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Aliases for YBX1 Gene

Aliases for YBX1 Gene

  • Y-Box Binding Protein 1 2 3 5
  • CCAAT-Binding Transcription Factor I Subunit A 3 4
  • Enhancer Factor I Subunit A 3 4
  • Y-Box Transcription Factor 3 4
  • Y-Box-Binding Protein 1 3 4
  • DNA-Binding Protein B 3 4
  • CBF-A 3 4
  • NSEP1 3 4
  • EFI-A 3 4
  • DBPB 3 4
  • YB-1 3 4
  • YB1 3 4
  • Major Histocompatibility Complex, Class II, Y Box-Binding Protein I 3
  • Nuclease Sensitive Element Binding Protein 1 2
  • Nuclease-Sensitive Element-Binding Protein 1 3
  • MDR-NF1 3
  • NSEP-1 3
  • CSDA2 3
  • BP-8 3
  • CSDB 3

External Ids for YBX1 Gene

Previous HGNC Symbols for YBX1 Gene

  • NSEP1

Previous GeneCards Identifiers for YBX1 Gene

  • GC01P042818
  • GC01P042920
  • GC01P043148
  • GC01P041268

Summaries for YBX1 Gene

Entrez Gene Summary for YBX1 Gene

  • This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]

GeneCards Summary for YBX1 Gene

YBX1 (Y-Box Binding Protein 1) is a Protein Coding gene. Diseases associated with YBX1 include Breast Cancer and Chondroblastic Osteosarcoma. Among its related pathways are mRNA Splicing - Major Pathway and SIDS Susceptibility Pathways. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX3.

UniProtKB/Swiss-Prot for YBX1 Gene

  • 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.

  • The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Gene Wiki entry for YBX1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YBX1 Gene

Genomics for YBX1 Gene

Regulatory Elements for YBX1 Gene

Enhancers for YBX1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around YBX1 on UCSC Golden Path with GeneCards custom track

Promoters for YBX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around YBX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for YBX1 Gene

Chromosome:
1
Start:
42,682,389 bp from pter
End:
42,702,363 bp from pter
Size:
19,975 bases
Orientation:
Plus strand

Genomic View for YBX1 Gene

Genes around YBX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YBX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YBX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YBX1 Gene

Proteins for YBX1 Gene

  • Protein details for YBX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P67809-YBOX1_HUMAN
    Recommended name:
    Nuclease-sensitive element-binding protein 1
    Protein Accession:
    P67809
    Secondary Accessions:
    • P16990
    • P16991
    • Q14972
    • Q15325
    • Q5FVF0

    Protein attributes for YBX1 Gene

    Size:
    324 amino acids
    Molecular mass:
    35924 Da
    Quaternary structure:
    • 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. Interacts with DERA. Interacts with FMR1; this interaction occurs in association with polyribosome (By similarity).
    SequenceCaution:
    • Sequence=AAA35750.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAA59949.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=AAA61308.1; Type=Frameshift; Positions=314; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for YBX1 Gene

neXtProt entry for YBX1 Gene

Post-translational modifications for YBX1 Gene

  • 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).
  • In the absence of phosphorylation the protein is retained in the cytoplasm.
  • Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability.
  • Ubiquitination at Lys 137, Lys 170, and Lys 264
  • Modification sites at PhosphoSitePlus

Other Protein References for YBX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for YBX1 Gene

Domains & Families for YBX1 Gene

Gene Families for YBX1 Gene

Suggested Antigen Peptide Sequences for YBX1 Gene

Graphical View of Domain Structure for InterPro Entry

P67809

UniProtKB/Swiss-Prot:

YBOX1_HUMAN :
  • Contains 1 CSD (cold-shock) domain.
Domain:
  • Contains 1 CSD (cold-shock) domain.
genes like me logo Genes that share domains with YBX1: view

Function for YBX1 Gene

Molecular function for YBX1 Gene

UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot Function:
The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

Gene Ontology (GO) - Molecular Function for YBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA 18809583
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA 18809583
GO:0003677 DNA binding TAS 2977358
GO:0003682 chromatin binding IEA --
GO:0003690 double-stranded DNA binding TAS 1738588
genes like me logo Genes that share ontologies with YBX1: view
genes like me logo Genes that share phenotypes with YBX1: view

Animal Models for YBX1 Gene

MGI Knock Outs for YBX1:

Animal Model Products

CRISPR Products

Transcription Factor Targets for YBX1 Gene

Selected GeneGlobe predicted Target genes for YBX1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for YBX1

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and HOMER Transcription for YBX1 Gene

Localization for YBX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YBX1 Gene

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
Jensen Localization Image for YBX1 Gene COMPARTMENTS Subcellular localization image for YBX1 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 4
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for YBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,TAS 3174636
GO:0005654 nucleoplasm TAS --
GO:0005689 U12-type spliceosomal complex IDA 15146077
GO:0005737 cytoplasm IEA,IDA 24965446
GO:0010494 cytoplasmic stress granule IDA 18335541
genes like me logo Genes that share ontologies with YBX1: view

