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YBX1 Gene

protein-coding   GIFtS: 58
GCID: GC01P043148

Y Box Binding Protein 1

(Previous name: nuclease sensitive element binding protein 1)
(Previous symbol: NSEP1)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Y Box Binding Protein 11 2     DNA-Binding Protein B2 3
NSEP11 2 3 5     Y-Box Transcription Factor2 3
DBPB2 3 5     Y-Box-Binding Protein 12 3
YB12 3 5     BP-82
Nuclease Sensitive Element Binding Protein 11 2     CSDA22
Enhancer Factor I Subunit A2 3     CSDB2
CBF-A2 3     MDR-NF12
EFI-A2 3     NSEP-12
YB-12 3     Major Histocompatibility Complex, Class II, Y Box-Binding Protein I2
CCAAT-Binding Transcription Factor I Subunit A2 3     Nuclease-Sensitive Element-Binding Protein 12

External Ids:    HGNC: 80141   Entrez Gene: 49042   Ensembl: ENSG000000659787   OMIM: 1540305   UniProtKB: P678093   

Export aliases for YBX1 gene to outside databases

Previous GC identifers: GC01P042818 GC01P042920 GC01P041268


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for YBX1 Gene:
YBX1 (Y box binding protein 1) is a protein-coding gene. GO annotations related to this gene include double-stranded DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is YBX3.

UniProtKB/Swiss-Prot: YBOX1_HUMAN, P67809
Function: Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates
splice site selection. Binds and stabilizes cytoplasmic mRNA. Contributes to the regulation of translation by
modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Regulates the
transcription of numerous genes. Its transcriptional activity on the multidrug resistance gene MDR1 is enhanced
in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box
(5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain
mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into
double-stranded DNA (in vitro). May play a role in DNA repair. Component of the CRD-mediated complex that
promotes MYC mRNA stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro
Function: The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation

Gene Wiki entry for YBX1 (Y box binding protein 1) Gene


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the YBX1 gene promoter:
         Max1   NF-1   AP-1   ATF-2   LCR-F1   YY1   FAC1   c-Jun   NF-Y   CBF(2)   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for YBX1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YBX1


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

Entrez Gene cytogenetic band: 1p34   Ensembl cytogenetic band:  1p34.2   HGNC cytogenetic band: 1p34

YBX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YBX1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P043148:  view genomic region     (about GC identifiers)

Start:
43,148,066 bp from pter      End:
43,168,020 bp from pter
Size:
19,955 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: YBOX1_HUMAN, P67809 (See protein sequence)
Recommended Name: Nuclease-sensitive element-binding protein 1  
Size: 324 amino acids; 35924 Da
Subunit: Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1
(By similarity). Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU,
IGF2BP1, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs.
Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Interacts with IGF2BP1 and RBBP6.
Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs). Interacts with AKT1, MBNL1, SFRS9,
ALYREF/THOC4, MSH2, XRCC5, WRN and NCL. Can bind to DNA as a homomeric form, (EFI-A)n or as a heteromeric form in
association with EFI-B. Homodimer in the presence of ATP. Interacts (via C-terminus) with APEX1 (via N-terminus);
the interaction is increased with APEX1 acetylated at 'Lys-6' and 'Lys-7'. Interacts with AGO1 and AGO2.
Interacts with ANKRD2
Sequence caution: Sequence=AAA35750.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=AAA59949.1; Type=Frameshift; Positions=Several; Sequence=AAA61308.1; Type=Frameshift; Positions=314;
1 PDB 3D structure from and Proteopedia for YBX1:
1H95 (3D)    
Secondary accessions: P16990 P16991 Q14972 Q15325 Q5FVF0

Explore the universe of human proteins at neXtProt for YBX1: NX_P67809

Explore proteomics data for YBX1 at MOPED

Post-translational modifications: 

  • Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability1
  • In the absence of phosphorylation the protein is retained in the cytoplasm1
  • Cleaved by a 20S proteasomal protease in response to agents that damage DNA. Cleavage takes place in the absence
    of ubiquitination and ATP. The resulting N-terminal fragment accumulates in the nucleus (By similarity)1
  • Ubiquitination2 at Lys64, Lys81, Lys92, Lys93, Lys137, Lys170, Lys264
  • Modification sites at PhosphoSitePlus

  • See YBX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004550.2  
    ENSEMBL proteins: 
     ENSP00000361626   ENSP00000405937   ENSP00000389639  
    Reactome Protein details: P67809

    YBX1 Human Recombinant Protein Products:

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    OriGene Purified Protein for YBX1
    OriGene Protein Over-expression Lysate for YBX1
    OriGene Custom MassSpec
    OriGene Custom Protein Services for YBX1
    GenScript Custom Purified and Recombinant Proteins Services for YBX1
    Novus Biologicals YBX1 Proteins
    Novus Biologicals YBX1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for YBX1

     
    Search eBioscience for Proteins for YBX1 

    YBX1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of YBX1
    Browse R&D Systems for Antibodies
    Cell Signaling Technology (CST) Antibodies for YBX1  (YB-1)
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    Novus Biologicals YBX1 Antibodies
    Abcam antibodies for YBX1
    Cloud-Clone Corp. Antibodies for YBX1
    ThermoFisher Antibodies for YBX1
    LSBio Antibodies in human, mouse, rat for YBX1

    YBX1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for YBX1
    Cell Signaling Technology (CST) Sandwich ELISA Kits for YBX1 (YB-1)
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for YBX1
    Cloud-Clone Corp. CLIAs for YBX1
    Search eBioscience for ELISAs for YBX1 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR019844 Cold-shock_CS
     IPR012340 NA-bd_OB-fold
     IPR011129 Cold_shock_prot
     IPR002059 CSP_DNA-bd

    Graphical View of Domain Structure for InterPro Entry P67809

    ProtoNet protein and cluster: P67809

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


    UniProtKB/Swiss-Prot: YBOX1_HUMAN, P67809
    Similarity: Contains 1 CSD (cold-shock) domain


    Find genes that share domains with YBX1           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: YBOX1_HUMAN, P67809
    Function: Mediates pre-mRNA alternative splicing regulation. Binds to splice sites in pre-mRNA and regulates
    splice site selection. Binds and stabilizes cytoplasmic mRNA. Contributes to the regulation of translation by
    modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Regulates the
    transcription of numerous genes. Its transcriptional activity on the multidrug resistance gene MDR1 is enhanced
    in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box
    (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain
    mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into
    double-stranded DNA (in vitro). May play a role in DNA repair. Component of the CRD-mediated complex that
    promotes MYC mRNA stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro
    Function: The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation

         Gene Ontology (GO): Selected molecular function terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding TAS2977358
    GO:0003690double-stranded DNA binding TAS1738588
    GO:0003697single-stranded DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS3174636
         
    Find genes that share ontologies with YBX1           About GenesLikeMe


    Phenotypes:
         13 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Ybx1):
     cardiovascular system  cellular  craniofacial  embryogenesis  growth/size/body 
     hematopoietic system  homeostasis/metabolism  integument  liver/biliary system  mortality/aging 
     nervous system  respiratory system  skeleton 

    Find genes that share phenotypes with YBX1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for YBX1: Ybx1tm1Ley Ybx1tm1Tuch

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for YBX1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for YBX1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for YBX1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for YBX1

