TNN Gene (Protein Coding)

Tenascin N

GC01P175067
GIFtS:
36
See more...

Aliases for TNN Gene

Aliases for TNN Gene

  • Tenascin N 2 3 5
  • Tenascin-W 2 3 4
  • TNW 2 3 4
  • Tenascin-N 3 4
  • TN-W 3 4
  • TN-N 3 4
  • Tenascin W 2
  • TNN 5

External Ids for TNN Gene

Previous GeneCards Identifiers for TNN Gene

  • GC01P171627
  • GC01P172286
  • GC01P172276
  • GC01P171768
  • GC01P173303
  • GC01P175036
  • GC01P146264

Summaries for TNN Gene

GeneCards Summary for TNN Gene

TNN (Tenascin N) is a Protein Coding gene. Diseases associated with TNN include Lipodystrophy, Congenital Generalized, Type 1. Among its related pathways are Degradation of the extracellular matrix and ECM proteoglycans. Gene Ontology (GO) annotations related to this gene include identical protein binding and integrin binding. An important paralog of this gene is TNR.

UniProtKB/Swiss-Prot Summary for TNN Gene

  • Extracellular matrix protein that seems to be a ligand for ITGA8:ITGB1, ITGAV:ITGB1 and ITGA4:ITGB1 (By similarity) (PubMed:17909022). Involved in neurite outgrowth and cell migration in hippocampal explants (By similarity). During endochondral bone formation, inhibits proliferation and differentiation of proteoblasts mediated by canonical WNT signaling (By similarity). In tumors, stimulates angiogenesis by elongation, migration and sprouting of endothelial cells (PubMed:19884327). Expressed in most mammary tumors, may facilitate tumorigenesis by supporting the migratory behavior of breast cancer cells (PubMed:17909022).

Additional gene information for TNN Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TNN Gene

Genomics for TNN Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TNN Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J175067 Enhancer 0.3 Ensembl CraniofacialAtlas 250.7 -0.2 -200 1.1 TNN HSALNG0008584 MRPS14
GH01J175071 Enhancer 0.9 ENCODE CraniofacialAtlas 22.9 +4.8 4760 2.7 ZNF600 ATF2 CEBPA POLR2A CEBPB ZNF341 YY1 MAX MYC INSM2 TNN MN309018 KIAA0040
GH01J175090 Enhancer 0.5 Ensembl 34.6 +23.2 23168 0.8 ZNF580 REST ZNF664 ZBTB21 ZXDB ZNF680 ZNF558 ZNF501 ZNF121 TNN MN309018 KIAA0040
GH01J175088 Enhancer 0.5 Ensembl 33.8 +21.3 21268 1 ATF2 ZNF316 JUND GATA2 JUN MAFK CHD2 ATF7 TNN MN309018 KIAA0040
GH01J174963 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 4.5 -100.1 -100085 9.2 BCLAF1 SP1 IKZF1 MYC NCOR1 POLR2A NFIC NONO BCL11A CEBPB RABGAP1L RNU6-307P CACYBP TNN KIAA0040 RABGAP1L-AS1 RF00026-084 GPR52
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TNN on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TNN

Top Transcription factor binding sites by QIAGEN in the TNN gene promoter:
  • AML1a
  • CREB
  • deltaCREB
  • E4BP4
  • FOXJ2
  • FOXJ2 (long isoform)
  • Pbx1a
  • RP58

Genomic Locations for TNN Gene

Latest Assembly
chr1:175,067,833-175,148,075
(GRCh38/hg38)
Size:
80,243 bases
Orientation:
Plus strand

Previous Assembly
chr1:175,036,969-175,117,211
(GRCh37/hg19 by Entrez Gene)
Size:
80,243 bases
Orientation:
Plus strand

chr1:175,036,994-175,117,202
(GRCh37/hg19 by Ensembl)
Size:
80,209 bases
Orientation:
Plus strand

Genomic View for TNN Gene

Genes around TNN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TNN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TNN Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TNN Gene

Proteins for TNN Gene

Products:

  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

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

    Protein Symbol:
    Q9UQP3-TENN_HUMAN
    Recommended name:
    Tenascin-N
    Protein Accession:
    Q9UQP3
    Secondary Accessions:
    • A0A0A6YY94
    • B9EGP3
    • Q5R360

