Cntn1 contactin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cntn1provided by RGD
Official Full Name: contactin 1provided by RGD
Primary source: RGD:621300
See related: Ensembl:ENSRNOG00000004438 AllianceGenome:RGD:621300
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: F3
Summary: Predicted to enable carbohydrate binding activity and cell-cell adhesion mediator activity. Involved in positive regulation of peptidyl-tyrosine phosphorylation. Located in membrane raft. Human ortholog(s) of this gene implicated in Compton-North congenital myopathy. Orthologous to human CNTN1 (contactin 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 826.3) and Lung (RPKM 58.6) See more
Orthologs: human mouse all
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Genomic context

Location:: 7q35

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (125142638..125440397)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (123263146..123560896)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (133290606..133588314)

Chromosome 7 - NC_086025.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression of alternatively spliced FnIII domains of tenascin-C is differentially regulated after brain injury, with strong increases of domains B and D that may well influence axonal regeneration and repair processes in the damaged nervous system.
Title: Analysis of combinatorial variability reveals selective accumulation of the fibronectin type III domains B and D of tenascin-C in injured brain.
Data show that the rat F3/contactin gene differs from the mouse gene in that it contains two additional untranslated exons that are alternatively spliced and lacks the homologue mouse untranslated exon 0.
Title: Polymorphism of the untranslated regions of the F3/contactin mRNA in the rat nervous system.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AU048466 (e-PCR)
- UniSTS:144916

Cntn1 (e-PCR), detects polymorphism
- UniSTS:141365

D7Got118 (e-PCR)
- UniSTS:115534

BF415915 (e-PCR)
- UniSTS:248970

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables carbohydrate binding	ISO Inferred from Sequence Orthology more info
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 brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in central nervous system myelin formation	IEA Inferred from Electronic Annotation more info
involved_in central nervous system myelin formation	ISO Inferred from Sequence Orthology more info
involved_in cerebellum development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cerebellum development	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of gene expression	ISO Inferred from Sequence Orthology more info
involved_in locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in myelination	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of peptidyl-tyrosine phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of sodium ion transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of sodium ion transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic membrane	ISO Inferred from Sequence Orthology more info
located_in side of membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: contactin-1

Names: neural cell surface protein F3

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)

NM_057118.2 → NP_476459.1 contactin-1 precursor

See identical proteins and their annotated locations for NP_476459.1

Status: PROVISIONAL

Source sequence(s)

D38492

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A0A8L2R3Y6, A6K7R9

Related

ENSRNOP00000006219.3, ENSRNOT00000006219.5

Conserved Domains (9) summary

cd05851
Location:241 → 328

IgI_3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) domains

cd00063
Location:612 → 699

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 ...

pfam00041
Location:813 → 895

fn3; Fibronectin type III domain

cd00096
Location:332 → 335

Ig; Ig strand A [structural motif]

cd04970
Location:503 → 603

Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin

cd05727
Location:142 → 230

Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2, and similar domains

cd05849
Location:40 → 134

IgI_1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains

cd05852
Location:413 → 501

Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1

cl11960
Location:332 → 408

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086025.1 Reference GRCr8

Range

125142638..125440397

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017594616.3 → XP_017450105.1 contactin-1 isoform X1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A0A8L2R3Y6, A6K7R9

Conserved Domains (9) summary

cd05851
Location:241 → 328

IgI_3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) domains

cd00063
Location:612 → 699

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 ...

pfam00041
Location:813 → 895

fn3; Fibronectin type III domain

cd00096
Location:332 → 335

Ig; Ig strand A [structural motif]

cd04970
Location:503 → 603

Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin

cd05727
Location:142 → 230

Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2, and similar domains

cd05849
Location:40 → 134

IgI_1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains

cd05852
Location:413 → 501

Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1

cl11960
Location:332 → 408

Ig; Immunoglobulin domain
XM_008765659.4 → XP_008763881.1 contactin-1 isoform X2

Conserved Domains (8) summary

cd04970
Location:520 → 604

Ig6_Contactin_like; Sixth Ig domain of contactin

cd05727
Location:134 → 230

Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2 and similar proteins

cd05849
Location:40 → 132

Ig1_Contactin-1; First Ig domain of contactin-1

cd05851
Location:241 → 328

Ig3_Contactin-1; Third Ig domain of contactin-1

cd05852
Location:429 → 501

Ig5_Contactin-1; Fifth Ig domain of contactin-1

smart00410
Location:422 → 501

IG_like; Immunoglobulin like

pfam07679
Location:331 → 408

I-set; Immunoglobulin I-set domain

cl11960
Location:332 → 408

Ig; Immunoglobulin domain
XM_063262899.1 → XP_063118969.1 contactin-1 isoform X1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A6K7R9
XM_063262902.1 → XP_063118972.1 contactin-1 isoform X1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A6K7R9
XM_039078298.1 → XP_038934226.1 contactin-1 isoform X1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A0A8L2R3Y6, A6K7R9

Conserved Domains (9) summary

cd05851
Location:241 → 328

IgI_3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) domains

cd00063
Location:612 → 699

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 ...

pfam00041
Location:813 → 895

fn3; Fibronectin type III domain

cd00096
Location:332 → 335

Ig; Ig strand A [structural motif]

cd04970
Location:503 → 603

Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin

cd05727
Location:142 → 230

Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2, and similar domains

cd05849
Location:40 → 134

IgI_1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains

cd05852
Location:413 → 501

Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1

cl11960
Location:332 → 408

Ig; Immunoglobulin domain
XM_063262901.1 → XP_063118971.1 contactin-1 isoform X1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A6K7R9
XM_063262904.1 → XP_063118974.1 contactin-1 isoform X2
XM_063262907.1 → XP_063118977.1 contactin-1 isoform X2
XM_063262905.1 → XP_063118975.1 contactin-1 isoform X2
XM_063262908.1 → XP_063118978.1 contactin-1 isoform X2
XM_063262903.1 → XP_063118973.1 contactin-1 isoform X2
XM_063262906.1 → XP_063118976.1 contactin-1 isoform X2
XM_006242177.5 → XP_006242239.1 contactin-1 isoform X1

See identical proteins and their annotated locations for XP_006242239.1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A0A8L2R3Y6, A6K7R9

Conserved Domains (9) summary

cd05851
Location:241 → 328

IgI_3_Contactin-1; Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) domains

cd00063
Location:612 → 699

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 ...

pfam00041
Location:813 → 895

fn3; Fibronectin type III domain

cd00096
Location:332 → 335

Ig; Ig strand A [structural motif]

cd04970
Location:503 → 603

Ig6_Contactin; Sixth immunoglobulin (Ig) domain of contactin

cd05727
Location:142 → 230

Ig2_Contactin-2-like; Second Ig domain of the neural cell adhesion molecule contactin-2, and similar domains

cd05849
Location:40 → 134

IgI_1_Contactin-1; First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains

cd05852
Location:413 → 501

Ig5_Contactin-1; Fifth immunoglobulin (Ig) domain of contactin-1

cl11960
Location:332 → 408

Ig; Immunoglobulin domain
XM_063262900.1 → XP_063118970.1 contactin-1 isoform X1

UniProtKB/Swiss-Prot

Q63198

UniProtKB/TrEMBL

A6K7R9