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TNXA Gene

pseudogene   GIFtS: 31
GCID: GC06M031979

Tenascin XA (Pseudogene)

(Previous name: tenascin XA)
(Previous symbol: TNX)
  See TNXA-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Tenascin XA (Pseudogene)1 2     D6S103E2
TNX1 2     HXBL2
XA2 3     TN-XA3
Tenascin XA1     

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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TNXA Gene:
TNXA (tenascin XA (pseudogene)) is a pseudogene. Diseases associated with TNXA include hypermobility syndrome, and scott syndrome.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   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
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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-,NT_167247 3,356,041-3,360,644      Chr6-,NT_167249 3,308,907-3,313,510      Chr6-,NT_167245 3,261,780-3,266,383     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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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

Explore proteomics data for TNXA at MOPED


See TNXA Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 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


Find genes that share domains with TNXA           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:
     Genatlas biochemistry entry for TNXA:
tenascin-like XA,homologous to XBS,included in YA and overlapping CYP21P,both in opposite orientation,(see XA)

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
     
Find genes that share ontologies with TNXA           About GenesLikeMe


Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for TNXA

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular2
plasma membrane2
endoplasmic reticulum1
golgi apparatus1
lysosome1
peroxisome1

Gene Ontology (GO): 1 cellular component term:    About this table

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

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TNXA
Interactions:

    GeneGlobe Interaction Network for TNXA

Gene Ontology (GO): 1 biological process term:    About this table

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

Find genes that share ontologies with TNXA           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for TNXA (TENXA)

Selected Novoseek inferred 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)



Find genes that share compounds with TNXA           About GenesLikeMe



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for TNXA gene: 
NM_007116.1  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000507684(uc021yvf.1)
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  QuantiFast Probe-based Assays in human, mouse, rat TNXA

5 AceView cDNA sequences:

CD634055 CD634052 CD629690 BQ955228 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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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TNXA expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TNXA Expression
About this image


TNXA expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Heart (Cardiovascular System)
         Subepicardial Cells Epicardium
 
 Adrenal Gland (Endocrine System)
TNXA Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TNXA Protein Expression

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

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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)
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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)
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Paralogs for TNXA gene
5 SIMAP similar genes for TNXA using alignment to 1 protein entry:     TENXA_HUMAN:
TNXB    TNC    TNC variant protein    XB    dJ34F7.1

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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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2 SNPs for TNXA    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs763107111,2
C--31977528(+) ATGTCC/GCAAAA 1 -- nc-transcript-variant2Minor allele frequency- G:0.08NA WA 120
rs774713771,2
C--31977552(+) CGCTCG/CCGGTT 1 -- nc-transcript-variant1Minor allele frequency- C:0.00NA 2

HapMap Linkage Disequilibrium report for TNXA (31976197 - 31980800 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for TNXA (see all 42):    About this table    
Variant IDTypeSubtypePubMed ID
esv2731825CNV Deletion23290073
dgv20n31CNV Duplication19718026
nsv884665CNV Loss21882294
dgv6631n71CNV Loss21882294
nsv884626CNV Loss21882294
nsv285CNV Loss15895083
dgv6624n71CNV Loss21882294
dgv6612n71CNV Loss21882294
dgv6613n71CNV Loss21882294
dgv6623n71CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
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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.)
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4 diseases for TNXA:    
About MalaCards
hypermobility syndrome    scott syndrome    burns    juvenile rheumatoid arthritis

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

Find genes that share disorders with TNXA           About GenesLikeMe

Selected Novoseek inferred 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)
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PubMed articles for TNXA gene, integrated from 10 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 FA1st G....Yu C.Y. (Int. Immunol. 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. (Hum. Immunol. 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. (Mol. Cell. Biol. 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. (J. Immunol. 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. (Proc. Natl. Acad. Sci. U.S.A. 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. (Exp. Clin. Immunogenet. 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.J.... Degenhart H.J. (Hum. Mol. Genet. 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. (Genomics 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. (J. Biol. Chem. 1994)
  10. Unfractionated heparin dose requirements targeting intermediate intensity antifactor Xa concentration during pregnancy. (PubMed id 20334457)9 Clark N.P....Witt D.M. (Pharmacotherapy 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 7146 HGNC: 11975 AceView: TNXA.1 Ensembl:ENSG00000248290 euGenes: HUgn7146
ECgene: TNXA H-InvDB: TNXA

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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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.)
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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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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