    Protein attributes for TNN Gene

    Size:
    1299 amino acids
    Molecular mass:
    144034 Da
    Quaternary structure:
    • Homohexamer.

neXtProt entry for TNN Gene

Protein Expression for TNN Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TNN Gene

  • Glycosylation at Asn1052, Asn1149, and Asn1168
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for TNN Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TNN Gene

Domains & Families for TNN Gene

Gene Families for TNN Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for TNN Gene

InterPro:
Blocks:
  • Fibrinogen, beta/gamma chain, C-terminal globular

Suggested Antigen Peptide Sequences for TNN Gene

GenScript: Design optimal peptide antigens:
  • Tenascin-N (TENN_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UQP3

UniProtKB/Swiss-Prot:

TENN_HUMAN :
  • Belongs to the tenascin family.
Family:
  • Belongs to the tenascin family.
genes like me logo Genes that share domains with TNN: view

Function for TNN Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for TNN Gene

UniProtKB/Swiss-Prot Function:
Extracellular matrix protein that seems to be a ligand for ITGA8:ITGB1, ITGAV:ITGB1 and ITGA4:ITGB1 (By similarity) (PubMed:17909022). Involved in neurite outgrowth and cell migration in hippocampal explants (By similarity). During endochondral bone formation, inhibits proliferation and differentiation of proteoblasts mediated by canonical WNT signaling (By similarity). In tumors, stimulates angiogenesis by elongation, migration and sprouting of endothelial cells (PubMed:19884327). Expressed in most mammary tumors, may facilitate tumorigenesis by supporting the migratory behavior of breast cancer cells (PubMed:17909022).

Phenotypes From GWAS Catalog for TNN Gene

Gene Ontology (GO) - Molecular Function for TNN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005178 integrin binding IEA,IBA 21873635
GO:0005515 protein binding IEA --
GO:0042802 identical protein binding IEA --
genes like me logo Genes that share ontologies with TNN: view
genes like me logo Genes that share phenotypes with TNN: view

Animal Models for research

  • Taconic Biosciences Mouse Models for TNN

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TNN

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for TNN Gene

Localization for TNN Gene

Subcellular locations from UniProtKB/Swiss-Prot for TNN Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TNN gene
Compartment Confidence
extracellular 4
plasma membrane 2
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for TNN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA 21873635
GO:0009986 cell surface IEA --
GO:0031012 extracellular matrix IEA --
genes like me logo Genes that share ontologies with TNN: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TNN Gene

Pathways & Interactions for TNN Gene

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

Pathways by source for TNN Gene

1 BioSystems pathway for TNN Gene
2 Reactome pathways for TNN Gene

Gene Ontology (GO) - Biological Process for TNN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002076 osteoblast development IEA,ISS --
GO:0007160 cell-matrix adhesion IEA,IBA 21873635
GO:0007409 axonogenesis IEA --
GO:0033689 negative regulation of osteoblast proliferation IEA,ISS --
GO:0045668 negative regulation of osteoblast differentiation IEA,ISS --
genes like me logo Genes that share ontologies with TNN: view

No data available for SIGNOR curated interactions for TNN Gene

Drugs & Compounds for TNN Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for TNN Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for TNN Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TNN

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

No ASD Table

Relevant External Links for TNN Gene

GeneLoc Exon Structure for
TNN

Expression for TNN Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TNN Gene

mRNA expression in normal human tissues for TNN Gene
mRNA expression by GTEx for TNN GenemRNA expression by BioGPS for TNN Gene

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

This gene is overexpressed in Breast - Mammary Tissue (x9.6), Skin - Not Sun Exposed (Suprapubic) (x9.2), Adipose - Subcutaneous (x6.5), and Adipose - Visceral (Omentum) (x4.5).

Protein differential expression in normal tissues from HIPED for TNN Gene

This gene is overexpressed in Plasma (44.7), Testis (9.5), and Lung (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TNN Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TNN

SOURCE GeneReport for Unigene cluster for TNN Gene:

Hs.156369

mRNA Expression by UniProt/SwissProt for TNN Gene:

Q9UQP3-TENN_HUMAN
Tissue specificity: Not detected in normal adult mammary tissues or brain but expressed in most breast tumors and brain tumors, such as glioblastomas, astrocytomas and oligodendrogliomas, tested (PubMed:17909022, PubMed:19884327). In brain tumors, detected around the endothelial cell layer of the clood vessels (PubMed:19884327).

