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YBX1 (Y box binding protein 1)

Written2010-11Valentina Evdokimova, Alexey Sorokin
Institute of Protein Research, Pushchino, Moscow Region 142290, Russian Federation

(Note : for Links provided by Atlas : click)

Identity

Alias_namesNSEP1
nuclease sensitive element binding protein 1
Alias_symbol (synonym)YB-1
YB1
DBPB
NSEP-1
MDR-NF1
BP-8
CSDB
CSDA2
Other aliasMGC104858
MGC110976
MGC117250
HGNC (Hugo) YBX1
LocusID (NCBI) 4904
Atlas_Id 46554
Location 1p34.2  [Link to chromosome band 1p34]
Location_base_pair Starts at 42682235 and ends at 42703803 bp from pter ( according to hg19-Feb_2009)  [Mapping YBX1.png]
Local_order The human YBX1 gene maps on 1p34 between the PPIH and the LOC100287607 loci.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ALDH1A1 (9q21.13) / YBX1 (1p34.2)YBX1 (1p34.2) / MUC1 (1q22)YBX1 (1p34.2) / NCBP2 (3q29)
YBX1 (1p34.2) / YBX1 (1p34.2)

DNA/RNA

 
  Genomic organization of YBX1. Box = exon (blue = 5'UTR, yellow = CDS, light red = 3'UTR). Line = intron.
Description The human YBX1 gene consists of 8 exons and 7 introns spanning a 19.2-kb genomic region. Intron number 1 is phase 1 (between 1st and 2nd base of codon). Introns number 2 and 6 are phase 2 (between 2nd and 3rd base of codon). Introns number 3, 4, 5 are phase 0 (between codons). According to the SNP source (dbSNP NCBI), non-synonymous polymorphism has been reported for the codons 30 (rs11558135), 237 (rs3887881), 251 (rs55676223), and 261 (rs3887879). The YBX1 promoter region contains no typical TATA or CCAAT box, but has multiple E-boxes located between -1855 and -422 nucleotides (relative to the start of exon 1) and several GT and GC boxes. The gene also contains a large and highly conserved CpG island at the immediate 5' promoter region which extends to the first exon encoding 5' UTR of YBX1 mRNA. The region between nucleotides -119 to +127 was shown to be essential for transcriptional activity in the reporter assays (Makino et al., 1996). YBX1 is constitutively expressed in multiple human tissues and its expression can be further induced by the E-box-binding transcription factors such as c-myc (Uramoto et al., 2002), Twist (Shiota et al., 2008) and Math2 (Ohashi et al., 2009).
Transcription The main processed mRNA is 1514 bp. It encompasses exons 1-8. The 70-amino acid cold-shock domain (CSD) is encoded separately by exons 2-5. Four additional splice variants in human were predicted (Ensembl), two of which (YBX1-004 and YBX1-201) preserve exons 2 and 3 coding for core elements of the CSD, the RNP1 and RNP2 motifs, respectively. An alternative transcript for ctYB-1, the YBX1 homologous gene in C. tentans, has been reported (Nashchekin et al., 2007).
Pseudogene
DescriptionSymbolNCBI gene IDPositionIntrons/exonsORFIdentity with YBX1Gaps
nuclease sensitive element binding protein 1 pseudogenebA327L3.41583739p13.1IntronlessStops after E881477/1515 (97%)2/1515 (0%)
Y box binding protein 1 pseudogene 1YBX1P1506314q23.3Intronless 1496 bp-1488/1531 (97%)20/1511 (1%)
Y box binding protein 1 pseudogene 2YBX1P26465317q22.32 exons, 1 intron, 1553 bpStops after E881431/1529 (93%)43/1529 (2%)
Y box binding protein 1 pseudogeneLOC1001310121001310127q36.1Intronless, 820 bp-287/353 (81%)26/353 (7%)

