LPJ_G0030991	protein coding gene	Chr6:106738514-107144526 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0030899	protein coding gene	Chr6:117642278-118123916 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031558	protein coding gene	Chr6:105337420-105726304 (+)
PWK/PhJ	MGP_PWKPhJ_G0029895	protein coding gene	Chr6:100709105-101087410 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029723	protein coding gene	Chr6:104199727-104585310 (+)
WSB/EiJ	MGP_WSBEiJ_G0030263	protein coding gene	Chr6:105847234-106236901 (+)

Human Ortholog

CNTN6, contactin 6

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CNTN6, contactin 6
Synonyms

NB3
Links

HGNC:2176

NCBI Gene ID: 27255

neXtProt AC: NX_Q9UQ52

UniProt: Q9UQ52
Chr Location

3p26.3; chr3:1092658-1404217 (+) GRCh38

MGI Vertebrate Homology

Cntn6 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: CNTN6
Gene Tree

Cntn6

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Phenotype Summary

3 phenotypes from 1 allele in 3 genetic backgrounds
1 phenotype from multigenic genotypes
18 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

5
Endonuclease-mediated

3
Spontaneous

1
Targeted

1
Genomic Mutations

1 involving Cntn6
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

64 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for disruption of this gene display impaired coordination without any obvious morphological of physiological abnormalities in the brain.

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All GO Annotations

21
GO References

5

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1138
Tissues

155
cDNA Data

9
Literature Summary

17

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA CNTN6

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All Sequences

89
RefSeq

52
UniProt

3
CCDS

CCDS20394.1

Ensembl

ENSMUSG00000030092 (Evidence)
NCBI Gene

53870

			Length	Strain/Species	Flank
genomic	ENSMUSG00000030092	Ensembl Gene Model \| MGI Sequence Detail	370617	C57BL/6J	± kb
transcript	ENSMUST00000162872	Ensembl \| MGI Sequence Detail	3467	Not Applicable
polypeptide	ENSMUSP00000124025	Ensembl \| MGI Sequence Detail	1028	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000005671 contactin-6

(term hierarchy)
PDB

5E55, 5E5U
InterPro Domains

IPR003961 Fibronectin type III

IPR036116 Fibronectin type III superfamily

IPR013098 Immunoglobulin I-set

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR003599 Immunoglobulin subtype

IPR003598 Immunoglobulin subtype 2
GlyGen

Q9JMB8 13 sites, 6 N-linked glycans (7 sites)

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All nucleic 12

cDNA 9

Primer pair 2

Other 1

Microarray probesets 3

Summaries

All 51

Developmental Gene Expression 17

Gene Ontology 5

Phenotypes 18
Earliest

J:61081 Lee S, et al., Expression and regulation of a gene encoding neural recognition molecule NB-3 of the contactin/F3 subgroup in mouse brain. Gene. 2000 Mar 21;245(2):253-66
Latest

J:357284 Lo Giudice Q, et al., Developmental emergence of first- and higher-order thalamic neuron molecular identities. Development. 2024 Sep 15;151(18)

TSS for Cntn6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr58028	Chr6:104469915-104469926 (+)	170 bp
Tssr58029	Chr6:104470010-104470072 (+)	290 bp
Tssr1956	Chr6:104470093-104470117 (+)	354 bp
Tssr58030	Chr6:104470122-104470177 (+)	399 bp
Tssr58031	Chr6:104470181-104470191 (+)	435 bp
Tssr58032	Chr6:104570123-104570127 (+)	100,374 bp
Tssr58033	Chr6:104759691-104759695 (+)	289,942 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/10/2024 MGI 6.24