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Aliases for TNR Gene

Aliases for TNR Gene

  • Tenascin R 2 3
  • Restrictin 2 3 4
  • Janusin 2 3 4
  • TN-R 3 4
  • Tenascin-R 3

External Ids for TNR Gene

Summaries for TNR Gene

Entrez Gene Summary for TNR Gene

  • 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]

GeneCards Summary for TNR Gene

TNR (Tenascin R) is a Protein Coding gene. Diseases associated with TNR include osteochondritis dissecans and familial osteochondritis dissecans. Among its related pathways are PI3K-Akt signaling pathway and MicroRNAs in cancer. An important paralog of this gene is TNC.

UniProtKB/Swiss-Prot for TNR Gene

  • Neural extracellular matrix (ECM) protein involved in interactions with different cells and matrix components. These interactions can influence cellular behavior by either evoking a stable adhesion and differentiation, or repulsion and inhibition of neurite growth. Binding to cell surface gangliosides inhibits RGD-dependent integrin-mediated cell adhesion and results in an inhibition of PTK2/FAK1 (FAK) phosphorylation and cell detachment. Binding to membrane surface sulfatides results in a oligodendrocyte adhesion and differentiation. Interaction with CNTN1 induces a repulsion of neurons and an inhibition of neurite outgrowth. Interacts with SCN2B may play a crucial role in clustering and regulation of activity of sodium channels at nodes of Ranvier. TNR-linked chondroitin sulfate glycosaminoglycans are involved in the interaction with FN1 and mediate inhibition of cell adhesion and neurite outgrowth. The highly regulated addition of sulfated carbohydrate structure may modulate the adhesive properties of TNR over the course of development and during synapse maintenance (By similarity).

Gene Wiki entry for TNR Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TNR Gene

Genomics for TNR Gene

Genomic Location for TNR Gene

Start:
175,315,194 bp from pter
End:
175,743,770 bp from pter
Size:
428,577 bases
Orientation:
Minus strand

Genomic View for TNR Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for TNR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TNR Gene

Regulatory Elements for TNR Gene

Proteins for TNR Gene

  • Protein details for TNR Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92752-TENR_HUMAN
    Recommended name:
    Tenascin-R
    Protein Accession:
    Q92752
    Secondary Accessions:
    • C9J563
    • Q15568
    • Q5R3G0

    Protein attributes for TNR Gene

    Size:
    1358 amino acids
    Molecular mass:
    149562 Da
    Quaternary structure:
    • Forms oligomers. Interacts with CNTN1, TNC, and FN1. Interacts with BCAN and ACAN in a calcium-dependent manner. Interacts with SCN2B, PTPRZ1, and CSPG3 (By similarity).

    Alternative splice isoforms for TNR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TNR Gene

Proteomics data for TNR Gene at MOPED

Post-translational modifications for TNR Gene

  • Contains N-linked oligosaccharides, O-linked sialylated structures and O-linked chondroitin sulfate glycosaminoglycans. Contains N-linked oligosaccharides with a sulfated carbohydrate structure (By similarity). O-glycosylated on Thr-36 or Thr-37 with a core 1 or possibly core 8 glycan.
  • Modification sites at PhosphoSitePlus
  • Glycosylation at Thr36, Thr37, Asn55, Asn180, Asn198, Asn278, Asn392, Asn470, Asn581, Asn791, Asn874, Asn1036, Asn1046, and Asn1261

Other Protein References for TNR Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for TNR Gene

Domains for TNR Gene

Gene Families for TNR Gene

HGNC:
  • FIBC :Fibrinogen C domain containing
  • FN3 :Fibronectin type III domain containing

UniProtKB/Swiss-Prot:

TENR_HUMAN
Domain:
  • The EGF-like domains mediate interaction with CNTN1. The fibronectin type-III domains 3-5 mediate interaction with BCAN. The fibronectin type-III domains 1-2 and 7-9 mediate interaction with SCN2B (By similarity).:
    • Q92752
  • Contains 5 EGF-like domains.:
    • Q92752
  • Contains 1 fibrinogen C-terminal domain.:
    • Q92752
  • Contains 9 fibronectin type-III domains.:
    • Q92752
Family:
  • Belongs to the tenascin family.:
    • Q92752
genes like me logo Genes that share domains with TNR: view