Protein

 
  Structural and functional organization of YB-1. YB-1 is composed by three domains: N-terminal Ala/Pro rich (AP) domain, cold shock domain (CSD) and the C-terminal domain (CTD) containing clusters of positively and negatively charged amino acids. Indicated are some known molecular partners of YB-1 and sites of their interactions (from Sorokin et al., 2005). The arrow indicates proteasomal cleavage sites.
Description The YBX1 gene encodes the Y-box protein 1 (YB-1) which consists of 324 amino acid residues and has the isoelectric point 10.3. Theoretical MW is 35924, however YB-1 is known to migrate as a ~45-50 kDa protein in SDS-polyacrylamide gels due to its anomalous electrophoretic mobility. YB-1 belongs to the family of multifunctional DNA/RNA binding proteins that are highly conserved throughout evolution and found in eukaryotes, prokaryotes and archaea. The most conserved region in YB-1 is the 80 amino acid CSD which exhibits >40% identity and >60% similarity to the major E. coli cold shock protein CspA (Matsumoto and Wolffe, 1998; Sommerville, 1999). The CSD possesses RNP1 and RNP2-like consensus motifs and is represented by a five-stranded beta-barrel structure which creates a surface rich in aromatic and basic amino acids that may act as a large nucleic acid-binding site (Wolffe et al., 1992; Wolffe, 1994). The CSD has a preference for binding single-stranded pyrimidine-rich sequences. The N-terminal AP domain of YB-1 is similar to that found in several other transcription factors and may thus be important for its transcriptional activity. This region is also essential for interaction with p53 and modulation of p53-mediated transcription (Okamoto et al., 2000), and for association with actin microfilaments and mRNA compartmentalization (Ruzanov et al., 1999). The C-terminal region of YB-1 is responsible for sequence-nonspecific binding to DNA and RNA and mediation of protein-protein interactions (Wolffe, 1994; Sommerville and Ladomery, 1996). An inverted CCAAT-box found in HLA class II gene promoters, a so-called Y-box, was originally determined as the YB-1 binding motif (Didier et al., 1988). Later studies have concluded that YB-1 rather recognizes the DNA structure than a defined nucleotide sequence, making prediction of its target genes not feasible with conventional in silico analyses (Swamynathan et al., 1998). YB-1 is also capable of unwinding DNA and RNA duplexes, especially those containing mismatches, thereby promoting strand exchange and formation of perfectly matched duplex structures (Skabkin et al., 2001; Gaudreault et al., 2004).
Expression According to Human Protein Atlas, YB-1 is variably expressed in most normal human tissues. Its expression is elevated in multiple cancer types (Kohno et al., 2003).
Localisation Mostly cytosolic. Shuttles between cytoplasm and nucleus. Localized in cytoplasmic stress granules and processing bodies containing untranslated mRNAs (Kedersha and Anderson, 2007). Nuclear translocation is induced in response to various stresses, including adenoviral infection (Holm et al., 2002), hyperthermia (Stein et al., 2001), DNA damage (Kohno et al., 2003) and activation of PI3K-Akt signaling (Sutherland et al., 2005).
Function The diverse biological functions of YB-1 appear to arise from its broad nucleic acid binding properties. YB-1 has been implicated in pre-mRNA splicing, transcriptional regulation, mRNA translation and stability as well as in chromatin remodelling, DNA repair and environmental stress responses (Kohno et al., 2003; Matsumoto and Bay, 2005).
Splicing. YB-1 regulates splice site selection via direct binding to splicing recognition motifs in pre-mRNA, including A/C-rich exon enhancers (Stickeler et al., 2001) or via interaction with splicing factors from the SR family (Li et al., 2003; Raffetseder et al., 2003).
