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CDH13 Gene

protein-coding   GIFtS: 60

GC16P081218
cadherin 13, H-cadherin (heart)
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
CDHH 1, 2, 3, 5
H-cadherin 2, 3
P105 2, 3
T-cad 2, 3
T-cadherin 2, 3
heart-cadherin 2
truncated-cadherin 2
Descriptions
Heart cadherin 3
Truncated cadherin 3
cadherin 13 2
cadherin 13, H-cadherin (heart) 2
External Ids
HGNC: 17531
Entrez Gene: 10122
UniProtKB: P552903
Ensembl: ENSG000001409457
Search outside databases for aliases for CDH13 gene

Previous GC identifers: GC16P073743 GC16P083625 GC16P082399 GC16P082440

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

EntrezGene summary for CDH13:
This gene is a member of the cadherin superfamily. The encoded protein is a calcium dependent
cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane
region but, unlike the typical cadherin superfamily member, lacks the highly conserved cytoplasmic
region. This particular cadherin is a putative mediator of cell-cell interaction in the heart and
may act as a negative regulator of neural cell growth. The gene locus is hypermethylated or
deleted in breast, ovarian and lung cancers. Two major mRNA transcripts encoding identical
proteins are found, products of alternative polyadenylation sites. [provided by RefSeq]

UniProtKB/Swiss-Prot: CAD13_HUMAN, P55290
Function: Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with
themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the
sorting of heterogeneous cell types. May act as a negative regulator of neural cell growth

Gene Wiki entry for CDH13 (T-cadherin)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16q24.2-q24.3   Ensembl cytogenetic band:  16q23.3   HGNC cytogenetic band: 16q23.3

CDH13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P081218:     (about GC identifiers)

Start:
81,218,079 bp from pter
End:
82,387,705 bp from pter
Size:
1,169,627 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000016.8  NT_010498.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: CAD13_HUMAN, P55290 (See protein sequence)
Recommended Name: Cadherin-13 precursor  
Size: 713 amino acids; 78287 Da
Subcellular location: Cell membrane; Lipid-anchor, GPI-anchor
Developmental stage: Expressed at higher levels in adult brain than in developing brain
PDB structures from and Proteopedia :
2V37 (3D)    
Secondary accessions: Q6GTW4 Q8TBX3

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_001248.1  

    ENSEMBL proteins: 
    ENSP00000268613 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (pan Cadherin, H Cadherin)
    Human Recombinant Proteins from Abnova (CDH13)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    5/7 Gene Ontology (GO) cellular component terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005615 extracellular space IDA16873731
    GO:0005737 cytoplasm IDA10737605
    GO:0005886 plasma membrane IEA--
    GO:0005901 caveola IDA9650591
    GO:0009897 external side of plasma membrane IEA--
    About this table

    Antibodies for CDH13: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for CDH13
    R&D Systems Antibodies for CDH13 (Cadherin-13)
    Antibodies from Abcam (pan Cadherin, H Cadherin), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (CDH13)
    Novus Biologicals Antibodies for CDH13

    Assays for CDH13: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    3 InterPro domains/families:
     IPR014868 Cadherin_pro
     IPR015489 Cadherin13
     IPR002126 Cadherin


       GeneDecks  CDH13 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry P55290

    ProtoNet protein and cluster: P55290

    1 Blocks protein family: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: CAD13_HUMAN, P55290
    Similarity: Contains 5 cadherin domains

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (CDH13)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (CDH13)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_001257

                  Applied Biosystems Silencer® siRNAs for CDH13

                  Sigma-Aldrich siRNA and siRNA Panels for CDH13  
                         Sigma-Aldrich shRNA Panels and shRNA for CDH13  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_001257
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_001257
                                     untagged cDNA clone in CMV expression vector: NM_001257 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_001257

    UniProtKB/Swiss-Prot: CAD13_HUMAN, P55290
    Function: Cadherins are calcium dependent cell adhesion proteins. They preferentially interact with
    themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the
    sorting of heterogeneous cell types. May act as a negative regulator of neural cell growth

    Genatlas biochemistry entry for CDH13:
    cadherin 13,H-cadherin,transmembrane glycoprotein component of adherens junction,expressed in the
    heart,deleted in lung carcinoma (see TSG16H),hypermethylated or deleted in ovarian tumors (see
    TSG16A)

    5 MGI mutant phenotypes (inferred from 1 allele(MGI details for Cdh13):

    homeostasis/metabolismlife span-post-weaning/agingreproductive systemtumorigenesis