Function for TNR Gene

Molecular function for TNR Gene

GENATLAS Biochemistry: tenascin-R,extracellular neural recognition molecule,expressed in glia and some neuronal subtypes,including horizontal cells in retina,putative ortholog of mouse loop-tail,interacting with fibronectin-dependent cell attachment and interaction,inhibitor of CD3-mediated T cell interaction
UniProtKB/Swiss-Prot Function: Neural extracellular matrix (ECM) protein involved in interactions with different cells and matrix components. These interactions can influence cellular behavior by either evoking a stable adhesion and differentiation, or repulsion and inhibition of neurite growth. Binding to cell surface gangliosides inhibits RGD-dependent integrin-mediated cell adhesion and results in an inhibition of PTK2/FAK1 (FAK) phosphorylation and cell detachment. Binding to membrane surface sulfatides results in a oligodendrocyte adhesion and differentiation. Interaction with CNTN1 induces a repulsion of neurons and an inhibition of neurite outgrowth. Interacts with SCN2B may play a crucial role in clustering and regulation of activity of sodium channels at nodes of Ranvier. TNR-linked chondroitin sulfate glycosaminoglycans are involved in the interaction with FN1 and mediate inhibition of cell adhesion and neurite outgrowth. The highly regulated addition of sulfated carbohydrate structure may modulate the adhesive properties of TNR over the course of development and during synapse maintenance (By similarity).

Gene Ontology (GO) - Molecular Function for TNR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with TNR: view

Phenotypes for TNR Gene

genes like me logo Genes that share phenotypes with TNR: view

Animal Models for TNR Gene

MGI Knock Outs for TNR:

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for TNR Gene

Localization for TNR Gene

Subcellular locations from UniProtKB/Swiss-Prot for TNR Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TNR Gene COMPARTMENTS Subcellular localization image for TNR gene
Compartment Confidence
extracellular 5
nucleus 4
plasma membrane 2
cytosol 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for TNR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA --
genes like me logo Genes that share ontologies with TNR: view

Pathways for TNR Gene

genes like me logo Genes that share pathways with TNR: view

Pathways by source for TNR Gene

1 GeneGo (Thomson Reuters Life Sciences Research) pathway for TNR Gene
1 BioSystems pathway for TNR Gene

Gene Ontology (GO) - Biological Process for TNR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion NAS 8940128
GO:0007158 neuron cell-cell adhesion IEA --
GO:0007411 axon guidance NAS 8940128
GO:0008306 associative learning IEA --
GO:0010977 negative regulation of neuron projection development --
genes like me logo Genes that share ontologies with TNR: view

Compounds for TNR Gene

(2) HMDB Compounds for TNR Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
Sodium
  • Sodium
7440-23-5

(6) Novoseek inferred chemical compound relationships for TNR Gene

Compound -log(P) Hits PubMed IDs
neurocan 88.3 7
chondroitin sulfate 38.9 1
calcium 0 2
tyrosine 0 1
testosterone 0 3
genes like me logo Genes that share compounds with TNR: view

Transcripts for TNR Gene

Unigene Clusters for TNR Gene

Tenascin R:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for TNR Gene

No ASD Table

Relevant External Links for TNR Gene

GeneLoc Exon Structure for
TNR
ECgene alternative splicing isoforms for
TNR

Expression for TNR Gene

mRNA expression in normal human tissues for TNR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TNR Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (6.7), Brain - Amygdala (6.3), Brain - Hippocampus (5.3), Brain - Frontal Cortex (BA9) (5.3), Brain - Substantia nigra (4.6), and Brain - Hypothalamus (4.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for TNR Gene

SOURCE GeneReport for Unigene cluster for TNR Gene Hs.659864

mRNA Expression by UniProt/SwissProt for TNR Gene

Q92752-TENR_HUMAN
Tissue specificity: Brain specific.
genes like me logo Genes that share expressions with TNR: view

Orthologs for TNR Gene

This gene was present in the common ancestor of animals.