Transcription. YB-1 is capable of binding to promoters of many genes, many of which lack the Y-box, and either activates or represses transcription. Among the genes activated by YB-1 are thymidine kinase, proliferating cell nuclear antigen (PCNA), cyclin A and cyclin B1, DNA topoisomerase II alpha, gelatinase A, matrix metalloproteinase 2, multidrug resistance 1 (MDR1), EGFR and protein tyrosine phosphatase 1B. Genes that are transcriptionally repressed by YB-1 include MHC class II, collagen alpha1, granulocyte-macrophage colony-stimulating factor (GM-CSF), etc (reviewed in Ladomery and Sommerville, 1995; Kohno et al., 2003; Kuwano et al., 2003). Overall, YB-1 is considered as an important regulator of growth- and stress-associated genes.
mRNA translation and stability. YB-1 (p50) is known as a major structural component of messenger ribonucleoprotein particles (mRNPs) which exerts positive or negative effects on translation, depending on the amount bound to mRNA (Evdokimova and Ovchinnikov, 1999). YB-1 regulates translational activity of many growth- and differentiation-associated mRNAs, including Snail1, and selectively protects capped mRNAs against degradation (Evdokimova et al., 2001; Evdokimova et al., 2006; Evdokimova et al., 2009). YB-1 appears vo pl`y(a role in stabilization of short-lived mRNAs, including IL-2 (Chen et al., 2000), GM-CSF (Capowski et al., 2001) and VEGF (Coles et al., 2004).
DNA repair and stress response. YB-1 is involved in base excision and mismatch repair pathways via interaction with multiple DNA repair proteins including glycosylase NEIL2, DNA polymerase beta and delta, DNA ligase III, APE1, MSH2, Ku80, WRN, endonuclease III, etc (Marenstein et al., 2001; Gaudreault et al., 2004; Das et al., 2007). YB-1 also directly binds and promotes separation of DNA strands that contain mismatches or are modified by cisplatin (Ise et al., 1999; Skabkin et al., 2001; Gaudreault et al., 2004). Various stresses, including DNA damage, adenovirus infection and hyperthermia, induce nuclear translocation of YB-1 (Ohga et al., 1996; Kohno et al., 2003) and its proteasomal cleavage (Sorokin et al., 2005). Accumulation of the full-length and/or truncated YB-1 proteins in the nucleus is associated with increased survival and multidrug resistance (Kohno et al., 2003; Sorokin et al., 2005). YB-1 knock-out in mice is lethal (Lu et al., 2005; Lu et al., 2006). Fibroblasts derived from YB-1(-/-) embryos exhibit a reduced ability to respond to oxidative, genotoxic and oncogene-induced stresses, further implicating YB-1 in stress responses and embryonic development.
Tumorigenesis. YB-1 is frequently overexpressed in multiple human cancers (reviewed in Kohno et al., 2003; Kuwano et al., 2003). In many cases, YB-1 levels are elevated in the nucleus, positively correlating with multiple drug resistance and poor patient outcome (Bargou et al., 1997; Janz et al., 2002). Ectopic expression of YB-1 in breast cancer cells and mouse models stimulated tumor growth (Bergmann et al., 2005; Sutherland et al., 2005). Yet, the role of YB-1 in tumorigenesis is controversial. YB-1 overexpression blocked oncogenic transformation caused by PI3K or Akt (Bader et al., 2003). These apparently contradictory results were proposed to be due to differential localization of YB-1; its interference with oncogenic transformation is associated with cytosolic localization and a consequent function in translational control (Bader and Vogt, 2004; Bader and Vogt, 2005).
Homology YB-1 is highly homologous to human DbpA (12p13; expressed predominantly in heart and muscle) and DbpC/contrin (17p11; expressed exclusively in germ cells). They share greater than 90% identity within the CSD and a high degree of similarity in the N- and C-terminal domains, including C-terminal clusters of basic and acidic amino acids. Mouse orthologues are YB-1 (encoded by Ybx1; 99% overall aminoacid identity with human YB-1), MSY2 (Ybx2; ~93% identity with contrin) and MSY4 (~86% identity with DbpA).

