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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TNXA Gene

pseudogene   GIFtS: 36
GCID: GC06M031979

tenascin XA (pseudogene)

(Previous name: tenascin XA )
(Previous symbol: TNX)
 Explore 32 diseases affiliated with
TNXA via our new
 Human Malady Compendium 
Biological research products
for TNXA
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Tenascin XA (Pseudogene)1 2     TNX1 2
XA1 2 3     Tenascin XA1
D6S103E1 2     TN-XA3
HXBL1 2     

External Ids:    HGNC: 119751   Entrez Gene: 71462   Ensembl: ENSG000002482907   UniProtKB: Q164733   

Export aliases for TNXA gene to outside databases

Previous GC identifers: GC06U990124 GC06M032084 GC06M031977


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

  --

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_007592.15  NT_167245.1  NT_167247.1  NT_167249.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TNXA gene promoter:
         CREB   Sp1   SREBP-1a   p53   AP-1   SREBP-1c   SREBP-1b   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for TNXA

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TNXA


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.3

TNXA Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TNXA gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M031979:  view genomic region     (about GC identifiers)

Start:
31,976,197 bp from pter      End:
31,980,800 bp from pter
Size:
4,604 bases      Orientation:
minus strand

3 alternative locations:
Chr6-,ALT_REF_LOCI_5 31,967,464-31,972,067      Chr6-,ALT_REF_LOCI_3 31,958,577-31,974,024      Chr6-,ALT_REF_LOCI_7 31,898,372-31,902,975     

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TENXA_HUMAN, Q16473 (See protein sequence)
Recommended Name: Putative tenascin-XA  
Size: 311 amino acids; 33740 Da
Miscellaneous: TNX genes are located in the class III HLA region within a complex locus, named RCCX module, containing
genes for RP1/STK19, C4B, CYP21B/CYP21A2 and TNXB. Most chromosomes bear 2 modules, but monomodular and trimodular
haplotypes are common in most populations. The bimodular haplotype results from the duplication of the RCCX module,
leading to a duplicate containing RP2/RP1 pseudogene, C4A, CYP21A/CYP21A1P and TNXA. TNXA is a duplicated section of
TNXB and probably consists in a truncated pseudogene: it contains a 120 bp deletion causing a frameshift and a
premature stop codon that probably render the gene non-functional. In some pathologies, an unequal crossover between
monomodular and bimodular RCCX results in a chromosome with a TNXB-TNXA hybrid gene, arising from a fusion between the
TNXB gene of a monomodular RCCX and the TNXA gene of a bimodular RCCX. The TNXB-TNXA hybrid may correspond to
TNXB-Short gene and may produce a functional protein
Caution: Could be the product of a pseudogene. TNXA is transcriptionally active in adrenal cortex but no protein
product has been observed

Explore the universe of human proteins at neXtProt for TNXA: NX_Q16473

TNXA Protein expression data from MOPED and PaxDb:    About this image 

Estimated protein expression log10 (pmol).


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Uscn Proteins for TNXA

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--


TNXA for ontologies           About GeneDecksing



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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

TNXA for domains           About GeneDecksing

2 InterPro domains/families:
 IPR003961 Fibronectin_type3
 IPR013783 Ig-like_fold

Graphical View of Domain Structure for InterPro Entry Q16473

ProtoNet protein and cluster: Q16473

UniProtKB/Swiss-Prot: TENXA_HUMAN, Q16473
Similarity: Contains 3 fibronectin type-III domains


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:
     Genatlas biochemistry entry for TNXA:
tenascin-like XA,homologous to XBS,included in YA and overlapping CYP21P,both in opposite orientation,(see XA)

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Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--


TNXA for ontologies           About GeneDecksing



(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for TNXA

Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--


TNXA for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

TNXA for compounds           About GeneDecksing

Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for TNXA
10/33 Novoseek chemical compound relationships for TNXA gene (see all 33)    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
heparin 84.4 146 11213853 (5), 17896889 (4), 10544915 (4), 15585445 (3) (see all 80)
fondaparinux 71.7 5 16637459 (1), 17635710 (1), 14760212 (1), 12820819 (1) (see all 5)
danaparoid 71.6 9 10544915 (2), 12407644 (2), 18349178 (1), 11307819 (1) (see all 5)
tinzaparin 65.5 2 11255277 (1), 11849226 (1)
nadroparin 62 2 11849226 (2)
protamine 58.4 1 17680178 (1)
hirudin 57.3 2 10715263 (1), 15387708 (1)
gamma-carboxyglutamic acid 55.2 1 9242658 (1)
argatroban 50.7 1 15387708 (1)
fibrinogen 46.3 2 15387708 (1), 11255277 (1)

