Human Gene TNR (uc009wwu.1) Description and Page Index
  Description: Homo sapiens tenascin R (TNR), mRNA.
RefSeq Summary (NM_003285): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:175,291,935-175,712,752 Size: 420,818 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg19 chr1:175,292,493-175,375,850 Size: 83,358 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:175,291,935-175,712,752)mRNA (may differ from genome)Protein (1358 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TENR_HUMAN
DESCRIPTION: RecName: Full=Tenascin-R; Short=TN-R; AltName: Full=Janusin; AltName: Full=Restrictin; Flags: Precursor;
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).
SUBUNIT: 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).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
TISSUE SPECIFICITY: Brain specific.
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).
PTM: 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.
SIMILARITY: Belongs to the tenascin family.
SIMILARITY: Contains 5 EGF-like domains.
SIMILARITY: Contains 1 fibrinogen C-terminal domain.
SIMILARITY: Contains 9 fibronectin type-III domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TNR
CDC HuGE Published Literature: TNR
Positive Disease Associations: Adiponectin , Blood Pressure , tonometry
Related Studies:
  1. Adiponectin
    James B Meigs et al. BMC medical genetics 2007, Genome-wide association with diabetes-related traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903298]
    Framingham 100K SNP data is a resource for association tests of known and novel genes with diabetes and related traits posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite. Framingham 100K data replicate the TCF7L2 association with diabetes.
  2. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  3. tonometry
    Levy ,et al. 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness, BMC medical genetics 2007 8 Suppl 1 : S3. [PubMed 17903302]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TNR
Diseases sorted by gene-association score: familial osteochondritis dissecans (9)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.70 RPKM in Brain - Amygdala
Total median expression: 172.99 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -197.59555-0.356 Picture PostScript Text
3' UTR -173.10558-0.310 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013032 - EGF-like_CS
IPR013111 - EGF_extracell
IPR002181 - Fibrinogen_a/b/g_C
IPR014716 - Fibrinogen_a/b/g_C_1
IPR014715 - Fibrinogen_a/b/g_C_2
IPR003961 - Fibronectin_type3
IPR013783 - Ig-like_fold

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00147 - Fibrinogen beta and gamma chains, C-terminal globular domain
PF07974 - EGF-like domain

SCOP Domains:
49265 - Fibronectin type III
56496 - Fibrinogen C-terminal domain-like
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q92752
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007155 cell adhesion
GO:0007158 neuron cell-cell adhesion
GO:0007411 axon guidance
GO:0008306 associative learning
GO:0010977 negative regulation of neuron projection development
GO:0022029 telencephalon cell migration
GO:0022408 negative regulation of cell-cell adhesion
GO:0030198 extracellular matrix organization
GO:0030517 negative regulation of axon extension
GO:0035641 locomotory exploration behavior
GO:0048692 negative regulation of axon extension involved in regeneration
GO:0050767 regulation of neurogenesis
GO:0050804 modulation of synaptic transmission
GO:0050805 negative regulation of synaptic transmission
GO:0050808 synapse organization
GO:0050885 neuromuscular process controlling balance
GO:0051968 positive regulation of synaptic transmission, glutamatergic
GO:0051971 positive regulation of transmission of nerve impulse
GO:0060291 long-term synaptic potentiation

Cellular Component:
GO:0005576 extracellular region
GO:0009986 cell surface
GO:0045121 membrane raft
GO:0072534 perineuronal net


-  Descriptions from all associated GenBank mRNAs
  Z67996 - H.sapiens mRNA for tenascin-R (restrictin).
X98085 - H.sapiens mRNA for tenascin-R.
BC129830 - Homo sapiens tenascin R (restrictin, janusin), mRNA (cDNA clone MGC:149328 IMAGE:40114168), complete cds.
AK295823 - Homo sapiens cDNA FLJ60578 complete cds, highly similar to Tenascin-R precursor.
Y13359 - Homo sapiens mRNA for tenascin-R, 5' UTR.
JD095101 - Sequence 76125 from Patent EP1572962.
JD440033 - Sequence 421057 from Patent EP1572962.
JD382399 - Sequence 363423 from Patent EP1572962.
JD386976 - Sequence 368000 from Patent EP1572962.
JD355525 - Sequence 336549 from Patent EP1572962.
JD261535 - Sequence 242559 from Patent EP1572962.
JD165196 - Sequence 146220 from Patent EP1572962.
JD239906 - Sequence 220930 from Patent EP1572962.
JD373642 - Sequence 354666 from Patent EP1572962.
JD239730 - Sequence 220754 from Patent EP1572962.
JD133874 - Sequence 114898 from Patent EP1572962.
JD239086 - Sequence 220110 from Patent EP1572962.
JD526868 - Sequence 507892 from Patent EP1572962.
JD259638 - Sequence 240662 from Patent EP1572962.
JD466726 - Sequence 447750 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction

Reactome (by CSHL, EBI, and GO)

Protein Q92752 (Reactome details) participates in the following event(s):

R-HSA-2424246 Tenascins C, R, (X, N) bind lecticans
R-HSA-2681681 Tenascins C, R, (X, N) bind fibronectin matrix
R-HSA-3000178 ECM proteoglycans
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: C9J563, NM_003285, NP_003276, Q15568, Q5R3G0, Q92752, TENR_HUMAN
UCSC ID: uc009wwu.1
RefSeq Accession: NM_003285
Protein: Q92752 (aka TENR_HUMAN)
CCDS: CCDS1318.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003285.2
exon count: 23CDS single in 3' UTR: no RNA size: 5190
ORF size: 4077CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 8340.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.