Tnr tenascin R [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tnrprovided by RGD
Official Full Name: tenascin Rprovided by RGD
Primary source: RGD:3886
See related: Ensembl:ENSRNOG00000002468 AllianceGenome:RGD:3886
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: J1NRM
Summary: Enables integrin binding activity. Involved in negative regulation of cell adhesion. Located in extracellular matrix. Is active in hippocampal mossy fiber to CA3 synapse and perisynaptic extracellular matrix. Orthologous to human TNR (tenascin R). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward (RPKM 158.8) See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 13q22

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (74285141..74706174)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (71751714..72172731)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (77602249..77678385)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Compared tenascin C and tenascin R in oligodendrocyte differentiation. Tnc and Tnr play antagonistic roles for differentiation and comparably inhibit morphologic maturation. conclude that independent molecular pathways regulate these processes.
Title: Tenascin C and tenascin R similarly prevent the formation of myelin membranes in a RhoA-dependent manner, but antagonistically regulate the expression of myelin basic protein via a separate pathway.
Beta 1 integrin-mediated effects of tenascin-R domains EGFL and FN6-8 on neural stem/progenitor cell proliferation and differentiation in vitro
Title: Beta 1 integrin-mediated effects of tenascin-R domains EGFL and FN6-8 on neural stem/progenitor cell proliferation and differentiation in vitro.
Perineuronal nets in the spinal cord are discovered as a site for synthesis of tenascin-R around many neuronal cell bodies and dendrites late in development.
Title: Distribution and synthesis of extracellular matrix proteoglycans, hyaluronan, link proteins and tenascin-R in the rat spinal cord.
TN-R plays a role in neuroprotection through distinct domains coordinating to modulate microglia function
Title: Tenascin-R plays a role in neuroprotection via its distinct domains that coordinate to modulate the microglia function.
Tenascin-R associates preferentially with the parvalbumin-positive subpopulation of interneurons within the cerebral cortex but is synthesized by another subpopulation of nerve cells in the adult rat cerebral cortex.
Title: Tenascin-R associates extracellularly with parvalbumin immunoreactive neurones but is synthesised by another neuronal population in the adult rat cerebral cortex.
An up-regulation of granular tenascin-R is found within pyramidal cells following epileptic seizure which parallels the degree of pyramidal cell loss, mossy fiber sprouting and astrogliosis.
Title: Up-regulation of the extracellular matrix glycoprotein tenascin-R during axonal reorganization and astrogliosis in the adult rat hippocampus.
spatial and temporal regulation of glycosylation in the cerebellum
Title: Spatial and temporal regulation of tenascin-R glycosylation in the cerebellum.
Tenascin R is expressed and glycosylated in neurons
Title: Neuronal-specific synthesis and glycosylation of tenascin-R.

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables integrin binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in associative learning	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within associative learning	ISO Inferred from Sequence Orthology more info
acts_upstream_of axon extension	ISO Inferred from Sequence Orthology more info
involved_in axon extension involved in regeneration	IEA Inferred from Electronic Annotation more info
acts_upstream_of axon extension involved in regeneration	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within extracellular matrix organization	ISO Inferred from Sequence Orthology more info
involved_in locomotory exploration behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within locomotory exploration behavior	ISO Inferred from Sequence Orthology more info
involved_in long-term synaptic potentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within long-term synaptic potentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within modulation of chemical synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in modulation of chemical synaptic transmission	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of axon extension	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of axon extension involved in regeneration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of axon extension involved in regeneration	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell-cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of cell-cell adhesion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron projection development	ISO Inferred from Sequence Orthology 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
acts_upstream_of_or_within negative regulation of synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
involved_in neuroblast migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuroblast migration	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuromuscular process controlling balance	ISO Inferred from Sequence Orthology more info
involved_in neuron cell-cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuron cell-cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transmission of nerve impulse	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transmission of nerve impulse	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation 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
acts_upstream_of_or_within synapse organization	ISO Inferred from Sequence Orthology more info
involved_in synaptic transmission, glutamatergic	IEA Inferred from Electronic Annotation more info
acts_upstream_of synaptic transmission, glutamatergic	ISO Inferred from Sequence Orthology more info
involved_in telencephalon cell migration	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within telencephalon cell migration	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Schaffer collateral - CA1 synapse	IEA Inferred from Electronic Annotation more info
is_active_in Schaffer collateral - CA1 synapse	ISO Inferred from Sequence Orthology more info
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISO Inferred from Sequence Orthology 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 matrix	ISO Inferred from Sequence Orthology more info
is_active_in extracellular matrix of synaptic cleft	IDA Inferred from Direct Assay more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in hippocampal mossy fiber to CA3 synapse	IDA Inferred from Direct Assay more info	PubMed
located_in membrane raft	IEA Inferred from Electronic Annotation more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in perineuronal net	IEA Inferred from Electronic Annotation more info
located_in perineuronal net	ISO Inferred from Sequence Orthology more info
is_active_in perisynaptic extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
part_of tenascin complex	IEA Inferred from Electronic Annotation more info
part_of tenascin complex	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

