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EFNB3 Gene

protein-coding   GIFtS: 60

GC17P007549
ephrin-B3
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: EPLG8)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
EFL6 2, 5
EPLG8 2, 3, 5
LERK-8 1, 3
LERK8 2, 3, 5
ephrin-B3 2
Descriptions
EPH-related receptor transmembrane ligand ELK-L3 3
EPH-related receptor tyrosine kinase ligand 8 2, 3
Ephrin B3 2
External Ids
HGNC: 32281
Entrez Gene: 19492
UniProtKB: Q157683
Ensembl: ENSG000001089477
Search outside databases for aliases for EFNB3 gene

Previous GC identifers: GC17U990024 GC17P008348 GC17P007551 GC17P007809

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

EntrezGene summary for EFNB3:
EFNB3, a member of the ephrin gene family, is important in brain development as well as in its
maintenance. Moreover, since levels of EFNB3 expression were particularly high in several
forebrain subregions compared to other brain subregions, it may play a pivotal role in forebrain
function. The EPH and EPH-related receptors comprise the largest subfamily of receptor
protein-tyrosine kinases and have been implicated in mediating developmental events, particularly
in the nervous system. EPH Receptors typically have a single kinase domain and an extracellular
region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin ligands and
receptors have been named by the Eph Nomenclature Committee (1997). Based on their structures and
sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to
the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are
transmembrane proteins. The Eph family of receptors are similarly divided into 2 groups based on
the similarity of their extracellular domain sequences and their affinities for binding ephrin-A
and ephrin-B ligands. [provided by RefSeq]

UniProtKB/Swiss-Prot: EFNB3_HUMAN, Q15768
Function: May play a pivotal role in forebrain function. Binds to, and induce the collapse of,
commissural axons/growth cones in vitro. May play a role in constraining the orientation of
longitudinally projecting axons (By similarity)

Gene Wiki entry for EFNB3

(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 EFNB3 gene  

Entrez Gene cytogenetic band: 17p13.1-p11.2   Ensembl cytogenetic band:  17p13.1   HGNC cytogenetic band: 17p13.1

EFNB3 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 17         GeneLoc Exon Structure

GeneLoc location for GC17P007549:     (about GC identifiers)

Start:
7,549,245 bp from pter
End:
7,555,418 bp from pter
Size:
6,174 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000017.9  NT_010718.15  
(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: EFNB3_HUMAN, Q15768 (See protein sequence)
Recommended Name: Ephrin-B3 precursor  
Size: 340 amino acids; 35835 Da
Subunit: Interacts with GRIP1 and GRIP2. Binds to Nipah virus G protein
Subcellular location: Membrane; Single-pass type I membrane protein
Secondary accessions: O00680 Q8TBH7 Q92875

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_001397.1  

    ENSEMBL proteins: 
    ENSP00000226091 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Sigma-Aldrich Proteins for EFNB3  
    R&D Systems Recombinant & Natural Proteins for EFNB3 (Ephrin-B3)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (Ephrin B3)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887 integral to plasma membrane TAS9126477
    GO:0016020 membrane IEA--
    About this table

    Antibodies for EFNB3: 
    Invitrogen Antibodies for EFNB3
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for EFNB3
    R&D Systems Antibodies for EFNB3 (Ephrin-B3)
    Antibodies from Abcam (Ephrin B3), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for EFNB3

    Assays for EFNB3: 
    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:
     IPR001799 Ephrin
     IPR008972 Cupredoxin
     IPR019765 Ephrin_CS


       GeneDecks  EFNB3 for the domains selected above  
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    Graphical View of Domain Structure for InterPro Entry Q15768

    ProtoNet protein and cluster: Q15768

    1 Blocks protein family: IPB001799 Ephrin signature

    UniProtKB/Swiss-Prot: EFNB3_HUMAN, Q15768
    Similarity: Belongs to the ephrin 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 (EFNB3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (EFNB3)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_001406

                  Applied Biosystems Silencer® siRNAs for EFNB3

                  Sigma-Aldrich siRNA and siRNA Panels for EFNB3  
                         Sigma-Aldrich shRNA for EFNB3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for EFNB3
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_001406
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_001406
                                     untagged cDNA clone in CMV expression vector: NM_001406 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_001406

