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

PRDM13 Gene

protein-coding   GIFtS: 45
GCID: GC06P100054

PR Domain Containing 13

  See 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)
About This Section

Aliases
PR Domain Containing 131 2     PR Domain Zinc Finger Protein 132
PFM102 3     PR-Domain Containing Protein 132
PR Domain-Containing Protein 132 3     PR-Domain Zinc Finger Protein 132
MU-MB-20.2202     EC 2.1.1.-3

External Ids:    HGNC: 139981   Entrez Gene: 593362   Ensembl: ENSG000001122387   UniProtKB: Q9H4Q33   

Export aliases for PRDM13 gene to outside databases

Previous GC identifers: GC06P099922 GC06P100071 GC06P100100 GC06P100161 GC06P097494


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

GeneCards Summary for PRDM13 Gene: 
PRDM13 (PR domain containing 13) is a protein-coding gene. Diseases associated with PRDM13 include large cell medulloblastoma, and childhood medulloblastoma. GO annotations related to this gene include DNA binding and zinc ion binding. An important paralog of this gene is MECOM.

UniProtKB/Swiss-Prot: PRD13_HUMAN, Q9H4Q3
Function: May be involved in transcriptional regulation




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PRDM13 gene promoter:
         Nkx3-1   AhR   Nkx3-1 v4   Pax-5   Nkx3-1 v1   Nkx2-5   Arnt   Nkx3-1 v2   HOXA5   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPRDM13 promoter sequence
   Search SABiosciences Chromatin IP Primers for PRDM13

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM13


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

Entrez Gene cytogenetic band: 6q16.2   Ensembl cytogenetic band:  6q16.2   HGNC cytogenetic band: 6q16.2

PRDM13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM13 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P100054:  view genomic region     (about GC identifiers)

Start:
100,054,606 bp from pter      End:
100,063,454 bp from pter
Size:
8,849 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PRD13_HUMAN, Q9H4Q3 (See protein sequence)
Recommended Name: PR domain zinc finger protein 13  
Size: 707 amino acids; 73981 Da
Subcellular location: Nucleus (Potential)
Sequence caution: Sequence=AAG13448.1; Type=Miscellaneous discrepancy; Note=Non-canonical splice intron-exon
junction; Sequence=CAI19763.1; Type=Erroneous gene model prediction; Sequence=CAI22063.1; Type=Erroneous gene
model prediction;
Secondary accessions: Q5TGC1 Q5TGC2

Explore the universe of human proteins at neXtProt for PRDM13: NX_Q9H4Q3

Explore proteomics data for PRDM13 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9H4Q3

  • PRDM13 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PRDM13 Protein Expression
    REFSEQ proteins: NP_067633.2  
    ENSEMBL proteins: 
     ENSP00000358217   ENSP00000358216  

    Human Recombinant Protein Products for PRDM13: 
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    Cloud-Clone Corp. Proteins for PRDM13 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    PRDM13 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    4 InterPro protein domains:
     IPR001214 SET_dom
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9H4Q3

    ProtoNet protein and cluster: Q9H4Q3

    UniProtKB/Swiss-Prot: PRD13_HUMAN, Q9H4Q3
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 4 C2H2-type zinc fingers
    Similarity: Contains 1 SET domain


    PRDM13 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PRD13_HUMAN, Q9H4Q3
    Function: May be involved in transcriptional regulation

         Enzyme Number (IUBMB): EC 2.1.1.-1

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0008168methyltransferase activity IEA--
    GO:0008270zinc ion binding ----
    GO:0046872metal ion binding IEA--
         
    PRDM13 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for PRDM13:
     Decreased POU5F1-GFP protein e  Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for PRDM13 
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    SwitchGear 3'UTR luciferase reporter plasmidPRDM13 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM13


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for PRDM13

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for PRDM13 (Q9H4Q33 ENSP000003582174) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KDM5BQ9UGL13, ENSP000003562344I2D: score=1 STRING: ENSP00000356234
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent IEA--
    GO:0022008neurogenesis IEA--

    PRDM13 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PRDM13 (PRD13)

    Search CenterWatch for drugs/clinical trials and news about PRDM13 / PRD13

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PRDM13 gene: 
    NM_021620.3  

    Unigene Cluster for PRDM13:

    PR domain containing 13
    Hs.287386
    Unigene Representative Sequence: AY004253
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369215 ENST00000369214(uc003pqg.1)
    miRNA
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    8/18 QIAGEN miScript miRNA Assays for microRNAs that regulate PRDM13 (see all 18):
    hsa-miR-607 hsa-miR-25 hsa-miR-340 hsa-miR-124 hsa-miR-376a* hsa-miR-891b hsa-miR-1208 hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidPRDM13 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PRDM13
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                         Customized lentivirus expression plasmids for stable overexpression of PRDM13 
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for PRDM13
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRDM13
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM13

    Additional mRNA sequence: 

    AY004253.1 AY130010.1 

    1 DOTS entry:

    DT.101977240 

    3 AceView cDNA sequences:

    NM_021620 AY004253 AY130010 

    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

    PRDM13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AATCTAAGAG
    PRDM13 Expression
    About this image


    See PRDM13 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PRDM13

    SOURCE GeneReport for Unigene cluster: Hs.287386
        SABiosciences Custom PCR Arrays for PRDM13
    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for PRDM13
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM13
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM13

    (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 animals.