Preferred Names: tenascin-R

Names: TN-R; Tenascin-R (Restrictin, janusin, J1-160/180); janusin; neural recognition molecule J1-160/180; restrictin; tenascin R (restrictin, janusin)

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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)

NM_013045.2 → NP_037177.2 tenascin-R precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/Swiss-Prot

Q05546

UniProtKB/TrEMBL

A0A096MJE6, A6ID49, F1LQ63

Related

ENSRNOP00000003407.6, ENSRNOT00000003407.6

Conserved Domains (5) 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:1134 → 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 ...

pfam18720
Location:203 → 231

EGF_Tenascin; Tenascin EGF domain

pfam00041
Location:865 → 944

fn3; Fibronectin type III domain

NF033759
Location:190 → 328

exchanger_TraA; outer membrane exchange protein TraA

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_086031.1 Reference GRCr8

Range

74285141..74706174

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090392.1 → XP_038946320.1 tenascin-R isoform X1

UniProtKB/Swiss-Prot

Q05546

UniProtKB/TrEMBL

A0A096MJE6, A6ID49, F1LQ63

Conserved Domains (5) 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:1134 → 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 ...

pfam18720
Location:203 → 231

EGF_Tenascin; Tenascin EGF domain

pfam00041
Location:865 → 944

fn3; Fibronectin type III domain

NF033759
Location:190 → 328

exchanger_TraA; outer membrane exchange protein TraA
XM_063272049.1 → XP_063128119.1 tenascin-R isoform X3
XM_039090391.1 → XP_038946319.1 tenascin-R isoform X1

UniProtKB/Swiss-Prot

Q05546

UniProtKB/TrEMBL

A0A096MJE6, A6ID49, F1LQ63

Conserved Domains (5) 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:1134 → 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 ...

pfam18720
Location:203 → 231

EGF_Tenascin; Tenascin EGF domain

pfam00041
Location:865 → 944

fn3; Fibronectin type III domain

NF033759
Location:190 → 328

exchanger_TraA; outer membrane exchange protein TraA
XM_063272048.1 → XP_063128118.1 tenascin-R isoform X2
XM_039090395.1 → XP_038946323.1 tenascin-R isoform X3

UniProtKB/Swiss-Prot

Q05546

Conserved Domains (5) summary

cd00063
Location:954 → 1039

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:1046 → 1254

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 ...

pfam18720
Location:203 → 231

EGF_Tenascin; Tenascin EGF domain

pfam00041
Location:777 → 856

fn3; Fibronectin type III domain

NF033759
Location:190 → 330

exchanger_TraA; outer membrane exchange protein TraA
XM_063272050.1 → XP_063128120.1 tenascin-R isoform X4
XM_063272051.1 → XP_063128121.1 tenascin-R isoform X5
XM_063272052.1 → XP_063128122.1 tenascin-R isoform X6
XM_063272053.1 → XP_063128123.1 tenascin-R isoform X7