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BAP1 Gene

protein-coding   GIFtS: 66

GC03M052410
BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)
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
DKFZp686N04275 2
EC 3.4.19.12 3
FLJ35406 2
FLJ37180 2
HUCEP-13 2
KIAA0272 1, 2, 3
UCHL2 1, 2
hucep-6 1, 2
Descriptions
BRCA1 associated protein-1 2
BRCA1 associated protein-1 (ubiquitin carboxy-terminal
hydrolase) 2
BRCA1-associated protein 1 3
Cerebral protein 6 3
cerebral protein-13 2
cerebral protein-6 2
ubiquitin carboxy-terminal hydrolase 2
External Ids
HGNC: 9501
Entrez Gene: 83142
UniProtKB: Q925603
Ensembl: ENSG000001639307
Search outside databases for aliases for BAP1 gene

Previous GC identifers: GC03M051527 GC03M051687 GC03M052290 GC03M052393

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

EntrezGene summary for BAP1:
The protein encoded by this gene localizes to the nucleus and it interacts with the RING finger
domain of the breast cancer 1, early onset protein (BRCA1). This gene is thought to be a tumor
suppressor gene that functions in the BRCA1 growth control pathway. There are multiple
polyadenylation sites found in this gene. [provided by RefSeq]

UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
Function: Deubiquitinating enzyme which may be involved in BRCA1 signal transduction pathway

Gene Wiki entry for BAP1

(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

 Transcription factor binding sites upstream to the BAP1 gene  

Entrez Gene cytogenetic band: 3p21.31-p21.2   Ensembl cytogenetic band:  3p21.1   HGNC cytogenetic band: 3p21.31-p21.2

BAP1 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 3         GeneLoc Exon Structure

GeneLoc location for GC03M052410:     (about GC identifiers)

Start:
52,410,064 bp from pter
End:
52,419,058 bp from pter
Size:
8,995 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000003.10  NT_022517.17  
(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)
About This Section

UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560 (See protein sequence)
Recommended Name: Ubiquitin carboxyl-terminal hydrolase BAP1  
Size: 729 amino acids; 80362 Da
Subunit: Interacts with the RING finger domain of BRCA1
Subcellular location: Nucleus
Secondary accessions: Q6LEM0 Q7Z5E8

Post-translational modifications:

  • Phosphorylated upon DNA damage, probably by ATM or ATR1
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_004647.1  

    ENSEMBL proteins: 
    ENSP00000296288 


    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
    Enzo Life Sciences proteins for BAP1
    Recombinant Proteins from Abcam (BAP1)
    Human Recombinant Proteins from Abnova (BAP1)
                  OriGene Purified Recombinant Human Protein: BAP1 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622 intracellular IEA--
    GO:0005634 nucleus TAS9528852
    About this table

    Antibodies for BAP1: 
    Browse Antibodies Central at Invitrogen
    Millipore Mono- and Polyclonal Antibodies for the study of BAP1
    Sigma-Aldrich Antibody Arrays and Antibodies for BAP1
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (BAP1), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (BAP1)
    Novus Biologicals Antibodies for BAP1

    Assays for BAP1: 
    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

    1 InterPro domain/family:
     IPR001578 Peptidase_C12


       GeneDecks  BAP1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q92560

    ProtoNet protein and cluster: Q92560

    1 Blocks protein family: IPB001578 Ubiquitin carboxyl-terminal hydrolase

    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
    Similarity: Belongs to the peptidase C12 family

    (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 (BAP1)
    Millipore RNAi Products for the Analysis of BAP1 Gene knock-down
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004656

                  Applied Biosystems Silencer® siRNAs for BAP1

                  Sigma-Aldrich siRNA and siRNA Panels for BAP1  
                         Sigma-Aldrich shRNA Panels and shRNA for BAP1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for BAP1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004656
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004656
                                     untagged cDNA clones in CMV expression vector (see all 3): NM_004656 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_004656

    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
    Function: Deubiquitinating enzyme which may be involved in BRCA1 signal transduction pathway
    Catalytic activity: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide
    bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an
    intracellular targeting signal)
    Enzyme Number (IUBMB): EC 3.4.19.12 

    Genatlas biochemistry entry for BAP1:
    BRCA1 associated protein 1,widely expressed,binding to the BRCA1 RING finger domain and enhancing
    BRCA1-mediated cell growth suppression
    1 MGI phenotypic allele for Bap1 (no phenotypes)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004221 ubiquitin thiolesterase activity IEA--
    GO:0005515 protein binding IPI9528852
    GO:0008233 peptidase activity NAS9528852
    GO:0008234 cysteine-type peptidase activity 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