Mutations

Note Mutations in YBX1 are not reported.

Implicated in

Note
  
Entity Breast cancer
Note Elevated expression and nuclear localization of YB-1 is associated with increased proliferation, multidrug resistance and tumor aggressiveness across all tumor subtypes. Nuclear localization positively correlates with increased expression of MDR1/P-gp and HER2/ErbB2 (Bargou et al., 1997; Saji et al., 2003; Fujii et al., 2008; Habibi et al., 2008). Enforced YB-1 expression in mammary glands of transgenic mice induced chromosomal instability and tumorigenesis (Bergmann et al., 2005). YB-1 effects on tumorigenesis are likely dependent on cellular signaling. It blocks oncogenic transformation induced by Akt or PI3K but not by Src, Jun or Qin oncoproteins (Bader et al., 2003), and decreases proliferation of tumor cells with activated MAPK-Ras signaling, while inducing their metastatic ability (Evdokimova et al., 2009).
Prognosis Nuclear YB-1 is considered as a marker of poor clinical outcome. Patients with high YB-1 levels are likely to benefit from dose-intensified chemotherapy regimens (Gluz et al., 2009).
  
  
Entity Prostate cancer
Note YB-1 is upregulated during prostate cancer tumor progression and is reported to increase P-glycoprotein activity (Giménez-Bonafé et al., 2004).
  
  
Entity Lung cancer
Note Nuclear YB-1 is associated with poor survival and expression of HER2/ErbB2 and HER3/ErbB3 in non-small cell lung cancer (Kashihara et al., 2009).
Prognosis Patients with nuclear YB-1 expression and p53 mutations appear to have the worst prognosis (median survival 3 months), while best outcome was found in patients with no nuclear YB-1 and wild-type p53 (Gessner et al., 2004).
  
  
Entity Colon cancer
Note YB-1 expression levels are elevated in colorectal carcinoma and positively correlate with DNA topoisomerase II alpha and PCNA expression but not with P-gp (Shibao et al., 1999). In colon cancer cells, YB-1 accumulates in the nuclei in response to vinblastin and is associated with development of vinblastin resistance and elevated expression of P-gp (Vaiman et al., 2007).
  
  
Entity Ovarian cancer
Note YB-1 levels are elevated in the nuclei of cisplatin-resistant cancer cell lines and cancer patients, indicating that nuclear YB-1 may be associated with acquired cisplatin resistance in ovarian cancers (Yahata et al., 2002).
Prognosis Co-expression of YB-1 and P-gp is indicative of unfavourable prognosis in ovarian cancer (Huang et al., 2004).
  
  
Entity Haematopoietic malignancies
Disease Large B-cell lymphoma, multiple myeloma.
Nuclear expression of YB-1 is associated with P-gp expression and poor response to chemotherapy in large B-cell lymphoma (Xu et al., 2009). YB-1 is strongly expressed in normal plasma cell precursor blasts as well as in a multiple myeloma tumor specimens and cell lines but not in normal bone marrow or plasma cells. Its expression is associated with an immature morphology, a highly proliferative phenotype and doxorubicin resistance, indicating its involvement in drug resistance and disease progression in multiple myeloma (Chatterjee et al., 2008).
  
  
Entity Bone and soft tissue tumors
Disease Rhabdomyosarcoma, synovial sarcoma and osteosarcoma.
Nuclear expression of YB-1 protein positively correlates with P-gp expression and a higher proliferative index in embryonal (ERMS) but not in alveolar rhabdomyosarcoma (ARMS) (Oda et al., 2008), synovial sarcoma (Oda et al., 2003) and osteosarcoma (Oda et al., 1998).
  
  
Entity Melanoma
Note YB-1 expression is increased in melanoma cells compared to benign melanocytes, and nuclear YB-1 is found in invasive and metastatic melanoma cells. YB-1 expression is associated with increased proliferation, tumor invasion and chemoresistance (Schittek et al., 2007).
  
  
Entity Nervous system tumors
Disease Glioblastoma, neuroblastoma.
YB-1 levels are elevated in pediatric glioblastoma (Faury et al., 2007) and neuroblastoma (Wachowiak et al., 2010).
Prognosis In neuroblastoma, no correlation of YB-1 expression with survival, risk factors or stage of the disease was found.
  