    Transcription Factor Targeting: 
    Selected GeneGlobe predicted Target genes for YBX1 (see all 427):
    AASS,  ABI3,  ACADSB,  ACSL3,  ADNP2,  ADORA2B,  ADRA2B,  AGBL5,  AGPAT5,  AKAP9

    miRNA
    Products:
        
    miRTarBase miRNAs that target YBX1:
    hsa-mir-605-5p (MIRT040476), hsa-mir-34a-5p (MIRT047343), hsa-mir-744-5p (MIRT037523), hsa-mir-1296-5p (MIRT036078), hsa-mir-16-5p (MIRT031527), hsa-mir-25-3p (MIRT050297), hsa-mir-106b-5p (MIRT044272), hsa-mir-935 (MIRT036695), hsa-mir-615-3p (MIRT039737), hsa-mir-484 (MIRT041860), hsa-mir-20a-5p (MIRT050595), hsa-mir-149-5p (MIRT045400), hsa-mir-137 (MIRT007092), hsa-mir-1307-3p (MIRT035821), hsa-mir-124-3p (MIRT022450), hsa-mir-1292-5p (MIRT035829)

    Block miRNA regulation of human, mouse, rat YBX1 using miScript Target Protectors
    6 qRT-PCR Assays for microRNAs that regulate YBX1:
    hsa-miR-548d-3p hsa-miR-3168 hsa-miR-137 hsa-miR-3662 hsa-miR-2116 hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidYBX1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for YBX1
    Predesigned siRNA for gene silencing in human, mouse, rat YBX1

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for YBX1

    Clone
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    OriGene clones in human, mouse for YBX1 (see all 7)
    OriGene ORF clones in mouse, rat for YBX1
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    GenScript: all cDNA clones in your preferred vector: YBX1 (NM_004559)
    Sino Biological Human cDNA Clone for YBX1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for YBX1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YBX1
    Addgene plasmids for YBX1 

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    Browse ESI BIO Cell Lines and PureStem Progenitors for YBX1 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YBX1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    YBOX1_HUMAN, P67809: Cytoplasm. Nucleus. Cytoplasmic granule. Secreted. Note=Localized in cytoplasmic mRNP
    granules containing untranslated mRNAs. Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in
    proliferating cells. Cytotoxic stress and DNA damage enhance translocation to the nucleus. Localized with DDX1,
    MBNL1 and TIAL1 in stress granules upon stress. Secreted by mesangial and monocytic cells after inflammatory
    challenges. Translocates from the cytoplasm to the nucleus after and colocalizes with APEX1 in nuclear speckles
    after genotoxic stress
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    nucleus5
    cytosol3
    cytoskeleton1

    Gene Ontology (GO): Selected cellular component terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus TAS3174636
    GO:0005654nucleoplasm TAS--
    GO:0005689U12-type spliceosomal complex IDA15146077
    GO:0005737cytoplasm IDA--
    GO:0010494cytoplasmic stress granule IDA18335541

    Find genes that share ontologies with YBX1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for YBX1 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA Splicing - Major Pathway0.78
    mRNA Splicing0.78
    Processing of Capped Intron-Containing Pre-mRNA0.78
    mRNA processing0.44
    2Gene Expression
    Gene Expression0.40
    3Translational Control
    Translational Control
    4Signaling events mediated by PTP1B
    Signaling events mediated by PTP1B
    5SIDS Susceptibility Pathways
    SIDS Susceptibility Pathways


    Find genes that share SuperPaths with YBX1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 Cell Signaling Technology (CST) Pathways for YBX1
        Translational Control
    PI3K / Akt Signaling

    4 BioSystems Pathways for YBX1
        mRNA processing
    SIDS Susceptibility Pathways
    BDNF signaling pathway
    Signaling events mediated by PTP1B


    1 Reactome Pathway for YBX1
        mRNA Splicing - Major Pathway


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for YBX1
    Interactions:

