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YBX2 Gene

protein-coding   GIFtS: 54

GC17M007132
Y box binding protein 2
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
CONTRIN 2
CSDA3 1, 2, 3
Contrin 3
DBPC 2
Dbpc 3
MGC45104 2
MSY2 1, 2, 3
Descriptions
DNA-binding protein C 3
Germ cell-specific Y-box-binding protein 3
MSY2 homolog 3
Y box binding protein 2 2
germ cell specific Y-box binding protein 2
External Ids
HGNC: 179481
Entrez Gene: 510872
UniProtKB: Q9Y2T73
Ensembl: ENSG000000060477
Search outside databases for aliases for YBX2 gene

Previous GC identifers: GC17M007549 GC17M007921 GC17M007134 GC17M007392

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

EntrezGene summary for YBX2:
YBX2 is a germ-cell specific member of the vertebrate Y box family of nucleic acid-binding proteins
(Gu et al., 1998 [PubMed 9780336]; Tekur et al., 1999 [PubMed 10100484]).[supplied by OMIM]

UniProtKB/Swiss-Prot: YBOX2_HUMAN, Q9Y2T7
Function: Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the
regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus
promoter element. Binds to full length mRNA with high affinity in a sequence-independent manner.
Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and
limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic
retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for
cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By
similarity)

Gene Wiki entry for YBX2

(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 YBX2 gene  

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

YBX2 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 GC17M007132:     (about GC identifiers)

Start:
7,132,295 bp from pter
End:
7,138,600 bp from pter
Size:
6,306 bases
Orientation:
minus 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: YBOX2_HUMAN, Q9Y2T7 (See protein sequence)
Recommended Name: Y-box-binding protein 2  
Size: 364 amino acids; 38518 Da
Subunit: Found in a mRNP complex with PABPC1 and CSDA (By similarity)
Subcellular location: Cytoplasm. Nucleus
Secondary accessions: Q8N4P0

Post-translational modifications:

  • Phosphorylated during oocyte maturation and dephosphorylated following egg activation.
    Phosphorylated in vitro by a kinase activity associated with testicular mRNPs. Dephosphorylation
    leads to a decrease in its affinity to bind RNA in vitro (By similarity)1


  • REFSEQ proteins: NP_057066.2  

    ENSEMBL proteins: 
    ENSP00000007699 


    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 (MSY2/YBOX2)
    Human Recombinant Proteins from Abnova (YBX2)
                    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:0005634 nucleus TAS10100484
    GO:0005737 cytoplasm TAS10100484
    About this table

    Antibodies for YBX2: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for YBX2
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (MSY2/YBOX2), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (YBX2)
    Novus Biologicals Antibody for YBX2

    Assays for YBX2: 
    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

    4 InterPro domains/families:
     IPR019844 Cold-shock_conserved_site
     IPR012340 NA-bd_OB-fold
     IPR011129 Cold_shock_prot
     IPR002059 CSP_DNA_bd


       GeneDecks  YBX2 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9Y2T7

    ProtoNet protein and cluster: Q9Y2T7

    2 Blocks protein families:
    IPB002059 Cold-shock DNA-binding domain
    IPB011129 Cold shock protein


    UniProtKB/Swiss-Prot: YBOX2_HUMAN, Q9Y2T7
    Similarity: Contains 1 CSD (cold-shock) domain

    (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 (YBX2)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (YBX2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015982

                  Applied Biosystems Silencer® siRNAs for YBX2

                  Sigma-Aldrich siRNA for YBX2  
                         Sigma-Aldrich shRNA for YBX2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for YBX2
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_015982
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_015982
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_015982 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_015982

    UniProtKB/Swiss-Prot: YBOX2_HUMAN, Q9Y2T7
    Function: Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the
    regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus
    promoter element. Binds to full length mRNA with high affinity in a sequence-independent manner.
    Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and
    limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic
    retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for
    cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By
    similarity)

    2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Ybx2):

    endocrine/exocrine glandreproductive system

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677 DNA binding IEA--
    GO:0003723 RNA 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



    4 Interacting proteins for YBX2 (ENSP000000076993) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SOHLH1ENSP000002984663STRING (score=.877)
    FIGLAENSP000003330973STRING (score=.868)
    PRM1ENSP000003105153STRING (score=.712)
    --ENSP000003739763STRING (score=.83)
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    GO:0006366 transcription from RNA polymerase II promoter TAS10100484
    GO:0007283 spermatogenesis TAS10100484
    GO:0009386 translational attenuation TAS10100484
    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 YBX2

    (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 (YBX2)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (YBX2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015982

                  Sigma-Aldrich siRNA for YBX2  
                         Sigma-Aldrich shRNA for YBX2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_015982  

    REFSEQ mRNAs for YBX2 gene: 

    NM_015982.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_015982  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_015982
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_015982
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_015982 

    Additional cDNA sequence: 

    AF096834.1 AK092747.1 AK315035.1 BC033800.1 BC047760.1 CR617829.1 

    10 DOTS entries:

    DT.424114  DT.75168027  DT.91683704  DT.100738000  DT.120957950  DT.75102929  DT.95151293  DT.409394 
    DT.91975859  DT.95218133 

    24/85 AceView cDNA sequences (see all 85 ):