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PMID 12565174
 
The increased expression of Y box-binding protein 1 in melanoma stimulates proliferation and tumor invasion, antagonizes apoptosis and enhances chemoresistance.
Schittek B, Psenner K, Sauer B, Meier F, Iftner T, Garbe C.
Int J Cancer. 2007 May 15;120(10):2110-8.
PMID 17266041
 
Enhanced coexpression of YB-1 and DNA topoisomerase II alpha genes in human colorectal carcinomas.
Shibao K, Takano H, Nakayama Y, Okazaki K, Nagata N, Izumi H, Uchiumi T, Kuwano M, Kohno K, Itoh H.
Int J Cancer. 1999 Dec 10;83(6):732-7.
PMID 10597187
 
Twist promotes tumor cell growth through YB-1 expression.
Shiota M, Izumi H, Onitsuka T, Miyamoto N, Kashiwagi E, Kidani A, Yokomizo A, Naito S, Kohno K.
Cancer Res. 2008 Jan 1;68(1):98-105.
PMID 18172301
 
The major messenger ribonucleoprotein particle protein p50 (YB-1) promotes nucleic acid strand annealing.
Skabkin MA, Evdokimova V, Thomas AA, Ovchinnikov LP.
J Biol Chem. 2001 Nov 30;276(48):44841-7. Epub 2001 Oct 3.
PMID 11585833
 
Activities of cold-shock domain proteins in translation control.
Sommerville J.
Bioessays. 1999 Apr;21(4):319-25. (REVIEW)
PMID 10377894
 
Proteasome-mediated cleavage of the Y-box-binding protein 1 is linked to DNA-damage stress response.
Sorokin AV, Selyutina AA, Skabkin MA, Guryanov SG, Nazimov IV, Richard C, Th'ng J, Yau J, Sorensen PH, Ovchinnikov LP, Evdokimova V.
EMBO J. 2005 Oct 19;24(20):3602-12. Epub 2005 Sep 29.
PMID 16193061
 
Hyperthermia-induced nuclear translocation of transcription factor YB-1 leads to enhanced expression of multidrug resistance-related ABC transporters.
Stein U, Jurchott K, Walther W, Bergmann S, Schlag PM, Royer HD.
J Biol Chem. 2001 Jul 27;276(30):28562-9. Epub 2001 May 21.
PMID 11369762
 
The RNA binding protein YB-1 binds A/C-rich exon enhancers and stimulates splicing of the CD44 alternative exon v4.
Stickeler E, Fraser SD, Honig A, Chen AL, Berget SM, Cooper TA.
EMBO J. 2001 Jul 16;20(14):3821-30.
PMID 11447123
 
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.
Sutherland BW, Kucab J, Wu J, Lee C, Cheang MC, Yorida E, Turbin D, Dedhar S, Nelson C, Pollak M, Leighton Grimes H, Miller K, Badve S, Huntsman D, Blake-Gilks C, Chen M, Pallen CJ, Dunn SE.
Oncogene. 2005 Jun 16;24(26):4281-92.
PMID 15806160
 
Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes.
Swamynathan SK, Nambiar A, Guntaka RV.
FASEB J. 1998 May;12(7):515-22. (REVIEW)
PMID 9576478
 
p73 Interacts with c-Myc to regulate Y-box-binding protein-1 expression.
Uramoto H, Izumi H, Ise T, Tada M, Uchiumi T, Kuwano M, Yasumoto K, Funa K, Kohno K.
J Biol Chem. 2002 Aug 30;277(35):31694-702. Epub 2002 Jun 21.
PMID 12080043
 
Development of drug resistance in the population of colon cancer cells under the effect of multifunctional protein YB-1.
Vaiman AV, Stromskaya TP, Rybalkina EY, Sorokin AV, Ovchinnikov LP, Stavrovskaya AA.
Bull Exp Biol Med. 2007 Apr;143(4):463-6.
PMID 18214301
 
Y-box-binding protein-1 is a potential novel tumour marker for neuroblastoma.
Wachowiak R, Thieltges S, Rawnaq T, Kaifi JT, Fiegel H, Metzger R, Quaas A, Mertens PR, Till H, Izbicki JR.
Anticancer Res. 2010 Apr;30(4):1239-42.
PMID 20530434
 
The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man.
Wolffe AP, Tafuri S, Ranjan M, Familari M.
New Biol. 1992 Apr;4(4):290-8. (REVIEW)
PMID 1622927
 
Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins.
Wolffe AP.
Bioessays. 1994 Apr;16(4):245-51. (REVIEW)
PMID 8031301
 