Evidence on tissue expression from TISSUES for TNN Gene

  • Bone marrow(4.1)
genes like me logo Genes that share expression patterns with TNN: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for TNN Gene

Orthologs for TNN Gene

This gene was present in the common ancestor of chordates.

Orthologs for TNN Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TNN 29 30
  • 98.87 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TNN 29 30
  • 87.76 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TNN 29 30
  • 87.51 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Tnn 29
  • 79.01 (n)
Mouse
(Mus musculus)
 Mammalia Tnn 29 16 30
  • 78.85 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TNN 30
  • 70 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia TNN 30
  • 68 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves TNN 29 30
  • 64.25 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TNN 30
  • 57 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia tnn 29
  • 53.04 (n)
Zebrafish
(Danio rerio)
 Actinopterygii tnw 30
  • 48 (a)
 OneToOne
tenw 29
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 30
  • 42 (a)
 OneToMany
Species where no ortholog for TNN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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 Vase (Ciona intestinalis)
  • 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 TNN Gene

ENSEMBL:
Gene Tree for TNN (if available)
TreeFam:
Gene Tree for TNN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TNN: view image
Alliance of Genome Resources:
Additional Orthologs for TNN

Paralogs for TNN Gene

Paralogs for TNN Gene

(8) SIMAP similar genes for TNN Gene using alignment to 1 proteins:

  • TENN_HUMAN
genes like me logo Genes that share paralogs with TNN: view

Variants for TNN Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TNN Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs201592719 Likely Benign: not provided 175,146,926(+) G/T
NM_022093.2(TNN):c.3760-5G>T 		INTRON
rs6664276 Benign: not provided 175,085,490(+) G/Tp.Arg440Ser
NM_022093.2(TNN):c.1320G>T (p.Arg440Ser) 		MISSENSE
rs10158841 -- p.Asp1135Glu
rs10798333 -- p.Thr941Met
rs16847812 -- p.Asp289Asn

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TNN Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv62e214 CNV gain 21293372
dgv81e199 CNV deletion 23128226
esv2159196 CNV deletion 18987734
esv2566793 CNV deletion 19546169
esv2719596 CNV deletion 23290073
esv2719607 CNV deletion 23290073
esv2719618 CNV deletion 23290073
esv28085 CNV gain 19812545
esv3587975 CNV loss 21293372
nsv1011472 CNV loss 25217958
nsv1113194 CNV deletion 24896259
nsv160653 CNV deletion 16902084
nsv3609 CNV deletion 18451855
nsv3620 CNV insertion 18451855
nsv498693 CNV loss 21111241
nsv508648 CNV deletion 20534489
nsv522101 CNV loss 19592680
nsv821166 CNV deletion 20802225
nsv825487 CNV gain 20364138

Variation tolerance for TNN Gene

Residual Variation Intolerance Score: 92.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.53; 97.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TNN Gene

Human Gene Mutation Database (HGMD)
TNN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TNN
Leiden Open Variation Database (LOVD)
TNN

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TNN Gene

Disorders for TNN Gene

MalaCards: The human disease database

(1) MalaCards diseases for TNN Gene - From: COP

Disorder Aliases PubMed IDs
lipodystrophy, congenital generalized, type 1
  • cgl1
- elite association - COSMIC cancer census association via MalaCards
Search TNN in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TNN

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TNN: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TNN Gene

Publications for TNN Gene

  1. Tenascin-W is a novel marker for activated tumor stroma in low-grade human breast cancer and influences cell behavior. (PMID: 17909022) Degen M … Chiquet-Ehrismann R (Cancer research 2007) 3 4
  2. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  3. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PMID: 16335952) Liu T … Smith RD (Journal of proteome research 2005) 3 4
  4. Tenascin-N: characterization of a novel member of the tenascin family that mediates neurite repulsion from hippocampal explants. (PMID: 12812753) Neidhardt J … Schachner M (Molecular and cellular neurosciences 2003) 3 22
  5. Agrin has a pathological role in the progression of oral cancer. (PMID: 29872149) Rivera C … Paes Leme AF (British journal of cancer 2018) 3

ExternalLinks

View latest publications for TNN gene in Mastermind

Products for TNN Gene

Sources for TNN Gene