        GeneGlobe Interaction Network for YBX1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for YBX1 (P678091, 2, 3 ENSP000003616264) via UniProtKB, MINT, STRING, and/or I2D (see all 392)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FBXO33Q7Z6M21, 2, 3, ENSP000002980974EBI-354065,EBI-8555452 MINT-2831655 MINT-2831487 MINT-2831514 MINT-2831737 MINT-2831765 I2D: score=2 STRING: ENSP00000298097
    PITX2Q996971, 2, 3, ENSP000003041694EBI-354065,EBI-1175211 MINT-6823857 MINT-6823877 MINT-6823902 I2D: score=1 STRING: ENSP00000304169
    GSK3BP498412, 3, ENSP000003248064MINT-65983 MINT-65986 I2D: score=3 STRING: ENSP00000324806
    HNRNPKP619782, 3, ENSP000003654394MINT-6823857 MINT-6823877 I2D: score=3 STRING: ENSP00000365439
    MAPK1P284822, 3, ENSP000002158324MINT-65982 MINT-65987 I2D: score=3 STRING: ENSP00000215832
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0000398mRNA splicing, via spliceosome TAS--
    GO:0001701in utero embryonic development IEA--
    GO:0006355regulation of transcription, DNA-templated IDA18809583
    GO:0006366transcription from RNA polymerase II promoter TAS3174636

    Find genes that share ontologies with YBX1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for YBX1 (YBOX1)

    Selected Novoseek inferred chemical compound relationships for YBX1 gene (see all 21)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    dbpa 87.8 31 7651426 (6), 16243807 (4), 7628487 (3), 1923758 (3) (see all 10)
    cisplatin 41.8 49 18571458 (7), 12458343 (6), 18307537 (5), 12080043 (3) (see all 12)
    selenocysteine 39.8 6 9488664 (3), 10760958 (1)
    etoposide 32.8 2 17266041 (1), 9155152 (1)
    agar 28.4 8 15806160 (1), 19284373 (1), 19996271 (1), 18974106 (1) (see all 5)
    camptothecin 24.5 2 9155152 (1), 18307537 (1)
    doxorubicin 18.6 1 9155152 (1)
    5fluorouracil 17.5 5 15750632 (3), 15703814 (1)
    vegf 16.2 4 16198352 (1), 16497437 (1), 17021746 (1)
    estrogen 15.1 6 18925950 (2), 18773210 (1), 20397575 (1), 15703814 (1) (see all 5)



    Find genes that share compounds with YBX1           About GenesLikeMe



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for YBX1 gene: 
    NM_004559.3  

    Unigene Cluster for YBX1:

    Y box binding protein 1
    Hs.473583  [show with all ESTs]
    Unigene Representative Sequence: BM907843
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000321358(uc001chs.3) ENST00000332220 ENST00000436427 ENST00000467957

    miRNA
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    6 qRT-PCR Assays for microRNAs that regulate YBX1:
    hsa-miR-548d-3p hsa-miR-3168 hsa-miR-137 hsa-miR-3662 hsa-miR-2116 hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidYBX1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat YBX1
    Clone
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    GenScript: all cDNA clones in your preferred vector: YBX1 (NM_004559)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for YBX1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YBX1
    Addgene plasmids for YBX1 
    Primer
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    OriGene qPCR primer pairs and template standards for YBX1
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat YBX1
      QuantiTect SYBR Green Assays in human, mouse, rat YBX1
      QuantiFast Probe-based Assays in human, mouse, rat YBX1

    Additional mRNA sequence: 

    AK309996.1 AK311708.1 BC000064.2 BC002411.2 BC013838.1 BC015208.1 BC018393.1 BC020164.1 
    BC038384.1 BC065571.1 BC070084.1 BC071708.1 BC072014.1 BC090038.1 BC098435.1 BC106045.1 
    J03827.1 L28809.1 Z70765.1 

    Selected DOTS entries (see all 79):

    DT.100710168  DT.100710149  DT.100875861  DT.97852954  DT.95313664  DT.95145401  DT.100710140  DT.91859349 
    DT.100710152  DT.100710161  DT.92051921  DT.100710159  DT.100060016  DT.91679588  DT.100848665  DT.121441173 
    DT.91959645  DT.100060019  DT.121441020  DT.100060018  DT.102825761  DT.121441112  DT.92464131  DT.100856136 

