Ybx1 Y box binding protein 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ybx1provided by RGD
Official Full Name: Y box binding protein 1provided by RGD
Primary source: RGD:61843
See related: EnsemblRapid:ENSRNOG00000023786 AllianceGenome:RGD:61843
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Yb1; Byb1; Cbfa; Dbpb; Ef1a; Msy1; YB-1; CBF-A; EFI-A; Nsep1
Summary: Enables nucleic acid binding activity and p53 binding activity. Involved in several processes, including negative regulation of apoptotic process; negative regulation of insulin receptor signaling pathway; and regulation of transcription by RNA polymerase II. Located in dendrite; neuronal cell body; and perinuclear region of cytoplasm. Part of protein-containing complex. Biomarker of myocardial infarction. Orthologous to human YBX1 (Y-box binding protein 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 1571.8), Muscle (RPKM 1024.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (138167444..138188155, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (132882137..132898885, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (138319754..138336721, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exosomal YB-1 facilitates ovarian restoration by MALAT1/miR-211-5p/FOXO3 axis.
Title: Exosomal YB-1 facilitates ovarian restoration by MALAT1/miR-211-5p/FOXO(3) axis.
MiR-379-5p Promotes Chondrocyte Proliferation via Inhibition of PI3K/Akt Pathway by Targeting YBX1 in Osteoarthritis.
Title: MiR-379-5p Promotes Chondrocyte Proliferation via Inhibition of PI3K/Akt Pathway by Targeting YBX1 in Osteoarthritis.
YBX1 Protects against Apoptosis Induced by Oxygen-Glucose Deprivation/Reoxygenation in PC12 Cells via Activation of the AKT/GSK3beta Pathway.
Title: YBX1 Protects against Apoptosis Induced by Oxygen-Glucose Deprivation/Reoxygenation in PC12 Cells via Activation of the AKT/GSK3β Pathway.
Y-box protein 1 promotes hypoxia/reoxygenation- or ischemia/reperfusion-induced cardiomyocyte apoptosis via SHP-1-dependent STAT3 inactivation.
Title: Y-box protein 1 promotes hypoxia/reoxygenation- or ischemia/reperfusion-induced cardiomyocyte apoptosis via SHP-1-dependent STAT3 inactivation.
Results show that follicle-stimulating hormone (FSH) promotes an increase in the phosphorylation of Y-box-binding protein-1 (YB-1) on serine Ser(102) within 15 min that is maintained at significantly increased levels until approximately 8 h post treatment.
Title: Extracellular Signal-regulated Kinase (ERK)-dependent Phosphorylation of Y-Box-binding Protein 1 (YB-1) Enhances Gene Expression in Granulosa Cells in Response to Follicle-stimulating Hormone (FSH).
YB-1 protein levels correlated with microglia phagocytic activity because its upregulation
Title: Constitutive and functional expression of YB-1 in microglial cells.
These studies define new roles for glucocorticoid receptor, Y-box binding protein 1, and RNase UK114 in the formation of a molecular complex that degrades MCP-1 mRNA.
Title: Y-box binding protein 1 and RNase UK114 mediate monocyte chemoattractant protein 1 mRNA stability in vascular smooth muscle cells.
YB-1 is activated during the hepatic acute phase response.
Title: Rat Mrp2 gene expression is regulated by an interleukin-1β-stimulated biphasic response with enhanced transcription and subcellular shuttling of YB-1.
Data demonstrate that extracellular YB-1 associates with outer cell membrane components and interacts with extracellular Notch-3 receptor domains.
Title: YB-1 acts as a ligand for Notch-3 receptors and modulates receptor activation.
YB-1 has an apparent stimulatory effect on c-Raf, MEK1/2, ERK1/2 and cell-cycle progression in messangial cells, after which activated ERK1/2 goes on to upregulate YB-1 expression and augment the proliferative effect of YB-1.
Title: Y-box protein 1 stimulates mesangial cell proliferation via activation of ERK1/2.

Submit: New GeneRIF Correction See all GeneRIFs (19)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH128187 (e-PCR)
- UniSTS:211495

Ybx1 (e-PCR), detects polymorphism
- UniSTS:265526

Ybx1 (e-PCR), detects polymorphism
- UniSTS:265527

Ybx1 (e-PCR), detects polymorphism
- UniSTS:265528

UniSTS:265529 (e-PCR)
- UniSTS:265529

Ybx1 (e-PCR), detects polymorphism
- UniSTS:265529

Nsep1 (e-PCR), detects polymorphism
- UniSTS:265530

Ybx1 (e-PCR), detects polymorphism
- UniSTS:498757

PMC140751P1 (e-PCR)
- UniSTS:270973

BF396960 (e-PCR)
- UniSTS:245894

RH79815 (e-PCR)
- UniSTS:85383

PMC127671P1 (e-PCR)
- UniSTS:270556

Ybx1 (e-PCR), detects polymorphism
- UniSTS:527608

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables C5-methylcytidine-containing RNA reader activity	ISO Inferred from Sequence Orthology more info
enables C5-methylcytidine-containing RNA reader activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables GTPase binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables miRNA binding	ISO Inferred from Sequence Orthology more info
enables miRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables nucleic acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables p53 binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in CRD-mediated mRNA stabilization	ISO Inferred from Sequence Orthology more info
involved_in CRD-mediated mRNA stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in RNA transport	ISO Inferred from Sequence Orthology more info
involved_in RNA transport	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within cellular response to interleukin-7	ISO Inferred from Sequence Orthology more info
involved_in embryonic morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in epidermis development	ISO Inferred from Sequence Orthology more info
involved_in epidermis development	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA stabilization	ISO Inferred from Sequence Orthology more info
involved_in mRNA stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in miRNA transport	ISO Inferred from Sequence Orthology more info
involved_in miRNA transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of RNA metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cellular senescence	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cellular senescence	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of insulin receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of macromolecule biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of striated muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of translation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell division	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cytoplasmic translation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein localization to cytoplasmic stress granule	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA transport	ISO Inferred from Sequence Orthology more info
involved_in tRNA transport	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of CRD-mediated mRNA stability complex	ISO Inferred from Sequence Orthology more info
located_in P-body	ISO Inferred from Sequence Orthology more info
part_of U12-type spliceosomal complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic stress granule	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic stress granule	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in extracellular exosome	ISO Inferred from Sequence Orthology more info
located_in extracellular exosome	ISS Inferred from Sequence or Structural Similarity more info
part_of histone pre-mRNA 3'end processing complex	ISO Inferred from Sequence Orthology more info
part_of histone pre-mRNA 3'end processing complex	ISS Inferred from Sequence or Structural Similarity more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synapse	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: Y-box-binding protein 1

Names: CCAAT-binding transcription factor 1 subunit A; CCAAT-binding transcription factor I subunit A; DNA binding protein B; Y box transcription factor; enhancer factor 1 alpha; enhancer factor 1 subunit A; enhancer factor I subunit A; nuclease-sensitive element-binding protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.