Search CenterWatch for drugs/clinical trials and news about TNXA 

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for TNXA gene: 
NM_007116.1  

Unigene Cluster for TNXA:

Tenascin XA (pseudogene)
Hs.708061  [show with all ESTs]
Unigene Representative Sequence: NR_001284
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000507684(uc021yvf.1)

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Inhib. RNA
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat TNXA

Additional cDNA sequence: NR_001284.2 

7 DOTS entries:

DT.99966274  DT.91940211  DT.102830673  DT.100726147  DT.446229  DT.91753286  DT.121361465 

5 AceView cDNA sequences:

CD634052 CD634055 BQ955228 CD629690 CD634057 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

TNXA expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)

About this image

TNXA expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
1 LifeMap In Vivo Development Anatomical Compartment/Cell 
Tissue Anatomical Compartment CellCategory (developmental path)
HeartEpicardiumSubepicardial CellsEpicardium
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization

See TNXA Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for TNXA

SOURCE GeneReport for Unigene cluster: Hs.708061

UniProtKB/Swiss-Prot: TENXA_HUMAN, Q16473
Tissue specificity: Expressed in the adrenal gland

    SABiosciences Custom PCR Arrays for TNXA
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TNXA

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of human and mouse.

Orthologs for TNXA gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tnxa5 tenascin XA (pseudogene)   --   17 (18.33 cM) 34771395 


ENSEMBL Gene Tree for TNXA (if available)
TreeFam Gene Tree for TNXA (if available) 

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/30 NCBI SNPs in TNXA are shown (see all 30    About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs797700491,2
--31977493(+) TGCCAC/TCCACC 2 -- int11Minor allele frequency- T:0.50NA 2
rs1846401041,2
--31977506(+) CCAGCC/TGCCCC 1 -- nc-transcript-variant0--------
rs763107111,2
C,--31977528(+) ATGTCC/GCAAAA 1 -- nc-transcript-variant2Minor allele frequency- G:0.08NA WA 120
rs1147081971,2
F,--31977535(+) AAAACA/CCGTTC 1 -- nc-transcript-variant1Minor allele frequency- C:0.05WA 118
rs774713771,2
C--31977552(+) CGCTCG/CCGGTT 1 -- nc-transcript-variant1Minor allele frequency- C:0.00NA 2
rs413161641,2
C--31978470(+) CTCAGC/GCCTGC 2 -- int10--------
rs1998495431,2
C,F--31978624(+) TCAGAA/GGGGTC 2 -- int11Minor allele frequency- G:0.06EU 295
rs577185501,2
C,F--31978635(+) CCCGCG/TGCTCT 2 -- int11Minor allele frequency- T:0.03EU 339
rs557612441,2
C,F,--31978746(+) ATGCCA/GTTTTC 2 -- int19Minor allele frequency- G:0.33WA NA CSA EU 563
rs285854921,2
C,F,--31978755(+) TCTTGA/GCTCCC 1 -- int13Minor allele frequency- G:0.05NA EA EU 807

HapMap Linkage Disequilibrium report for TNXA (31976197 - 31980800 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 13 variations for TNXA
     13 CNVs: 0599 36512 36511 31278 36507 3602 0600 69404 32785 36509 64474 59325 36510

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

TNXA for disorders           About GeneDecksing

20/32 diseases for TNXA (see all 32):    About MalaCards
disseminated intravascular coagulation    heparin-induced thrombocytopenia    deep vein thrombosis    21-hydroxylase deficiency
glanzmann's thrombasthenia    mitral valve prolapse    ehlers-danlos syndrome    adrenal hyperplasia
arterial tortuosity syndrome    pulmonary embolism    scott syndrome    thrombasthenia
thrombosis    antiphospholipid syndrome    juvenile rheumatoid arthritis    venous thrombosis
hypermobility syndrome    thrombophilia    thrombocytopenia    rheumatoid arthritis