Orthologs for TNR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TNR 36
  • 99.46 (n)
  • 99.63 (a)
TNR 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TNR 36
  • 90.38 (n)
  • 93.45 (a)
TNR 37
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TNR 36
  • 89.81 (n)
  • 93.15 (a)
TNR 37
  • 73 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Tnr 36
  • 88.27 (n)
  • 93.23 (a)
Tnr 16
Tnr 37
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TNR 37
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 91 (a)
OneToMany
-- 37
  • 84 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Tnr 36
  • 87.48 (n)
  • 92.99 (a)
chicken
(Gallus gallus)
Aves TNR 36
  • 75.66 (n)
  • 75.46 (a)
TNR 37
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TNR 37
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tnr 36
  • 64.68 (n)
  • 63.69 (a)
zebrafish
(Danio rerio)
Actinopterygii -- 36
tnr 36
  • 63.84 (n)
  • 61.97 (a)
tnr 37
  • 62 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG1889 38
  • 41 (a)
CG30281 38
  • 38 (a)
CG1791 38
  • 40 (a)
sca 38
  • 36 (a)
CG30280 38
  • 38 (a)
CG9500 38
  • 34 (a)
CG5550 38
  • 42 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 45 (a)
OneToMany
Species with no ortholog for TNR:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TNR Gene

ENSEMBL:
Gene Tree for TNR (if available)
TreeFam:
Gene Tree for TNR (if available)

Paralogs for TNR Gene

Paralogs for TNR Gene

Selected SIMAP similar genes for TNR Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with TNR: view

Variants for TNR Gene

Sequence variations from dbSNP and Humsavar for TNR Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs484813 -- 175,674,123(+) AGGTG(C/T)CCATT intron-variant
rs487574 -- 175,667,834(+) ATCTG(C/G)TTGCC intron-variant
rs512371 -- 175,674,795(+) ACAGA(C/G)AGGAG intron-variant
rs516500 -- 175,733,315(+) AATAG(C/T)GAAAG intron-variant
rs519395 -- 175,696,904(+) aatat(A/C)ataat intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TNR Gene

Variant ID Type Subtype PubMed ID
nsv831948 CNV Loss 17160897
esv2719629 CNV Deletion 23290073
esv2719640 CNV Deletion 23290073
esv2719651 CNV Deletion 23290073
esv1005191 CNV Deletion 20482838
esv1283541 CNV Deletion 17803354
nsv159978 CNV Loss 16902084
nsv524232 CNV Loss 19592680
esv2670531 CNV Deletion 23128226
esv21661 CNV Loss 19812545
nsv517137 CNV Loss 19592680
nsv527256 CNV Gain 19592680
nsv466072 CNV Gain 19166990
nsv528975 CNV Gain 19592680
nsv3633 CNV Insertion 18451855
esv33328 CNV Gain 17666407
nsv508659 CNV Loss 20534489
nsv3644 CNV Insertion 18451855
esv2719662 CNV Deletion 23290073
esv2719673 CNV Deletion 23290073
nsv831959 CNV Gain 17160897
nsv872560 CNV Gain 21882294

Relevant External Links for TNR Gene

HapMap Linkage Disequilibrium report
TNR
Human Gene Mutation Database (HGMD)
TNR

Disorders for TNR Gene

(1) University of Copenhagen DISEASES for TNR Gene

(2) Novoseek inferred disease relationships for TNR Gene

Disease -log(P) Hits PubMed IDs
tumors 0 1
multiple sclerosis 0 2

Relevant External Links for TNR

Genetic Association Database (GAD)
TNR
Human Genome Epidemiology (HuGE) Navigator
TNR
genes like me logo Genes that share disorders with TNR: view

No data available for UniProtKB/Swiss-Prot for TNR Gene

Publications for TNR Gene

  1. Human tenascin-R: complete primary structure, pre-mRNA alternative splicing and gene localization on chromosome 1q23-q24. (PMID: 8626505) Carnemolla B. … Zardi L. (J. Biol. Chem. 1996) 2 3 4 23
  2. The human tenascin-R gene. (PMID: 8940128) Leprini A. … Zardi L. (J. Biol. Chem. 1996) 2 3 23
  3. Parallel genotyping of 10,204 single nucleotide polymorphisms to screen for susceptible genes for IgA nephropathy. (PMID: 19890582) Woo K.T. … Chan C.M. (Ann. Acad. Med. Singap. 2009) 3 23 49
  4. Association of the NPAS3 gene and five other loci with response to the antipsychotic iloperidone identified in a whole genome association study. (PMID: 18521090) Lavedan C. … Polymeropoulos M.H. (Mol. Psychiatry 2009) 3 23 49
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4

Products for TNR Gene

Sources for TNR Gene

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