Nuclear expression of YB-1 in diffuse large B-cell lymphoma: correlation with disease activity and patient outcome.
Xu W, Zhou L, Qin R, Tang H, Shen H.
Eur J Haematol. 2009 Oct;83(4):313-9. Epub 2009 Jun 2.
PMID 19500133
 
Increased nuclear localization of transcription factor YB-1 in acquired cisplatin-resistant ovarian cancer.
Yahata H, Kobayashi H, Kamura T, Amada S, Hirakawa T, Kohno K, Kuwano M, Nakano H.
J Cancer Res Clin Oncol. 2002 Nov;128(11):621-6. Epub 2002 Oct 22.
PMID 12458343
 

Citation

This paper should be referenced as such :
Evdokimova, V ; Sorokin, A
YBX1 (Y box binding protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2011;15(7):598-604.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/YBX1ID46554ch1p34.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(9;13)(p12;q21) PAX5/DACH1


External links

Nomenclature
HGNC (Hugo)YBX1   8014
Cards
AtlasYBX1ID46554ch1p34
Entrez_Gene (NCBI)YBX1  4904  Y-box binding protein 1
AliasesBP-8; CBF-A; CSDA2; CSDB; 
DBPB; EFI-A; MDR-NF1; NSEP-1; NSEP1; YB-1; YB1
GeneCards (Weizmann)YBX1
Ensembl hg19 (Hinxton)ENSG00000065978 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000065978 [Gene_View]  chr1:42682235-42703803 [Contig_View]  YBX1 [Vega]
ICGC DataPortalENSG00000065978
TCGA cBioPortalYBX1
AceView (NCBI)YBX1
Genatlas (Paris)YBX1
WikiGenes4904
SOURCE (Princeton)YBX1
Genetics Home Reference (NIH)YBX1
Genomic and cartography
GoldenPath hg38 (UCSC)YBX1  -     chr1:42682235-42703803 +  1p34.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)YBX1  -     1p34.2   [Description]    (hg19-Feb_2009)
EnsemblYBX1 - 1p34.2 [CytoView hg19]  YBX1 - 1p34.2 [CytoView hg38]
Mapping of homologs : NCBIYBX1 [Mapview hg19]  YBX1 [Mapview hg38]
OMIM154030   
Gene and transcription
Genbank (Entrez)AK309996 AK311708 BC000064 BC002411 BC010430
RefSeq transcript (Entrez)NM_004559
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)YBX1
Cluster EST : UnigeneHs.473583 [ NCBI ]
CGAP (NCI)Hs.473583
Alternative Splicing GalleryENSG00000065978
Gene ExpressionYBX1 [ NCBI-GEO ]   YBX1 [ EBI - ARRAY_EXPRESS ]   YBX1 [ SEEK ]   YBX1 [ MEM ]
Gene Expression Viewer (FireBrowse)YBX1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4904
GTEX Portal (Tissue expression)YBX1
Human Protein AtlasENSG00000065978-YBX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP67809   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP67809  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP67809
Splice isoforms : SwissVarP67809
PhosPhoSitePlusP67809
Domaine pattern : Prosite (Expaxy)COLD_SHOCK (PS00352)   
Domains : Interpro (EBI)Cold-shock_CS    CSD    CSP_DNA-bd    NA-bd_OB-fold   
Domain families : Pfam (Sanger)CSD (PF00313)   
Domain families : Pfam (NCBI)pfam00313   
Domain families : Smart (EMBL)CSP (SM00357)  
Conserved Domain (NCBI)YBX1
DMDM Disease mutations4904
Blocks (Seattle)YBX1
PDB (SRS)1H95   
PDB (PDBSum)1H95   
PDB (IMB)1H95   
PDB (RSDB)1H95   
Structural Biology KnowledgeBase1H95   
SCOP (Structural Classification of Proteins)1H95   
CATH (Classification of proteins structures)1H95   
SuperfamilyP67809
Human Protein Atlas [tissue]ENSG00000065978-YBX1 [tissue]
Peptide AtlasP67809
HPRD01095
IPIIPI00031812   IPI00041601   IPI00479509   IPI00450235   IPI00643351   IPI00643807   
Protein Interaction databases
DIP (DOE-UCLA)P67809
IntAct (EBI)P67809
FunCoupENSG00000065978
BioGRIDYBX1
STRING (EMBL)YBX1
ZODIACYBX1
Ontologies - Pathways
QuickGOP67809