2 diseases from the University of Copenhagen DISEASES database for TNXA:
Ehlers-Danlos syndrome     Hypermobility syndrome

10/21 Novoseek disease relationships for TNXA gene (see all 21)    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
scott syndrome 65.6 2 1730083 (1), 9057642 (1)
thrombosis 54.6 4 2251671 (1), 9241747 (1), 17723080 (1), 8857926 (1)
bleeding 54.4 7 15264185 (2), 1317657 (1), 9421696 (1), 16999658 (1) (see all 6)
thromboembolism 51.3 5 2166971 (1), 9768037 (1), 15585445 (1), 12820819 (1)
arterial thrombosis 50.4 3 11307818 (1), 8857926 (1), 10598121 (1)
thrombophilia 50 1 17635710 (1)
venous thrombosis 46.9 1 7919374 (1)
deep vein thrombosis 40.9 1 11849226 (1)
pulmonary embolism 38.1 1 11849226 (1)
glanzmann thrombasthenia 34.4 1 9057642 (1)

Genetic Association Database (GAD): TNXA
Human Genome Epidemiology (HuGE) Navigator: TNXA (2 documents)

Export disorders for TNXA gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for TNXA gene, integrated from 9 sources (see all 221):
(articles sorted by number of sources associating them with TNXA)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Genetic basis of tobacco smoking: strong association of a specific major histocompatibility complex haplotype on chromosome 6 with smoking behavior. (PubMed id 15339882)1, 4 Fust G....Yu C.Y. (2004)
  2. An unequal crossover event in RCCX modules of the human MHC resulting in the formation of a TNXB/TNXA hybrid and deletion of the CYP21A. (PubMed id 12121677)1, 2 Jaatinen T.... Lokki M.-L. (2002)
  3. Mechanism and consequences of the duplication of the human C4/P450c21/gene X locus. (PubMed id 1373808)1, 2 Gitelman S.E....Miller W.L. (1992)
  4. The complete exon-intron structure of a human complement component C4A gene. DNA sequences, polymorphism, and linkage to the 21- hydroxylase gene. (PubMed id 1988494)1, 3 Yu C.Y. (1991)
  5. Transcript encoded on the opposite strand of the human steroid 21- hydroxylase/complement component C4 gene locus. (PubMed id 2475872)1, 3 Morel Y.... Miller W.L. (1989)
  6. An unequal crossover between the RCCX modules of the human MHC leading to the presence of a CYP21B gene and a tenascin TNXB/TNXA-RP2 recombinant between C4A and C4B genes in a patient with juvenile rheumatoid arthritis. (PubMed id 10343159)1, 9 Rupert K.L.... Yu C.Y. (1999)
  7. Carriership of a defective tenascin-X gene in steroid 21-hydroxylase deficiency patients: TNXB -TNXA hybrids in apparent large-scale gene conversions. (PubMed id 12354783)2 Koppens P.F....Degenhart H.J. (2002)
  8. Sequences promoting the transcription of the human XA gene overlapping P450c21A correctly predict the presence of a novel, adrenal-specific, truncated form of tenascin-X. (PubMed id 8530023)1 Tee M.K.... Miller W.L. (1995)
  9. Structure and genetics of the partially duplicated gene RP located immediately upstream of the complement C4A and the C4B genes in the HLA class III region. Molecular cloning, exon-intron structure, composite retroposon, and breakpoint of gene duplication. (PubMed id 8132574)1 Liming S.... Yu C. (1994)
  10. Unfractionated heparin dose requirements targeting in termediate intensity antifactor Xa concentration during pregnancy. (PubMed id 20334457)9 Clark N.P....Witt D.M. (2010)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Disorders
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 7146 HGNC: 11975 AceView: TNXA.1 Ensembl:ENSG00000248290 euGenes: HUgn7146
ECgene: TNXA H-InvDB: TNXA

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for TNXA Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for TNXA gene:
Search GeneIP for patents involving TNXA

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section

 
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