    Orthologs for PRDM13 gene from 4/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prdm131 , 5 PR domain containing 131, 5 83.89(n)1
    86.17(a)1
      4 (8.78 cM)5
    2300251  NM_001080771.11  NP_001074240.11 
     216774805 
    lizard
    (Anolis carolinensis)
    Reptilia PRDM136
    Uncharacterized protein
    49(a)
    1 ↔ 1
    1(171613139-171643310)
    zebrafish
    (Danio rerio)
    Actinopterygii prdm131 PR domain containing 13 64.39(n)
    64.39(a)
      796276  XM_001336555.3  XP_001336591.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG132966
    CG103486
    --
    26(a)
    11(a)
    1 ↔ 1
    possible ortholog
    3L(6156257-6157782)
    2L(18714615-18731419)


    ENSEMBL Gene Tree for PRDM13 (if available)
    TreeFam Gene Tree for PRDM13 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PRDM13 gene
    MECOM2  PRDM162  
    14 SIMAP similar genes for PRDM13 using alignment to 1 protein entry:     PRD13_HUMAN:
    ZNF55    PLZF    ZNF78L1    ZNF72    ZNF702P    ZFS-5
    kr-znf3    ZNF    ZFS-2    ZNF697    DKFZp547H249    ZFS-6
    HZF16    ZNF808

    PRDM13 for paralogs           About GeneDecksing



    (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) 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

    10/228 SNPs in PRDM13 are shown (see all 228)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1876412821,2
    --100052665(+) CCCCCC/GGGCTT 1 -- us2k10--------
    rs3308371,2
    C,F,A,H--100052699(+) CAAAGG/CCTCCC 1 -- us2k1 tfbs316Minor allele frequency- C:0.10NS EA NA WA CSA 840
    rs119615951,2
    C,F,H--100052886(+) CCATGT/AATACA 1 -- us2k110Minor allele frequency- A:0.21NS EA WA NA CSA 752
    rs772037061,2
    C,F--100053031(+) ATGCAC/TGCACT 1 -- us2k11Minor allele frequency- T:0.01EA 120
    rs121915791,2
    C,F,H--100053112(+) CCCATT/ATTACA 1 -- us2k112Minor allele frequency- A:0.06NS EA NA WA 1188
    rs1145418711,2
    --100053154(+) CTAAAG/TGTTCC 1 -- us2k11Minor allele frequency- T:0.01WA 118
    rs1157359691,2
    C,F--100053178(+) GGGAGA/GGCACA 1 -- us2k11Minor allele frequency- G:0.04WA 118
    rs1925606651,2
    --100053214(+) TCCTGC/GCCAGT 1 -- us2k10--------
    rs1393667781,2
    C--100053242(+) CGAGTA/GAGGGG 1 -- us2k10--------
    rs121917541,2
    C,F,H--100053427(+) GTGGTT/CGGGCC 1 -- us2k18Minor allele frequency- C:0.01NS EA NA 898

    HapMap Linkage Disequilibrium report for PRDM13 (100054606 - 100063454 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for PRDM13:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv830741CNV Gain17160897

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing PRDM13
    DNA2.0 Custom Variant and Variant Library Synthesis for PRDM13

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    3 diseases for PRDM13:    About MalaCards
    large cell medulloblastoma    childhood medulloblastoma    medulloblastoma


    PRDM13 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PRDM13

    Export disorders for PRDM13 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 PRDM13 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PRDM13)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Thirty new loci for age at menarche identified by a m eta-analysis of genome-wide association studies. (PubMed id 21102462)1, 4 Elks C.E....Murray A. (2010)
    2. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    3. The PcG protein hPc2 interacts with the N-terminus of histone demethylase JARID1B and acts as a transcriptional co-repressor. (PubMed id 19336002)1 Zhou W....Zhang L. (2009)
    4. Novel tumor antigens identified by autologous antibody screening of childhood medulloblastoma cDNA libraries. (PubMed id 12800201)1 Behrends U.... Mautner J. (2003)
    5. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (2001)
    6. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    (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, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 59336 HGNC: 13998 AceView: PRDM13 Ensembl:ENSG00000112238 euGenes: HUgn59336
    ECgene: PRDM13 H-InvDB: PRDM13

    (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 PRDM13 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 PRDM13 gene:
    Search GeneIP for patents involving PRDM13

    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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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