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  mRNA splicing, via spliceosome  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  in utero embryonic development  DNA binding  DNA binding  chromatin binding  double-stranded DNA binding  single-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  RNA binding  protein binding  nucleus  nucleoplasm  U12-type spliceosomal complex  cytoplasm  cytosol  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  cytoplasmic stress granule  intracellular ribonucleoprotein complex  nuclear membrane  intracellular membrane-bounded organelle  positive regulation of transcription from RNA polymerase II promoter  GTPase binding  negative regulation of striated muscle cell differentiation  positive regulation of cell division  extracellular exosome  CRD-mediated mRNA stabilization  CRD-mediated mRNA stability complex  histone pre-mRNA 3'end processing complex  protein localization to cytoplasmic stress granule  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  mRNA splicing, via spliceosome  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  in utero embryonic development  DNA binding  DNA binding  chromatin binding  double-stranded DNA binding  single-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  RNA binding  protein binding  nucleus  nucleoplasm  U12-type spliceosomal complex  cytoplasm  cytosol  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  cytoplasmic stress granule  intracellular ribonucleoprotein complex  nuclear membrane  intracellular membrane-bounded organelle  positive regulation of transcription from RNA polymerase II promoter  GTPase binding  negative regulation of striated muscle cell differentiation  positive regulation of cell division  extracellular exosome  CRD-mediated mRNA stabilization  CRD-mediated mRNA stability complex  histone pre-mRNA 3'end processing complex  protein localization to cytoplasmic stress granule  
Pathways : BIOCARTATranscriptional activation of dbpb from mRNA [Genes]   
REACTOMEP67809 [protein]
REACTOME PathwaysR-HSA-72165 [pathway]   
NDEx NetworkYBX1
Atlas of Cancer Signalling NetworkYBX1
Wikipedia pathwaysYBX1
Orthology - Evolution
OrthoDB4904
GeneTree (enSembl)ENSG00000065978
Phylogenetic Trees/Animal Genes : TreeFamYBX1
HOVERGENP67809
HOGENOMP67809
Homologs : HomoloGeneYBX1
Homology/Alignments : Family Browser (UCSC)YBX1
Gene fusions - Rearrangements
Tumor Fusion PortalYBX1
Fusion Cancer (Beijing)YBX1 [1p34.2]  -  MUC1 [1q22]  [FUSC003046]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerYBX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)YBX1
dbVarYBX1
ClinVarYBX1
1000_GenomesYBX1 
Exome Variant ServerYBX1
ExAC (Exome Aggregation Consortium)ENSG00000065978
GNOMAD BrowserENSG00000065978
Genetic variants : HAPMAP4904
Genomic Variants (DGV)YBX1 [DGVbeta]
DECIPHERYBX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisYBX1 
Mutations
ICGC Data PortalYBX1 
TCGA Data PortalYBX1 
Broad Tumor PortalYBX1
OASIS PortalYBX1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICYBX1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDYBX1
intOGen PortalYBX1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch YBX1
DgiDB (Drug Gene Interaction Database)YBX1
DoCM (Curated mutations)YBX1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)YBX1 (select a term)
intoGenYBX1
NCG5 (London)YBX1
Cancer3DYBX1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM154030   
Orphanet
DisGeNETYBX1
MedgenYBX1
Genetic Testing Registry YBX1
NextProtP67809 [Medical]
TSGene4904
GENETestsYBX1
Target ValidationYBX1
Huge Navigator YBX1 [HugePedia]
snp3D : Map Gene to Disease4904
BioCentury BCIQYBX1
ClinGenYBX1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4904
Chemical/Pharm GKB GenePA31791
Clinical trialYBX1
Miscellaneous
canSAR (ICR)YBX1 (select the gene name)
Probes
Litterature
PubMed329 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineYBX1
EVEXYBX1
GoPubMedYBX1
iHOPYBX1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 15:06:38 CET 2017

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