    AL041670 BC047760 AI653298 CD359924 BC033800 BM772139 AA383400 AI805280 
    AK092747 CB268201 AI203057 AI968077 CR617829 BM553247 AL041569 AA883961 
    AL042395 AA579771 BM854748 BM563498 AI738586 AA504349 NM_015982 AW273185 

    highest scoring ESTs for YBX2:

    AF096834 AL042395 BC033800 BC047760 BI825507 BI825872 BI826336 BI828225 BI828701 BI829851 

    Unigene Cluster for YBX2:

    Y box binding protein 2
    Hs.567494  [show with all ESTs]
    Unigene Representative Sequence: AK092747


    GeneLoc Exon Structure

    1 Ensembl transcript including schematic representation:
    ENST00000007699  
    (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

    YBX2 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for YBX2

    1 / 2 / 3

    4 probe-sets matching YBX2 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    52203_s_at2, 3 U95-B 1 1.00 1.00 0.87 1.43 AI968077 0.60 1.00 0.82 1

    59991_at2, 3 U95-C 1 1.00 1.00 0.89 0.58 AL042395 0.80 1.00 0.91 1

    219704_at2, 3 U133-A 1 1.00 1.00 -- -- NM_015982 0.60 1.00 0.82 1

    219704_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TGCCACCTGA

    SOURCE GeneReport for Unigene cluster: Hs.567494

    UniProtKB/Swiss-Prot: YBOX2_HUMAN, Q9Y2T7
    Tissue specificity: Expressed in oocytes and testicular germ cells in the stage of spermatogonia to
    spermatocyte. Also observed placental trophoblasts, as well as in vascular smooth muscle cells in
    the pulmonary artery, myocardium, and skeletal muscle. Undetectable in epithelial cells in
    respiratory, gastrointestinal, and urogenital tracts. Up-regulated in various carcinomas and germ
    cell tumors (at protein level)

    (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 YBX2 gene from 5/7 species (see all 7 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    YBX21   -- Y box binding protein 2 89.6(n)
    91.92(a)
    489467  XM_546585.2  XP_546585.1 
    chimpanzee
    (Pan troglodytes)
    YBX21   -- Y box binding protein 2 99.27(n)
    98.9(a)
    455231  XM_511973.2  XP_511973.2 
    cow
    (Bos taurus)
    YBX21   -- Y box binding protein 2 90.69(n)
    91.06(a)
    614429  XM_865925.2  XP_871018.1 
    rat
    (Rattus norvegicus)
    Ybx21   -- Y box binding protein 2 90.6(n)
    91.62(a)
    303250  XM_220618.4  XP_220618.3 
    mouse
    (Mus musculus)
    Ybx21, 5 115
    Y box protein 21, 5 90.32(n)1
    91.62(a)1
    534221  NM_016875.21  NP_058571.21 
     AF0739545  AF0739555  (see all 12)
    About this table        Species with no ortholog for YBX2

    ENSEMBL Gene Tree for YBX2
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for YBX2 gene
    CSDA2  YBX12  

    Pseudogenes
    1 related pseudogene


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


    10/36 NCBI SNPs in YBX2 are shown (see all 36 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 49)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 17 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs2228421,2
    A,C,F,H7132815(+) GTCCTC/TTGAGT 1 -- ut31 ese37Minor allele frequency- T:0.35EA EU WA NA 2072
    --
    rs2228591,2
    C,F,H7138518(+) tagccA/Cccgct 1 G/V mis12Minor allele frequency- C:0.09EU WA 240
    --
    rs47963941,2
    A,C7139385(+) cgctaC/Taacct 1 -- ng310--------
    --
    rs47962991,2
    A7139565(+) CGCCCA/GGGCTG 1 -- ng310--------
    --
    rs80695331,2
    A7138357(+) GCGGGA/GGCCCG 1 S/P mis1 ese30--------
    rs37444051,2
    A,C,F,H7133979(+) GGAAGG/AGGAAG 1 -- int1 trp39Minor allele frequency- A:0.34EA EU WA 2298
    rs2228381,2
    A,C,F,H7134172(+) GCCAGA/GTTATC 1 -- int18Minor allele frequency- G:0.43EA NA EU WA 546
    rs16343821,2
    A,C,F7134985(+) CTAGCA/GTTAAG 1 -- int11Minor allele frequency- G:0.32EA 1116
    rs2228401,2
    A,C7133407(+) GGAGGC/GGGCAC 1 -- int10--------
    --
    rs19103231,2
    A,C7133420(-) ACCCCC/TCTGGC 1 -- int10--------
    About this table

    HapMap Linkage Disequilibrium images for YBX2 (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: 611447

    1 Novoseek disease relationship for YBX2 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    shock 35.09 1 9155152 (1)
    About this table

    Human Gene Mutation Database: YBX2
    Human Genome Epidemiology Navigator: YBX2 (2 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

    10/12 PubMed articles for YBX2 gene (see all 12 ):
    (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: 51087 HGNC: 17948 AceView: YBX2 Ensembl:ENSG00000006047 euGenes: HUgn51087
    ECgene: YBX2 H-InvDB: YBX2
    (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 YBX2:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Millipore Custom Antibody & Bulk Services
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     Predesigned and custom siRNAs for YBX2 Antibodies for YBX2
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for YBX2 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Antibodies for YBX2

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