    Selected AceView cDNA sequences (see all 1998):

    BQ925361 BU956506 BU507912 BE046834 BU682383 BQ921784 CR609077 AI905848 
    BQ671834 BQ223674 CR595367 AI678502 AW243927 BG576562 AI274447 CA424023 
    CD364482 BM848836 BM470028 BQ898662 BM763503 CB215189 BM994309 BQ719868 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    YBX1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGTTTTTAT
    YBX1 Expression
    About this image


    YBX1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 18) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Colon (Gastrointestinal Tract)
     
     Uterus (Reproductive System)
    YBX1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    YBX1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.473583
        Custom PCR Arrays for YBX1
    Primer
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    OriGene qPCR primer pairs and template standards for YBX1
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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for YBX1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ybx11 , 5 Y box protein 11, 5 96.48(n)1
    99.07(a)1
      4 (55.34 cM)5
    226081  NM_011732.21  NP_035862.21 
     1192779815 
    chicken
    (Gallus gallus)
    Aves YBX16
    Gallus gallus Y box binding protein 1 (YBX1), mRNA...
    95(a)
    1 ↔ 1
    21(6384970-6392015)
    African clawed frog
    (Xenopus laevis)
    Amphibia nsep1-prov2 nuclease sensitive element binding protein 1 85.34(n)    BC042217.1 
    zebrafish
    (Danio rerio)
    Actinopterygii nsep12 nuclease sensitive element binding protein 1 81.53(n)   58144  BC050156.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta yps6
    ypsilon schachtel
    39(a)
    1 → many
    3L(12114374-12118250)
    worm
    (Caenorhabditis elegans)
    Secernentea cey-16
    cey-46
    (see all 4)
    Protein CEY-4 (cey-4) mRNA, complete cds
    (see all 4)
    45(a)
    34(a)
    (see all 4)
    many ↔ many
    many ↔ many
    (see all 4)
    II(11039449-11041206) WBGene00000472
    III(10866946-10868727) WBGene00000475


    ENSEMBL Gene Tree for YBX1 (if available)
    TreeFam Gene Tree for YBX1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for YBX1 gene
    YBX32  YBX22  
    3 SIMAP similar genes for YBX1 using alignment to 6 protein entries:     YBOX1_HUMAN (see all proteins):
    YB-1    YBX3    YBX2

    Find genes that share paralogs with YBX1           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for YBX1 (see all 9)
    PGOHUM00000247142 PGOHUM00000240350 PGOHUM00000241021 PGOHUM00000238138 PGOHUM00000250901


    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for YBX1 (see all 468)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1884025281,2
    --43146081(+) TATCCA/TGCAGC 1 -- us2k10--------
    rs66594001,2
    C,F,H--43146208(+) GTAATG/AGTAGT 1 -- us2k121Minor allele frequency- A:0.27NS EA NA WA CSA 939
    rs1930131661,2
    --43146210(+) AATAGC/TAGTCA 1 -- us2k10--------
    rs1409993711,2
    --43146254(+) AGATAA/GATGTT 1 -- us2k10--------
    rs1450404461,2
    --43146283(+) CTGTTC/GTGGTG 1 -- us2k10--------
    rs1401196521,2
    C--43146354(+) ATGCT-/AGGGGT 1 -- us2k10--------
    rs1851492121,2
    --43146436(+) GTTGAA/GAATAT 1 -- us2k10--------
    rs1887000631,2
    --43146493(+) AACCTG/TAGTAG 1 -- us2k10--------
    rs1916137381,2
    C--43146547(+) TTTGGC/TTCTCA 1 -- us2k10--------
    rs1388145281,2
    --43146590(+) ATTGGC/TGATGA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for YBX1 (43148066 - 43168020 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for YBX1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv829682CNV Loss17160897

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing YBX1
    DNA2.0 Custom Variant and Variant Library Synthesis for YBX1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 154030    OMIM disorders: --