    UniProtKB/Swiss-Prot: EFNB3_HUMAN, Q15768
    Function: May play a pivotal role in forebrain function. Binds to, and induce the collapse of,
    commissural axons/growth cones in vitro. May play a role in constraining the orientation of
    longitudinally projecting axons (By similarity)

    Genatlas biochemistry entry for EFNB3:
    ephrin B-3,eph-related receptor tyrosine kinase,class B,ligand,involved in short-range
    contact-mediated axonal guidance,expressed in fetal brain,and in adult forebrain

    3 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Efnb3):

    behavior/neurologicalnervous systemnormal

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005005 transmembrane-ephrin receptor activity TAS9126477
    GO:0046875 ephrin receptor binding IDA8808709
    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

    1 Invitrogen iPath™ Online BioAtlas - Pathway for EFNB3 (Maps provided by GeneGo):
     Pleckstrin homology proteins interactions. Part V

       GeneDecks  EFNB3 for the pathways selected above  
    About GeneDecksing

    2 Millipore Pathways for EFNB3
     Cytoskeleton remodeling Reverse signaling by ephrin B
     Cell adhesion Ephrins signaling

       GeneDecks  EFNB3 for the pathways selected above  
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    2 Sigma-Aldrich "Your Favorite Gene" Pathways for  EFNB3  (Your Favorite Gene powered by Ingenuity) 
     Ephrin Receptor Signaling
     Axonal Guidance Signaling

       GeneDecks  EFNB3 for the pathways selected above  
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    1 Kegg Pathway  (Kegg details for EFNB3):
     hsa04360 Axon guidance

       GeneDecks  EFNB3 for the pathways selected above  
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     Gene Network CentralTM Interacting Genes and Proteins Network for  EFNB3 


    5/32 Interacting proteins for EFNB3 (ENSP000002260913) via UniProtKB, MINT, and/or STRING (see all 32 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EPHA4ENSP000002818213STRING (score=.998)
    EPHB3ENSP000003321183STRING (score=.992)
    EPHB2ENSP000003637613STRING (score=.984)
    EPHB1ENSP000003541913STRING (score=.982)
    EPHB6ENSP000002228473STRING (score=.977)
    About this table

    5/8 Gene Ontology (GO) biological process terms (links to tree view) (see all 8 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007267 cell-cell signaling TAS9126477
    GO:0007275 multicellular organismal development IEA--
    GO:0007399 nervous system development TAS9126477
    GO:0007628 adult walking behavior IEA--
    GO:0016198 axon choice point recognition IEA--
    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 EFNB3
    1 Novoseek chemical compound relationship for EFNB3 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    tyrosine 36.66 5 15720813 (1), 9126477 (1), 16951161 (1)
    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 (EFNB3)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (EFNB3)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_001406

                  Sigma-Aldrich siRNA and siRNA Panels for EFNB3  
                         Sigma-Aldrich shRNA for EFNB3  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_001406  

    REFSEQ mRNAs for EFNB3 gene: 

    NM_001406.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_001406  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_001406
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_001406
                                     untagged cDNA clone in CMV expression vector: NM_001406 

    Additional cDNA sequence: 

    AK027329.1 AK314841.1 BC022499.1 BC042944.2 U57001.1 

    6 DOTS entries:

    DT.100813533  DT.445474  DT.91680350  DT.100813537  DT.120949968  DT.120950010 

    24/67 AceView cDNA sequences (see all 67 ):

    AA973977 BU859261 BU557245 BM974629 AI088793 NM_001406 BU854800 BI913360 
    BU554039 AA417565 BI488464 AA932672 AA291485 BU685648 BG751869 BC042944 
    BX352973 BM971890 AI350400 AW303554 F01548 T09017 AA055762 BG701666 

    highest scoring ESTs for EFNB3:

    AA055762 AA219737 AA291485 AA404693 AA417565 AA417681 AA485665 AA485795 AA875969 AA973977 

    Unigene Cluster for EFNB3:

    Ephrin-B3
    Hs.26988  [show with all ESTs]
    Unigene Representative Sequence: NM_001406


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000226091  
    (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

    EFNB3 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for EFNB3

    1 / 2 / 3

    5 probe-sets matching EFNB3 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    469_at2, 3 U95-A 2 1.00 0.97 1.00 1.00 U66406 0.80 1.00 0.91 1