    5 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509 calcium ion binding IEA--
    GO:0030169 low-density lipoprotein binding IDA16013438
    GO:0042803 protein homodimerization activity IEA--
    GO:0045296 cadherin binding IDA10601632
    GO:0055100 adiponectin binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


     Gene Network CentralTM Interacting Genes and Proteins Network for  CDH13 


    5/26 Interacting proteins for CDH13 (ENSP000002686133) via UniProtKB, MINT, and/or STRING (see all 26 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RASSF1ENSP000003523233STRING (score=.965)
    ADIPOQENSP000003207093STRING (score=.835)
    RASSF5ENSP000003560853STRING (score=.82)
    FHITENSP000003420873STRING (score=.816)
    MLH1ENSP000002317903STRING (score=.815)
    About this table

    5/21 Gene Ontology (GO) biological process terms (links to tree view) (see all 21 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001938 positive regulation of endothelial cell proliferation IMP15364621
    GO:0001954 positive regulation of cell-matrix adhesion IMP17573778
    GO:0002040 sprouting angiogenesis IDA16873731
    GO:0007156 homophilic cell adhesion IEA--
    GO:0007162 negative regulation of cell adhesion IDA14729458
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for CDH13
    5 Novoseek chemical compound relationships for CDH13 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    matrigel 9.67 1 17486418 (2), 17077306 (1)
    progesterone 4.75 5 16516410 (1), 16603640 (1), 16397211 (1)
    lipid 0.00 2 11171368 (1), 15552364 (1)
    calcium 0.00 4 1400585 (1), 9610389 (1), 15821437 (1)
    tyrosine 0.00 5 17631504 (3)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (CDH13)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (CDH13)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_001257

                  Sigma-Aldrich siRNA and siRNA Panels for CDH13  
                         Sigma-Aldrich shRNA Panels and shRNA for CDH13  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001257  

    REFSEQ mRNAs for CDH13 gene: 

    NM_001257.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001257  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_001257
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_001257
                                     untagged cDNA clone in CMV expression vector: NM_001257 

    Additional cDNA sequence: 

    AK294277.1 AK295886.1 AK298612.1 AK304592.1 AK304733.1 AK307862.1 BC012615.1 BC028624.2 
    BC030653.2 EU190357.1 EU190358.1 L34058.1 U59288.1 

    10 DOTS entries:

    DT.214971  DT.120686349  DT.92425049  DT.100791986  DT.75175565  DT.95091153  DT.120686309  DT.100791980 
    DT.120686344  DT.99999594 

    24/25 AceView cDNA sequences (see all 25 ):

    AL708705 BX281335 CA433353 BF432251 BX281642 BC012615 AU132542 AL048601 
    BF105192 BX500121 AU123178 BI829166 BG212777 AI359109 AU280768 AI493289 
    BP336793 BP336568 L34058 NM_001257 BC028624 BC030653 BP337622 BU632738 

    highest scoring ESTs for CDH13:

    L34058 BC028624 BC030653 U59288 U59289 AA042897 AA043035 AA150490 AA156693 AA161471 

    Unigene Cluster for CDH13:

    Cadherin 13, H-cadherin (heart)
    Hs.654386  [show with all ESTs]
    Unigene Representative Sequence: NM_001257


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000268613  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    CDH13 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for CDH13

    1 / 2 / 3

    6 probe-sets matching CDH13 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    483_g_at2, 3 U95-A 1 1.00 1.00 0.95 1.25 U59289 0.80 1.00 0.91 1
    2073_s_at2, 3 U95-A 1 1.00 1.00 0.94 0.75 L34058 1.00 1.00 1.00 1
    84974_at2, 3 U95-D 1 1.00 1.00 0.92 1.14 AI493289 0.60 1.00 0.82 1
    482_at2, 3 U95-A 1 0.56 1.00 0.96 1.00 U59289 0.80 1.00 0.91 1

    204726_at2, 3 U133-A 1 0.73 1.00 -- -- NM_001257 0.60 1.00 0.82 1

    204726_at2 U133Plus2 1 0.73 1.00 -- -- -- -- -- -- --
    GeneDecks  CDH13 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: GTGGCATATG

    SOURCE GeneReport for Unigene cluster: Hs.654386

    Expression variation in blood from EXPOLDB for CDH13

    UniProtKB/Swiss-Prot: CAD13_HUMAN, P55290
    Tissue specificity: Highly expressed in heart. In the CNS, expressed in cerebral cortex, medulla,
    hippocampus, amygdala, thalamus and substantia nigra. No expression detected in cerebellum or
    spinal cord