    2 Millipore Pathways for BAP1
     Selected targets of ESR1
     Common schema of ubiquitination

       GeneDecks  BAP1 for the pathways selected above  
    About GeneDecksing

    1 Sigma-Aldrich "Your Favorite Gene" Pathway for  BAP1  (Your Favorite Gene powered by Ingenuity) 
     Protein Ubiquitination Pathway

       GeneDecks  BAP1 for the pathways selected above  
    About GeneDecksing

     Gene Network CentralTM Interacting Genes and Proteins Network for  BAP1 


    1 Interacting protein for BAP1 (ENSP000002962883 Q925601) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BRCA1P383981STRING (score=.752) EBI-1791447, EBI-349905
    About this table

    3 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006464 protein modification process NAS9528852
    GO:0006511 ubiquitin-dependent protein catabolic process IEA--
    GO:0008285 negative regulation of cell proliferation TAS9528852
    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 BAP1

    (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 (BAP1)
    Millipore RNAi Products for the Analysis of BAP1 Gene knock-down
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004656

                  Sigma-Aldrich siRNA and siRNA Panels for BAP1  
                         Sigma-Aldrich shRNA Panels and shRNA for BAP1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_004656  

    REFSEQ mRNAs for BAP1 gene: 

    NM_004656.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_004656  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004656
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004656
                                     untagged cDNA clones in CMV expression vector (see all 3): NM_004656 

    Additional cDNA sequence: 

    AB002534.1 AF045581.1 AK092725.1 AK094499.1 AK225494.1 AK292608.1 AK295395.1 AK307274.1 
    AY130008.1 BC001596.1 BX647318.1 D87462.2 D88812.1 

    18 DOTS entries:

    DT.217303  DT.91763316  DT.102820838  DT.100795050  DT.100795049  DT.120914317  DT.120914340  DT.120914236 
    DT.100032503  DT.120914364  DT.86854177  DT.97791879  DT.100029516  DT.100795048  DT.102820839  DT.120914363 
    DT.120914282  DT.80100384 

    24/369 AceView cDNA sequences (see all 369 ):

    BU846231 BX508658 AI963987 Z45707 BE713073 AI917782 BU145192 CK430805 
    BE535499 AI675206 BM451889 BQ941857 AI401328 AA742202 BQ058097 BM556538 
    BQ955178 BQ217330 BC001596 BE464104 Z41371 BF196085 AU125284 BX500239 

    highest scoring ESTs for BAP1:

    AF045581 BC001596 BE207318 BE277104 BE730762 BE736910 BF309296 BF966464 BF967313 BG036825 

    Unigene Cluster for BAP1:

    BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)
    Hs.106674  [show with all ESTs]
    Unigene Representative Sequence: NM_004656


    GeneLoc Exon Structure

    5/13 Alternative Splicing Database (ASD) splice patterns (SP) for BAP1 (see all 13 )

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18a ·
    SP1:                                                  -     -     -                 -           -                                                     -         
    SP2:                                -     -                                                                                                                     
    SP3:                                                                                                                                                  -         
    SP4:                          -                                                                                                                                 
    SP5:              -                                                                                                                                             

    ExUns: 18b · 18c ^ 19 ^ 20a · 20b · 20c · 20d · 20e
    SP1:                                                
    SP2:                                                
    SP3:                                                
    SP4:                                                
    SP5:                                                

    About this scheme

    ECgene alternative splicing isoforms for BAP1

    1 Ensembl transcript including schematic representation:
    ENST00000296288  
    (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

    BAP1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for BAP1

    1 / 2 / 3

    4 probe-sets matching BAP1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    38682_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 AF045581 1.00 1.00 1.00 1

    201419_at2, 3 U133-A 1 1.00 1.00 -- -- NM_004656 0.60 1.00 0.82 1

    201419_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    1555735_a_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  BAP1 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: GCCTCTGCCA

    SOURCE GeneReport for Unigene cluster: Hs.106674

    Expression variation in blood from EXPOLDB for BAP1

    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
    Tissue specificity: Highly expressed in testis, placenta and ovary. Expressed in breast

