ID:YBOX1_HUMAN DESCRIPTION: RecName: Full=Nuclease-sensitive element-binding protein 1; AltName: Full=CCAAT-binding transcription factor I subunit A; Short=CBF-A; AltName: Full=DNA-binding protein B; Short=DBPB; AltName: Full=Enhancer factor I subunit A; Short=EFI-A; AltName: Full=Y-box transcription factor; AltName: Full=Y-box-binding protein 1; Short=YB-1; 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. 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 mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and 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 EIF2C1 and EIF2C2. INTERACTION: Q08705:CTCF (xeno); NbExp=2; IntAct=EBI-354065, EBI-932806; Q09472:EP300; NbExp=2; IntAct=EBI-354065, EBI-447295; Q14103-4:HNRNPD; NbExp=3; IntAct=EBI-354065, EBI-432545; SUBCELLULAR LOCATION: 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. PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability. PTM: In the absence of phosphorylation the protein is retained in the cytoplasm. PTM: 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). SIMILARITY: Contains 1 CSD (cold-shock) domain. 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;
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on P67809
Front
Top
Side
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.
Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
LF206595 - JP 2014500723-A/14098: Polycomb-Associated Non-Coding RNAs. LF356427 - JP 2014500723-A/163930: Polycomb-Associated Non-Coding RNAs. AK311708 - Homo sapiens cDNA, FLJ18750. AK309996 - Homo sapiens cDNA, FLJ17038. M83234 - Human nuclease-sensitive element DNA-binding protein mRNA, complete cds. M85234 - Human nuclease sensitive element binding protein-1 mRNA, complete cds. BC070084 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:87414 IMAGE:5272578), complete cds. BC098435 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:104858 IMAGE:4859074), complete cds. Z70765 - H.sapiens mRNA, clone ICRFp507B2047. BC106045 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:117250 IMAGE:6062615), complete cds. J03827 - Y box binding protein-1 (YB-1) mRNA. BC072014 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone IMAGE:5556363), partial cds. BC065571 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:75111 IMAGE:6171221), complete cds. BC071708 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:87995 IMAGE:4361396), complete cds. BC090038 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:110976 IMAGE:6526492), complete cds. BC038384 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:5173 IMAGE:3449398), complete cds. BC000064 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone IMAGE:3510030), partial cds. BC010430 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:15819 IMAGE:3506647), complete cds. M24070 - Human DNA-binding protein B (dbpB) gene, 3' end. BC002411 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:8655 IMAGE:2961659), complete cds. L28809 - Homo sapiens dbpB-like protein mRNA, complete cds. BC015208 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone MGC:17203 IMAGE:3914485), complete cds. LF356425 - JP 2014500723-A/163928: Polycomb-Associated Non-Coding RNAs. DQ894802 - Synthetic construct Homo sapiens clone IMAGE:100009262; FLH178597.01L; RZPDo839E12127D Y box binding protein 1 (YBX1) gene, encodes complete protein. DQ891609 - Synthetic construct clone IMAGE:100004239; FLH178601.01X; RZPDo839E12128D Y box binding protein 1 (YBX1) gene, encodes complete protein. AB385072 - Synthetic construct DNA, clone: pF1KB5258, Homo sapiens YBX1 gene for nuclease sensitive element-binding protein 1, complete cds, without stop codon, in Flexi system. JD460829 - Sequence 441853 from Patent EP1572962. JD131737 - Sequence 112761 from Patent EP1572962. BC013838 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone IMAGE:4154898). JD522871 - Sequence 503895 from Patent EP1572962. JD019839 - Sequence 863 from Patent EP1572962. JD029061 - Sequence 10085 from Patent EP1572962. BC020164 - Homo sapiens Y box binding protein 1, mRNA (cDNA clone IMAGE:3906774), partial cds. JD411599 - Sequence 392623 from Patent EP1572962. JD354278 - Sequence 335302 from Patent EP1572962. JD129902 - Sequence 110926 from Patent EP1572962. JD511036 - Sequence 492060 from Patent EP1572962. JD447578 - Sequence 428602 from Patent EP1572962. JD058818 - Sequence 39842 from Patent EP1572962. MA442172 - JP 2018138019-A/14098: Polycomb-Associated Non-Coding RNAs. MA592004 - JP 2018138019-A/163930: Polycomb-Associated Non-Coding RNAs. MA592002 - JP 2018138019-A/163928: Polycomb-Associated Non-Coding RNAs.
Biochemical and Signaling Pathways
BioCarta from NCI Cancer Genome Anatomy Project h_dbpbPathway - Transcriptional activation of dbpb from mRNA
Reactome (by CSHL, EBI, and GO)
Protein P67809 (Reactome details) participates in the following event(s):
R-HSA-72107 Formation of the Spliceosomal E complex R-HSA-9017797 NOTCH3 binds YBX1 R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage R-HSA-72139 Formation of the active Spliceosomal C (B*) complex R-HSA-72124 Formation of the Spliceosomal A Complex R-HSA-72127 Formation of the Spliceosomal B Complex R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex R-HSA-75080 Formation of AT-AC A complex R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation R-HSA-156661 Formation of Exon Junction Complex R-HSA-75081 Formation of AT-AC B Complex R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage R-HSA-75079 Formation of AT-AC C complex R-HSA-72163 mRNA Splicing - Major Pathway R-HSA-9017802 Noncanonical activation of NOTCH3 R-HSA-72165 mRNA Splicing - Minor Pathway R-HSA-72172 mRNA Splicing R-HSA-9013507 NOTCH3 Activation and Transmission of Signal to the Nucleus R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA R-HSA-9012852 Signaling by NOTCH3 R-HSA-8953854 Metabolism of RNA R-HSA-157118 Signaling by NOTCH R-HSA-162582 Signal Transduction
US Server
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