    2 diseases from the University of Copenhagen DISEASES database for YBX1:
    Breast cancer     Sarcoma

    Find genes that share disorders with YBX1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for YBX1 gene (see all 28)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    breast cancer 46.3 101 19284373 (6), 18925950 (6), 18974106 (5), 19930682 (5) (see all 31)
    shock 45 21 11069676 (2), 9409758 (1), 15494450 (1), 18224398 (1) (see all 18)
    tumors 42.1 126 16489918 (5), 10357417 (5), 19517610 (4), 18974106 (4) (see all 50)
    cancer 33.6 45 20079629 (4), 17418094 (4), 18773210 (4), 18172301 (2) (see all 23)
    aggressiveness 28.8 9 15703814 (2), 15735691 (1), 19411069 (1), 19901122 (1) (see all 5)
    ovarian cancer 23.9 14 12458343 (4), 17072343 (3), 16964697 (2), 17459055 (1) (see all 7)
    nsclc 18.1 23 11595709 (5), 16101161 (4), 19648825 (3), 14738225 (2) (see all 5)
    glioblastoma 17.4 3 16409125 (2), 17401009 (1)
    liposarcoma 16.2 1 12168660 (1)
    breast carcinoma 13.2 4 15899797 (1), 19713745 (1), 12565174 (1), 19411069 (1)


    Export disorders for YBX1 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)
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    PubMed articles for YBX1 gene, integrated from 10 sources (see all 375):
    (articles sorted by number of sources associating them with YBX1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein. (PubMed id 1891370)1, 2, 3 Kolluri R. and Kinniburgh A.J. (Nucleic Acids Res. 1991)
    2. Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box. (PubMed id 3174636)1, 2, 3 Didier D.K.... Schwartz B.D. (Proc. Natl. Acad. Sci. U.S.A. 1988)
    3. Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection. (PubMed id 12604611)1, 2, 9 Raffetseder U.... Mertens P.R. (J. Biol. Chem. 2003)
    4. YB-1 promotes strand separation in vitro of duplex DNA containing either mispaired bases or cisplatin modifications, exhibits endonucleolytic activities and binds several DNA repair proteins. (PubMed id 14718551)1, 2, 9 Gaudreault I.... Lebel M. (Nucleic Acids Res. 2004)
    5. Y-box protein-1 is actively secreted through a non-classical pathway and acts as an extracellular mitogen. (PubMed id 19483673)1, 2, 9 Frye B.C.... Mertens P.R. (EMBO Rep. 2009)
    6. Akt phosphorylates the Y-box binding protein 1 at Ser102 located in the cold shock domain and affects the anchorage-independent growth of breast cancer cells. (PubMed id 15806160)1, 2, 9 Sutherland B.W.... Dunn S.E. (Oncogene 2005)
    7. Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA stabilization during T-cell activation. (PubMed id 10817758)1, 2, 9 Chen C.-Y.... Karin M. (Genes Dev. 2000)
    8. The Ankrd2 protein, a link between the sarcomere and the nucleus in skeletal muscle. (PubMed id 15136035)1, 2, 9 Kojic S....Faulkner G. (J. Mol. Biol. 2004)
    9. A human protein containing a 'cold shock' domain binds specifically to H-DNA upstream from the human gamma-globin genes. (PubMed id 8188694)1, 2, 9 Horwitz E.M.... Ley T.J. (J. Biol. Chem. 1994)
    10. Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic RNPs. (PubMed id 19029303)1, 2 Weidensdorfer D.... Huettelmaiery S. (RNA 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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)
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    Entrez Gene: 4904 HGNC: 8014 AceView: NSEP1 Ensembl:ENSG00000065978 euGenes: HUgn4904
    ECgene: YBX1 H-InvDB: YBX1

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for YBX1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for YBX1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for YBX1 gene:
    Search GeneIP for patents involving YBX1

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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