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for CDH13 gene from 5/7 species (see all 7 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    CDH131   -- cadherin 13, H-cadherin (heart) 91.43(n)
    95.92(a)
    489689  XM_546809.2  XP_546809.2 
    chimpanzee
    (Pan troglodytes)
    CDH131   -- cadherin 13, H-cadherin (heart) 98.66(n)
    98(a)
    454273  XM_001149641.1  XP_001149641.1 
    cow
    (Bos taurus)
    CDH131   -- cadherin 13, H-cadherin (heart) 91.44(n)
    95.09(a)
    512302  NM_001035277.1  NP_001030354.1 
    rat
    (Rattus norvegicus)
    Cdh131   -- cadherin 13 87.89(n)
    94.37(a)
    192248  NM_138889.2  NP_620244.1 
    mouse
    (Mus musculus)
    Cdh131, 5 8 (64.00 cM)5
    cadherin 131, 5 87.65(n)1
    93.94(a)1
    125541  NM_019707.31  NP_062681.21 
     AB0221005  AI4150445  (see all 14)
    About this table        Species with no ortholog for CDH13

    ENSEMBL Gene Tree for CDH13
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for CDH13 gene
    CDH42  CDH22  CDH152  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/10714 NCBI SNPs in CDH13 are shown (see all 10714 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 4278)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 16 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs71974231,2
    A,C,F,H82388190(+) GCACTG/ATCACG 1 -- ng3111Minor allele frequency- A:0.08EU EA WA NA 980
    rs72044541,2
    A,C,F,H81216695(+) CAGTAG/CAATTT 1 -- ng518Minor allele frequency- C:0.47EU EA WA 838
    rs65650511,2
    A,C,F,H81216229(+) CTGGAA/GTGGAG 1 -- ng517Minor allele frequency- G:0.37EA WA EU 690
    rs10486131,2
    C,F,H82387027(+) CCTGTC/TATCAT 1 -- ut316Minor allele frequency- T:0.03NA EU EA 440
    rs37436211,2
    C,F,H82386630(+) CAGGGC/TCTCCC 1 -- ut31 ese312Minor allele frequency- T:0.04EA NA EU WA 2458
    rs116415151,2
    C,F,H82388125(+) AGGGAC/TAGGGG 1 -- ng314Minor allele frequency- T:0.01EU EA WA 420
    rs4607961,2
    C,F,H82387800(+) ACCATT/GTGGGG 1 -- ng318Minor allele frequency- G:0.11EU EA WA 834
    rs177078621,2
    C,F,H82387306(+) TTGTTC/TTAAGA 1 -- ut3111Minor allele frequency- T:0.13NA EU EA WA 982
    rs10486141,2
    C,F,H82387047(+) ACATGC/GATACA 1 -- ut31 ese311Minor allele frequency- G:0.12NA EU EA WA 980
    rs22398571,2
    C,F81217444(+) ATATAC/GAAAAA 1 -- ng513Minor allele frequency- G:0.30EA 1130
    About this table

    HapMap Linkage Disequilibrium images for CDH13 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 601364

    10/34 Novoseek disease relationships for CDH13 gene (see all 34 )

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    nsclc stage i 54.57 1 18337602 (1)
    nsclc 54.27 30 11410507 (4), 15197197 (3), 17606310 (2), 15201980 (2) (see all 12)
    cancer 47.30 31 12489108 (3), 15292927 (2), 15245595 (2), 15704093 (2) (see all 18)
    cancer lung 46.84 19 9737784 (3), 11389090 (2), 11355171 (1), 17960794 (1) (see all 10)
    tumors 46.04 90 10493953 (5), 11410507 (3), 16222700 (3), 17077306 (3) (see all 37)
    allelic loss 39.55 5 12489108 (2), 9737784 (1)
    familial adenomatous polyposis 37.48 7 17873900 (1), 12467239 (1), 15042681 (1)
    carcinoma squamous cell 36.31 16 12177241 (3), 15816843 (2), 12932231 (1), 12455028 (1) (see all 7)
    endometrial cancer 33.52 7 18519763 (3), 16928264 (2), 15159323 (1)
    cervical cancer 29.67 6 16928264 (2), 17548682 (1), 19054549 (1), 14750164 (1) (see all 5)
    About this table

    Human Genome Epidemiology Navigator: CDH13 (7 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

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

    10/178 PubMed articles for CDH13 gene (see all 178 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    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, and/or H-InvDB)
    About This Section

    Entrez Gene: 1012 HGNC: 1753 AceView: CDH13 Ensembl:ENSG00000140945 euGenes: HUgn1012
    ECgene: CDH13 H-InvDB: CDH13
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for CDH13 Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for CDH13:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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