ENSMUSG00000028639


Mus musculus

Features
Gene ID: ENSMUSG00000028639
  
Biological name :Ybx1
  
Synonyms : P62960 / Y box protein 1 / Ybx1
  
Possible biological names infered from orthology : P67809 / Y-box binding protein 1
  
Species: Mus musculus
  
Chr. number: 4
Strand: -1
Band: D2.1
Gene start: 119277981
Gene end: 119294604
  
Corresponding Affymetrix probe sets: 10515878 (MoGene1.0st)   10544015 (MoGene1.0st)   1418624_at (Mouse Genome 430 2.0 Array)   1430720_at (Mouse Genome 430 2.0 Array)   1438064_at (Mouse Genome 430 2.0 Array)   
  
Cross references: Ensembl peptide - ENSMUSP00000078589
Ensembl peptide - ENSMUSP00000117225
NCBI entrez gene - 22608     See in Manteia.
MGI - MGI:99146
RefSeq - XM_006502934
RefSeq - NM_011732
RefSeq - XM_006502933
RefSeq Peptide - NP_035862
swissprot - P62960
swissprot - Q3UBT1
swissprot - A2BGG7
Ensembl - ENSMUSG00000028639
  

This gene has been taged as a transcription factor by TFT
See expression report in BioGPS
See gene description in Wikigenes
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 ybx1ENSDARG00000004757Danio rerio
 YBX1ENSGALG00000004848Gallus gallus
 YBX1ENSG00000065978Homo sapiens


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
Ybx3 / Q9JKB3 / Y box protein 3 / P16989* / Y-box binding protein 3*ENSMUSG0000003018958
Ybx2 / Y box protein 2 / Q9Y2T7* / Y-box binding protein 2*ENSMUSG0000001855446


Protein motifs (from Interpro)
Interpro ID Name
 IPR002059  Cold-shock protein, DNA-binding
 IPR011129  Cold shock domain
 IPR012340  Nucleic acid-binding, OB-fold
 IPR019844  Cold-shock conserved site


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0000122 negative regulation of transcription by RNA polymerase II IGI
 biological_processGO:0001701 in utero embryonic development IMP
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated ISO
 biological_processGO:0006366 transcription by RNA polymerase II IEA
 biological_processGO:0006397 mRNA processing IEA
 biological_processGO:0008380 RNA splicing IEA
 biological_processGO:0045944 positive regulation of transcription by RNA polymerase II IEA
 biological_processGO:0051154 negative regulation of striated muscle cell differentiation IDA
 biological_processGO:0051781 positive regulation of cell division IEA
 biological_processGO:0070934 CRD-mediated mRNA stabilization IEA
 biological_processGO:1903608 protein localization to cytoplasmic stress granule IEA
 cellular_componentGO:0005576 extracellular region IEA
 cellular_componentGO:0005634 nucleus IGI
 cellular_componentGO:0005689 U12-type spliceosomal complex IEA
 cellular_componentGO:0005737 cytoplasm IEA
 cellular_componentGO:0005829 cytosol IEA
 cellular_componentGO:0010494 cytoplasmic stress granule IEA
 cellular_componentGO:0031965 nuclear membrane IEA
 cellular_componentGO:0043231 intracellular membrane-bounded organelle IEA
 cellular_componentGO:0070937 CRD-mediated mRNA stability complex IEA
 cellular_componentGO:0071204 histone pre-mRNA 3"end processing complex IDA
 molecular_functionGO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA
 molecular_functionGO:0001077 transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding IEA
 molecular_functionGO:0003676 nucleic acid binding IEA
 molecular_functionGO:0003677 DNA binding ISO
 molecular_functionGO:0003682 chromatin binding IDA
 molecular_functionGO:0003697 single-stranded DNA binding IDA
 molecular_functionGO:0003723 RNA binding ISO
 molecular_functionGO:0005515 protein binding IPI
 molecular_functionGO:0051020 GTPase binding IEA


Pathways (from Reactome)
Pathway description
mRNA Splicing - Major Pathway
mRNA Splicing - Minor Pathway
Noncanonical activation of NOTCH3


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 MP:0000358 abnormal cell content/ morphology "structural anomalies of the minute protoplasmic masses that make up organized tissues and which are the fundamental structural and functional units of living organisms" [cwg:Carroll-Ann W. Goldsmith , Mouse Genome Informatics curator, MeSH:National Library of Medicine - Medical Subject Headings , 2003]
Show

Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0000428 abnormal craniofacial morphology "anomalous structure or development of the face and/or cranium" [Stedman s Medical Dictionary:ISBN 0-683-40008-8]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0000455 abnormal maxilla morphology "malformation of the upper bony framework of the mouth where the superior teeth are held" [Stedman s Medical Dictionary , 27th edition:ISBN 0-683-40008-8]
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Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0000458 abnormal mandible morphology "malformation of the lower bony framework of the mouth where the inferior teeth are held" [Stedman s Medical Dictionary , 27th edition:ISBN 0-683-40008-8]
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Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0000600 liver hypoplasia "reduced size of liver due to decreased cell number " [J:57631]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0000601 small liver "reduced size of the liver" [J:23170]
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Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0000913 abnormal brain development "malformed or incomplete differentiation of the brain" [MGI:cls, J:49840]
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Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0000914 exencephaly "neurocranial defects resulting in exposure or extrusion of the brain" [Stedman s Medical Dictionary:ISBN 0-683-40008-8, J:49840]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

Allelic Composition: Ybx3tm1Ley/Ybx3+,Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

Allelic Composition: Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

Allelic Composition: Ybx1tm1Tuch/Ybx1tm1Tuch
Genetic Background: involves: 129S/SvEv * C57BL/6