    (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 BAP1 gene from 5/10 species (see all 10 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    BAP11   -- BRCA1 associated protein-1 (ubiquitin carboxy-terminal more 90.77(n)
    94.63(a)
    484737  XM_854401.1  XP_859494.1 
    chimpanzee
    (Pan troglodytes)
    BAP11   -- BRCA1 associated protein-1 (ubiquitin carboxy-terminal more 99.54(n)
    99.73(a)
    460426  XM_001171970.1  XP_001171970.1 
    rat
    (Rattus norvegicus)
    Bap11   -- BRCA1 associated protein-1 (ubiquitin carboxy-terminal more 89.27(n)
    93.95(a)
    306257  XM_224614.4  XP_224614.4 
    mouse
    (Mus musculus)
    Bap11, 5 145
    Brca1 associated protein 11, 5 88.64(n)1
    93.54(a)1
    1044161  NM_027088.21  NP_081364.11 
     AA9897615  AB0478205  (see all 26)
    chicken
    (Gallus gallus)
    BAP11   -- BRCA1 associated protein-1 (ubiquitin carboxy-terminal more 80.83(n)
    85.55(a)
    415944  NM_001030590.1  NP_001025761.1 
    About this table        Species with no ortholog for BAP1

    ENSEMBL Gene Tree for BAP1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for BAP1 gene
    UCHL52  

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


    10/46 NCBI SNPs in BAP1 are shown (see all 46 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 42)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 3 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs1235981,2
    A,C,F,H52410900(+) AGTTGG/AGACCG 1 -- ut31 ese310Minor allele frequency- A:0.02EA NA EU WA 872
    rs353537811,2
    C,F52412237(+) GCCTCA/TCCATC 1 V/E mis15Minor allele frequency- T:0.48NA EU EA WA 446
    rs98554791,2
    F,H52410370(+) ACCCTG/AAGTGC 1 -- ut31 ese34Minor allele frequency- A:0.01EU EA WA 410
    rs347361171,2
    F52412788(+) CTCCCA/CGCCCC 1 A/A syn11Minor allele frequency- C:0.04NA 46
    rs1236021,2
    A,C,F,H,O52417394(+) AGTTCG/CTTCTG 1 -- int110Minor allele frequency- C:0.07EA MN EU WA NA 2343
    rs98429601,2
    A,F,H52413308(+) GCTTAC/TGTGCT 1 -- int14Minor allele frequency- T:0.01EU EA WA 410
    rs4196041,2
    C,F,H52416646(+) TTCTTA/TAAAGG 1 -- int18Minor allele frequency- T:0.02EU EA WA 838
    rs38218401,2
    F,H52417245(-) AGAAGG/AGGAGT 1 -- int1 trp34Minor allele frequency- A:0.04EA EU 1758
    rs98486281,2
    C,H52414487(+) AAGCTC/TTAAGT 1 -- int14Minor allele frequency- T:0.00EU EA WA 410
    rs98483431,2
    H52414351(+) ACCATC/TTGAGA 1 -- int1 spl34Minor allele frequency- T:0.00EU EA WA 420
    About this table

    HapMap Linkage Disequilibrium images for BAP1 (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: 603089

    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
  • Defects in BAP1 are found in non-small cell lung cancer (NSCLC) cell lines
  • Tumor-associated antigen found in several childhood medulloblastoma
  • 3 Novoseek disease relationships for BAP1 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    parkinson disease 36.72 2 12775255 (1), 10203348 (1)
    breast cancer 20.08 4 9528852 (2), 19197335 (1)
    tumors 0.00 2 12800201 (1), 9528852 (1)
    About this table

    Human Genome Epidemiology Navigator: BAP1 (4 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

    10/32 PubMed articles for BAP1 gene (see all 32 ):
    (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: 8314 HGNC: 950 AceView: BAP1 Ensembl:ENSG00000163930 euGenes: HUgn8314
    ECgene: BAP1 H-InvDB: BAP1
    (According to HUGE)
    About This Section

    HUGE: KIAA0272
    (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 BAP1 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 BAP1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for BAP1 Antibodies for BAP1
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     Lentivirus-delivered shRNAs for BAP1 Browse small molecules at Sigma-Aldrich
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     Recombinant Proteins
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     Tagged/untagged cDNA clones
     Validated SYBR primer pairs
     Purified proteins from HEK293T cells
     Western blot validated antibodies
     shRNA in GFP-retroviral vector
     Search Tocris compounds for BAP1




     Proteins for BAP1
     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Antibodies for BAP1

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    Version 2.41.1
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