Pathways & Interactions for YBX1 Gene

genes like me logo Genes that share pathways with YBX1: view

SIGNOR curated interactions for YBX1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for YBX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0001701 in utero embryonic development IEA --
GO:0006355 regulation of transcription, DNA-templated IDA 18809583
GO:0006366 transcription from RNA polymerase II promoter TAS 3174636
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IDA 18809583
genes like me logo Genes that share ontologies with YBX1: view

Drugs & Compounds for YBX1 Gene

(15) Drugs for YBX1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(6) Additional Compounds for YBX1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with YBX1: view

Transcripts for YBX1 Gene

mRNA/cDNA for YBX1 Gene

Unigene Clusters for YBX1 Gene

Y box binding protein 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for YBX1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for YBX1 Gene

No ASD Table

Relevant External Links for YBX1 Gene

GeneLoc Exon Structure for
YBX1
ECgene alternative splicing isoforms for
YBX1

Expression for YBX1 Gene

mRNA expression in normal human tissues for YBX1 Gene

Protein differential expression in normal tissues from HIPED for YBX1 Gene

This gene is overexpressed in Nasal epithelium (10.6) and Bone marrow stromal cell (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YBX1 Gene



Protein tissue co-expression partners for YBX1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of YBX1 Gene:

YBX1

SOURCE GeneReport for Unigene cluster for YBX1 Gene:

Hs.473583
genes like me logo Genes that share expression patterns with YBX1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for YBX1 Gene

Orthologs for YBX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for YBX1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia YBX1 34
  • 97.63 (n)
  • 100 (a)
YBX1 35
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LOC607025 34
  • 97.74 (n)
  • 100 (a)
-- 35
  • 85 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Ybx1 34
  • 96.48 (n)
  • 99.07 (a)
Ybx1 16
Ybx1 35
  • 99 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia YBX1 34
  • 99.9 (n)
  • 100 (a)
YBX1 35
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ybx1 34
  • 96.58 (n)
  • 99.07 (a)
oppossum
(Monodelphis domestica)
Mammalia YBX1 35
  • 99 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia YBX1 35
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves YBX1 35
  • 95 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.8793 34
ybx1 34
  • 82.55 (n)
  • 89.82 (a)
African clawed frog
(Xenopus laevis)
Amphibia nsep1-prov 34
zebrafish
(Danio rerio)
Actinopterygii nsep1 34
ybx1 34
  • 69.45 (n)
  • 71.91 (a)
ybx1 35
  • 73 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8781 34
fruit fly
(Drosophila melanogaster)
Insecta yps 35
  • 39 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cey-1 35
  • 45 (a)
ManyToMany
cey-2 35
  • 27 (a)
ManyToMany
cey-3 35
  • 26 (a)
ManyToMany
cey-4 35
  • 34 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10127 35
  • 44 (a)
OneToMany
Species where no ortholog for YBX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for YBX1 Gene

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

Paralogs for YBX1 Gene

Paralogs for YBX1 Gene

(3) SIMAP similar genes for YBX1 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with YBX1: view

Variants for YBX1 Gene

Sequence variations from dbSNP and Humsavar for YBX1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs9428 -- 42,702,137(+) TTTAC(A/C)TAAAG utr-variant-3-prime
rs2208926 -- 42,684,072(-) AGAAC(G/T)GAAGA intron-variant
rs3850847 -- 42,700,556(-) CATGG(A/C)ATGAT intron-variant
rs3862218 -- 42,686,939(+) TAGCC(A/G)TTTTC intron-variant
rs3862219 -- 42,700,612(+) CATCC(C/G)CCCCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for YBX1 Gene

Variant ID Type Subtype PubMed ID
esv3577249 CNV gain 25503493
nsv1118116 CNV deletion 24896259
nsv829682 CNV loss 17160897
nsv945906 CNV duplication 23825009
nsv945907 CNV duplication 23825009
nsv945908 CNV duplication 23825009

Variation tolerance for YBX1 Gene

Residual Variation Intolerance Score: 36.1% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for YBX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YBX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YBX1 Gene

Disorders for YBX1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for YBX1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
breast cancer
  • breast cancer, invasive ductal
chondroblastic osteosarcoma
  • chondrosarcomatous osteogenic sarcoma
- elite association - COSMIC cancer census association via MalaCards
Search YBX1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for YBX1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
YBX1
genes like me logo Genes that share disorders with YBX1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YBX1 Gene

Publications for YBX1 Gene

  1. Y-box protein-1 is actively secreted through a non-classical pathway and acts as an extracellular mitogen. (PMID: 19483673) Frye B.C. … Mertens P.R. (EMBO Rep. 2009) 3 4 22 65
  2. 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. (PMID: 15806160) Sutherland B.W. … Dunn S.E. (Oncogene 2005) 3 4 22 65
  3. 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. (PMID: 14718551) Gaudreault I. … Lebel M. (Nucleic Acids Res. 2004) 3 4 22 65
  4. Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection. (PMID: 12604611) Raffetseder U. … Mertens P.R. (J. Biol. Chem. 2003) 3 4 22 65
  5. A human protein containing a 'cold shock' domain binds specifically to H-DNA upstream from the human gamma-globin genes. (PMID: 8188694) Horwitz E.M. … Ley T.J. (J. Biol. Chem. 1994) 3 4 22 65

Products for YBX1 Gene

Sources for YBX1 Gene

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