    210883_x_at2, 3 U133-A 1 1.00 1.00 -- -- U57001 0.80 1.00 0.91 1

    205031_at2, 3 U133-A 1 1.00 1.00 -- -- NM_001406 0.60 1.00 0.82 1

    210883_x_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    205031_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  EFNB3 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: GTGGCGGGAT

    SOURCE GeneReport for Unigene cluster: Hs.26988

    Expression variation in blood from EXPOLDB for EFNB3

    UniProtKB/Swiss-Prot: EFNB3_HUMAN, Q15768
    Tissue specificity: Highly expressed in brain; expressed in embryonic floor plate, roof plate and
    hindbrain segments

    (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 EFNB3 gene from 5/7 species (see all 7 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    EFNB31   -- ephrin-B3 93.61(n)
    97.01(a)
    607903  XM_844752.1  XP_849845.1 
    chimpanzee
    (Pan troglodytes)
    EFNB31   -- ephrin-B3 99.65(n)
    100(a)
    750632  XM_001174846.1  XP_001174846.1 
    cow
    (Bos taurus)
    EFNB31   -- ephrin-B3 94.71(n)
    96.76(a)
    617714  XM_870023.2  XP_875116.1 
    rat
    (Rattus norvegicus)
    Efnb31   -- ephrin B3 93.43(n)
    96.76(a)
    360546  XM_340824.3  XP_340825.1 
    mouse
    (Mus musculus)
    Efnb31, 5 11 (40.00 cM)5
    ephrin B31, 5 91.96(n)1
    95.59(a)1
    136431  NM_007911.41  NP_031937.11 
     AF0252885  AK0483055  (see all 13)
    About this table        Species with no ortholog for EFNB3

    ENSEMBL Gene Tree for EFNB3
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for EFNB3 gene
    EFNB12  EFNB22  

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


    10/21 NCBI SNPs in EFNB3 are shown (see all 21 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 47)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 17 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs71411,2
    A,C,F,H7555326(+) GCGGGA/GTATGC 1 -- ut31 ese315Minor allele frequency- N:0.00MN EA NA EU WA 2890
    rs37442621,2
    A,C,F,H7554490(-) CTGTCC/TGGGCC 1 -- ut31 ese310Minor allele frequency- T:0.40EA MN CSAM EU WA 2288
    rs37442631,2
    C,F,H7554433(-) CATTCG/AGCATC 1 -- ut31 ese313Minor allele frequency- A:0.46EA NA MN CSAM EU 2190
    rs129419811,2
    C,F,H7549187(+) CCCTCC/AACCAT 1 -- ng51 trp34Minor allele frequency- A:0.15EU EA WA 352
    rs37442641,2
    F7553972(-) GGCGGT/CGCCAA 1 -- ut311Minor allele frequency- C:0.03EA 1474
    rs124510951,2
    H7552850(+) CCTGCC/AGTCAC 1 -- int14Minor allele frequency- A:0.00EU EA WA 418
    --
    rs99123341,2
    --7548200(+) GGGTGA/GGGGAC 1 -- ng510--------
    --
    rs32105531,2
    --7555416(+) gttgaA/Caaaaa 1 -- ut310--------
    --
    rs713879901,2
    --7548233(+) CTCCT-/CCCCTC 1 -- ng510--------
    --
    rs80722351,2
    --7549170(+) CTCCAA/GCTCCG 1 -- ng510--------
    About this table

    HapMap Linkage Disequilibrium images for EFNB3 (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: 602297

    3 Novoseek disease relationships for EFNB3 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    brain tumors 31.03 2 16596216 (1)
    glioma 26.17 4 16951161 (3), 15720813 (1)
    tumors 16.55 8 10984508 (1), 16596216 (1), 16951161 (1), 12695554 (1) (see all 5)
    About this table

    Human Genome Epidemiology Navigator: EFNB3 (1 document)

    (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

    10/39 PubMed articles for EFNB3 gene (see all 39 ):
    (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: 1949 HGNC: 3228 AceView: EFNB3 Ensembl:ENSG00000108947 euGenes: HUgn1949
    ECgene: EFNB3 H-InvDB: EFNB3
    (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

      --
    (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 EFNB3:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for EFNB3 Antibodies for EFNB3
     Explore super-pooled esiRNAs Proteins for EFNB3
     Lentivirus-delivered shRNAs for EFNB3 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Search OriGene for EFNB3
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     Search Novus for antibodies for EFNB3

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