Human Gene TNN (ENST00000239462.9_4) from GENCODE V47lift37
  Description: tenascin N (from RefSeq NM_022093.2)
Gencode Transcript: ENST00000239462.9_4
Gencode Gene: ENSG00000120332.17_8
Transcript (Including UTRs)
   Position: hg19 chr1:175,036,969-175,117,211 Size: 80,243 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr1:175,046,555-175,116,207 Size: 69,653 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:175,036,969-175,117,211)mRNA (may differ from genome)Protein (1299 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TENN_HUMAN
DESCRIPTION: RecName: Full=Tenascin-N; Short=TN-N; Flags: Precursor;
FUNCTION: Involved in neurite outgrowth and cell migration in hippocampal explants (By similarity).
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix.
SIMILARITY: Belongs to the tenascin family.
SIMILARITY: Contains 3 EGF-like domains.
SIMILARITY: Contains 1 fibrinogen C-terminal domain.
SIMILARITY: Contains 9 fibronectin type-III domains.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/TNNID44209ch1q25.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: TNN
Diseases sorted by gene-association score: adhesive otitis media (17), chronic purulent otitis media (8)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 2.96 RPKM in Breast - Mammary Tissue
Total median expression: 13.68 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 -50.10138-0.363 Picture PostScript Text
3' UTR -283.301004-0.282 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
IPR002181 - Fibrinogen_a/b/g_C
IPR014716 - Fibrinogen_a/b/g_C_1
IPR014715 - Fibrinogen_a/b/g_C_2
IPR020837 - Fibrinogen_CS
IPR003961 - Fibronectin_type3
IPR013783 - Ig-like_fold

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00147 - Fibrinogen beta and gamma chains, C-terminal globular domain
PF18720 - Tenascin EGF domain

SCOP Domains:
49265 - Fibronectin type III
49319 - Actinoxanthin-like
49785 - Galactose-binding domain-like
159133 - EutN/CcmL-like
56496 - Fibrinogen C-terminal domain-like
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q9UQP3
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005178 integrin binding
GO:0042802 identical protein binding

Biological Process:
GO:0002076 osteoblast development
GO:0007160 cell-matrix adhesion
GO:0007409 axonogenesis
GO:0033689 negative regulation of osteoblast proliferation
GO:0045668 negative regulation of osteoblast differentiation
GO:0070593 dendrite self-avoidance
GO:1905240 negative regulation of canonical Wnt signaling pathway involved in osteoblast differentiation
GO:2001223 negative regulation of neuron migration

Cellular Component:
GO:0005575 cellular_component
GO:0005576 extracellular region
GO:0009986 cell surface
GO:0043005 neuron projection
GO:0043025 neuronal cell body
GO:0097442 CA3 pyramidal cell dendrite
GO:1990026 hippocampal mossy fiber expansion


-  Descriptions from all associated GenBank mRNAs
  AK127044 - Homo sapiens cDNA FLJ45101 fis, clone BRAWH3032298, highly similar to Tenascin-N precursor.
BC136619 - Homo sapiens tenascin N, mRNA (cDNA clone MGC:168232 IMAGE:9020609), complete cds.
BC144305 - Homo sapiens cDNA clone MGC:177842 IMAGE:9052825, complete cds.
AL049689 - Novel human mRNA from chromosome 1, similar to Tenascin-R.
AK127654 - Homo sapiens cDNA FLJ45752 fis, clone LYMPB2002458, weakly similar to Tenascin precursor.
JD181031 - Sequence 162055 from Patent EP1572962.
JD094323 - Sequence 75347 from Patent EP1572962.
JD304854 - Sequence 285878 from Patent EP1572962.
JD047353 - Sequence 28377 from Patent EP1572962.
JD355259 - Sequence 336283 from Patent EP1572962.
JD349770 - Sequence 330794 from Patent EP1572962.
JD178589 - Sequence 159613 from Patent EP1572962.
JD279422 - Sequence 260446 from Patent EP1572962.
JD488708 - Sequence 469732 from Patent EP1572962.
JD290584 - Sequence 271608 from Patent EP1572962.
JD226120 - Sequence 207144 from Patent EP1572962.
JD359668 - Sequence 340692 from Patent EP1572962.
JD251362 - Sequence 232386 from Patent EP1572962.
JD261541 - Sequence 242565 from Patent EP1572962.
JD095607 - Sequence 76631 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UQP3 (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: A0A0A6YY94, B9EGP3, ENST00000239462.1, ENST00000239462.2, ENST00000239462.3, ENST00000239462.4, ENST00000239462.5, ENST00000239462.6, ENST00000239462.7, ENST00000239462.8, NM_022093, Q5R360, Q9UQP3, TENN_HUMAN, TNN , TNW , uc317efv.1, uc317efv.2
UCSC ID: ENST00000239462.9_4
RefSeq Accession: NM_022093.2
Protein: Q9UQP3 (aka TENN_HUMAN)

-  Gene Model Information
  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.