 MP:0000928 incomplete cephalic closure "arrest of the fusion of the cephalic neural folds" [J:12622]
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Allelic Composition: Ybx1tm1Tuch/Ybx1tm1Tuch
Genetic Background: involves: 129S/SvEv * C57BL/6

 MP:0001575 cyanosis "a dark bluish or purple skin discoloration resulting from deficient oxygenation of the blood" [Stedman s Medical Dictionary:ISBN 0-683-40008-8, J:60159]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0001698 reduced embryo size "smaller proportions of embryo compared to littermates" [J:61790]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

Allelic Composition: Ybx3tm1Ley/Ybx3+,Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

Allelic Composition: Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

 MP:0001785 edema "an accumulation of an excessive amount of watery fluid in cells or intercellular tissues" [Stedman s Medical Dictionary:ISBN 0-683-40008-8, J:54065]
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Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0001916 intracerebral hemorrhage "bleeding within the cerebrum" [cwg:Carroll-Ann W. Goldsmith , Mouse Genome Informatics curator]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0001953 respiratory failure "cessation of or failure to commence breathing" [MGI:cls, J:60159]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0002082 postnatal lethality "premature death anytime after postnatal day 1 to weaning age (3 weeks)" [csmith:Cynthia L. Smith , Mouse Genome Informatics Curator]
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Allelic Composition: Otx1tm1Sia/Otx1+,Otx2tm2(Otx1)Sia/Otx2+
Genetic Background: involves: C57BL/6 * CBA

 MP:0002123 abnormal hematopoiesis "abnormal development of the enucleated fetal and adult erythrocytes that develop in the aorta, genital ridge and mesonephros region and later in the fetal and adult liver" [csmith:Cynthia L. Smith , Mouse Genome Informatics Curator]
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Allelic Composition: Hps3coa-7J/Hps3coa-7J
Genetic Background: C3H/HeJ-Hps3coa-7J/GrsrJ

 MP:0003186 abnormal redox activity "defect in the processes that maintain the redox environment of a cell or compartment within a cell " [csmith:Cynthia L. Smith , Mouse Genome Informatics Curator]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0003717 pallor "an unnatural paleness to the skin, generally attributable to anemia" [MeSH:National Library of Medicine - Medical Subject Headings , 2003]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0003720 abnormal neural tube closure "abnormal invagination and fusion of the neuroepithelial layer in early development" [monikat:Monika Tomczuk, Mouse Genome Informatics Curator, J:99099]
Show

Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0003984 embryonic growth retardation "slow or limited development before birth" [csmith:Cynthia L. Smith , Mouse Genome Informatics Curator]
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Allelic Composition: Ybx1tm1Tuch/Ybx1tm1Tuch
Genetic Background: involves: 129S/SvEv * C57BL/6

 MP:0004200 reduced fetal size "smaller proportions of a fetus compared to littermates (sensu Mus: from E14 through birth)" [MGI:csmith "Cynthia L. Smith, Mouse Genome Informatics Curator"]
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Allelic Composition: Ybx3tm1Ley/Ybx3+,Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

Allelic Composition: Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

 MP:0008008 early cellular replicative senescence "increase in the progression of the process in which a cell progresses from its inception to the end of its lifespan, which occurs as the cell continues cycles of growth and division" [MGI:smb "Susan M. Bello, Mouse Genome Informatics Curator"]
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Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0011087 complete neonatal lethality "death of all organisms of a given genotype in a population within the neonatal period after birth (Mus: P0)" [MGI:csmith]
Show

Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0011092 complete embryonic lethality "death of all organisms of a given genotype in a population within the embryonic period prior to organogenesis (Mus: prior to E14)" [MGI:csmith]
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Allelic Composition: Szt2Gt(XH662)Byg/Szt2+
Genetic Background: involves: 129P2/OlaHsd * C57BL/6J

 MP:0011099 complete lethality throughout fetal growth and development "death of all organisms of a given genotype in a population between the completion of organogenesis and birth (Mus: E14 to approximately E18.5)" [MGI:csmith]
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Allelic Composition: Ybx1tm1Tuch/Ybx1tm1Tuch
Genetic Background: involves: 129S/SvEv * C57BL/6

 MP:0011108 partial embryonic lethality during organogenesis "the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between embryo turning and the completion of organogenesis (Mus: E9 to less than E14)" [MGI:csmith]
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Allelic Composition: Otx1tm1Sia/Otx1+,Otx2tm2(Otx1)Sia/Otx2+
Genetic Background: involves: C57BL/6 * CBA

 MP:0011109 partial lethality throughout fetal growth and development "the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and birth (Mus: E14 to approximately E18.5)" [MGI:csmith]
Show

Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

 MP:0011111 complete lethality during fetal growth through weaning "the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and weaning age (Mus: E14 to approximately 3 weeks of age)" [MGI:csmith]
Show

Allelic Composition: Ybx1tm1Ley/Ybx1tm1Ley
Genetic Background: involves: 129X1/SvJ * C57BL/6

 MP:0011704 decreased fibroblast proliferation "reduction in the expansion rate of a fibroblast cell population by cell division" [MGI:csmith]
Show

Allelic Composition: Sox2lcc/Sox2+
Genetic Background: involves: 101/H * C3H/HeH

Allelic Composition: Ybx1tm1Tuch/Ybx1tm1Tuch
Genetic Background: involves: 129S/SvEv * C57BL/6

  


Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSMUSG00000038146 Notch3 / Q61982 / Neurogenic locus notch homolog protein 3 Notch 3 extracellular truncation Notch 3 intracellular domain / Q9UM47*  / complex / reaction






 

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