TNR tenascin R [Homo sapiens (human)] - Gene

Summary

Official Symbol: TNRprovided by HGNC
Official Full Name: tenascin Rprovided by HGNC
Primary source: HGNC:HGNC:11953
See related: Ensembl:ENSG00000116147 MIM:601995; AllianceGenome:HGNC:11953
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TN-R; NEDSTO
Summary: This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The encoded protein is restricted to the central nervous system. The protein may play a role in neurite outgrowth, neural cell adhesion and modulation of sodium channel function. It is a constituent of perineuronal nets. [provided by RefSeq, Aug 2013]
Expression: Restricted expression toward brain (RPKM 22.5) See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.1

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (175315194..175743595, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (174669251..175098445, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (175284330..175712731, complement)

Chromosome 1 - NC_000001.11 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TNR is a novel candidate for Biopolar Disorder in humans and anxiety in mice
Title: A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder.
Study observed a genome-wide significant association between attention deficit hyperactivity disorder and rs6686722, mapped to the Tenascin R (TNR) gene.
Title: A case-control genome-wide association study of ADHD discovers a novel association with the tenascin R (TNR) gene.
Two genes, TNR (and TNK2), were found to have genetic variations linked to familial Parkinson's Disease.
Title: Whole-Exome Sequencing in Familial Parkinson Disease.
TnC and TnR play important roles in nervous and immune systems. [Review]
Title: Tenascins and inflammation in disorders of the nervous system.
citation presents comparison with human gene.
Title: Structure of the murine tenascin-R gene and functional characterisation of the promoter.
results show that tenascin-R expression is tightly regulated in a spatiotemporal manner during brain development, especially cortical plate formation; its pattern of expression suggests a role for tenascin-R in corticogenesis
Title: Spatiotemporal distribution of tenascin-R in the developing human cerebral cortex parallels neuronal migration.
Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
Title: Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia: B3GAT2 is associated with disease risk and cortical surface area.
KIAA0510, the 3'-untranslated region of the tenascin-R gene, and tenascin-R are overexpressed in pilocytic astrocytomas
Title: KIAA0510, the 3'-untranslated region of the tenascin-R gene, and tenascin-R are overexpressed in pilocytic astrocytomas.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
The researchers found evidence that the tenascin R gene is a potential susceptiblity or marker gene for IgA nephropathy.
Title: Parallel genotyping of 10,204 single nucleotide polymorphisms to screen for susceptible genes for IgA nephropathy.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder, nonprogressive, with spasticity and transient opisthotonus MedGen: C5562040 OMIM: 619653 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL034091 (e-PCR)
- UniSTS:93445

AL034092 (e-PCR)
- UniSTS:93446

AL034093 (e-PCR)
- UniSTS:93447

AL034094 (e-PCR)
- UniSTS:93448

AL034095 (e-PCR)
- UniSTS:93449

AL034096 (e-PCR)
- UniSTS:93450

AL034097 (e-PCR)
- UniSTS:93451

AL034098 (e-PCR)
- UniSTS:93452

AL034099 (e-PCR)
- UniSTS:93453

D1S370 (e-PCR)
- UniSTS:42287

SHGC-85092 (e-PCR)
- UniSTS:103472

B327YG9 (e-PCR)
- UniSTS:5426

AL034184 (e-PCR)
- UniSTS:94010

GDB:637251 (e-PCR)
- UniSTS:158553

RH123916 (e-PCR)
- UniSTS:136291

D1S1565 (e-PCR)
- UniSTS:26225

AL034056 (e-PCR)
- UniSTS:93818

AL033939 (e-PCR)
- UniSTS:93833

D1S537 (e-PCR)
- UniSTS:54163

D1S2411 (e-PCR)
- UniSTS:64669

SHGC-132782 (e-PCR)
- UniSTS:181946

D1S2643 (e-PCR), detects polymorphism
- UniSTS:58594

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in associative learning	IEA Inferred from Electronic Annotation more info
involved_in axon extension involved in regeneration	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	NAS Non-traceable Author Statement more info	PubMed
involved_in cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in extracellular matrix organization	IEA Inferred from Electronic Annotation more info
involved_in locomotory exploration behavior	IEA Inferred from Electronic Annotation more info
involved_in long-term synaptic potentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of axon extension involved in regeneration	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in neuroblast migration	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
involved_in neuron cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transmission of nerve impulse	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in synapse organization	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info
involved_in telencephalon cell migration	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
located_in cell surface	IEA Inferred from Electronic Annotation more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	ISO Inferred from Sequence Orthology more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in membrane raft	IEA Inferred from Electronic Annotation more info
located_in perineuronal net	ISO Inferred from Sequence Orthology more info
part_of tenascin complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tenascin-R

Names: janusin; restrictin

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.

Genomic

NG_050931.2 RefSeqGene

Range

5000..433401

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001328635.2 → NP_001315564.1 tenascin-R isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice junction compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AL021919, AL023285, Z94055, Z94057

UniProtKB/TrEMBL

A1L306
NM_003285.3 → NP_003276.3 tenascin-R isoform 1 precursor

See identical proteins and their annotated locations for NP_003276.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AV650210, BC129830, DA804585, DB068074, Z67996, Z94057

Consensus CDS

CCDS1318.1

UniProtKB/Swiss-Prot

C9J563, Q15568, Q5R3G0, Q92752

UniProtKB/TrEMBL

A1L306

Related

ENSP00000356646.1, ENST00000367674.7

Conserved Domains (4) summary

cd00063
Location:1042 → 1127

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 ...

cd00087
Location:1133 → 1342

FReD; Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular ...

pfam00041
Location:687 → 766

fn3; Fibronectin type III domain

pfam07974
Location:299 → 323

EGF_2; EGF-like domain