Ybx1 Y box protein 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ybx1provided by MGI
Official Full Name: Y box protein 1provided by MGI
Primary source: MGI:MGI:99146
See related: Ensembl:ENSMUSG00000028639 AllianceGenome:MGI:99146
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: EF1A; MSY1; YB-1; dbpB; Nsep1; mYB-1a; 1700102N10Rik
Summary: Enables chromatin binding activity; mRNA binding activity; and single-stranded DNA binding activity. Involved in epidermis development and negative regulation of cellular senescence. Acts upstream of or within several processes, including cellular response to interleukin-7; negative regulation of striated muscle cell differentiation; and negative regulation of transcription by RNA polymerase II. Located in P-body and nucleus. Part of histone pre-mRNA 3'end processing complex. Is active in synapse. Is expressed in several structures, including brain; branchial arch; facial prominence; gonad; and retina. Orthologous to human YBX1 (Y-box binding protein 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis adult (RPKM 192.5), CNS E11.5 (RPKM 174.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4; 4 D2.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (119134524..119153462, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (119277327..119296265, complement)

Chromosome 4 - NC_000070.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Microglia-derived exosomes selective sorted by YB-1 alleviate nerve damage and cognitive outcome in Alzheimer's disease.
Title: Microglia-derived exosomes selective sorted by YB-1 alleviate nerve damage and cognitive outcome in Alzheimer's disease.
YBX1 promotes type H vessel-dependent bone formation in an m5C-dependent manner.
Title: YBX1 promotes type H vessel-dependent bone formation in an m5C-dependent manner.
Decreased YB-1 expression denervates brown adipose tissue and contributes to age-related metabolic dysfunction.
Title: Decreased YB-1 expression denervates brown adipose tissue and contributes to age-related metabolic dysfunction.
Y-box binding protein 1 promotes chromatin accessibility to aggravate liver fibrosis.
Title: Y-box binding protein 1 promotes chromatin accessibility to aggravate liver fibrosis.
YBX1 as an oncogenic factor in T-cell acute lymphoblastic leukemia.
Title: YBX1 as an oncogenic factor in T-cell acute lymphoblastic leukemia.
DNA binding protein YB-1 is a part of the neutrophil extracellular trap mediation of kidney damage and cross-organ effects.
Title: DNA binding protein YB-1 is a part of the neutrophil extracellular trap mediation of kidney damage and cross-organ effects.
Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1.
Title: Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1.
Splicing factor YBX1 regulates bone marrow stromal cell fate during aging.
Title: Splicing factor YBX1 regulates bone marrow stromal cell fate during aging.
YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m[6]A-mediated YWHAZ stability.
Title: YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m(6)A-mediated YWHAZ stability.
The formation of HuR/YB1 complex is required for the stabilization of target mRNA to promote myogenesis.
Title: The formation of HuR/YB1 complex is required for the stabilization of target mRNA to promote myogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (71)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Gene trapped (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

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

RH126663 (e-PCR)
- UniSTS:207711

PMC140751P1 (e-PCR)
- UniSTS:270973

RH79815 (e-PCR)
- UniSTS:85383

PMC127671P1 (e-PCR)
- UniSTS:270556

D5Mit392.1 (e-PCR), detects polymorphism
- UniSTS:130544

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

Gene Ontology Provided by MGI

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 GTPase binding	IEA Inferred from Electronic Annotation more info
enables GTPase binding	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay 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	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
involved_in embryonic morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in epidermis development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
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 cellular senescence	IMP Inferred from Mutant Phenotype more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within 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	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
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 cytoplasmic translation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation 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 DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity 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	IDA Inferred from Direct Assay more info	PubMed
part_of U12-type spliceosomal complex	IEA Inferred from Electronic Annotation more info
part_of U12-type spliceosomal complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IGI Inferred from Genetic Interaction more info	PubMed
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
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	EXP Inferred from Experiment more info	PubMed
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: Y-box-binding protein 1

Names: CBF-A; CCAAT-binding transcription factor I subunit A; DNA-binding protein B; EFI-A; Y-box transcription factor; 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.

mRNA and Protein(s)

NM_011732.2 → NP_035862.2 Y-box-binding protein 1

See identical proteins and their annotated locations for NP_035862.2

Status: VALIDATED

Source sequence(s)

AK150821, BG066506, BU512458, BX470153

Consensus CDS

CCDS18579.1

UniProtKB/Swiss-Prot

P22568, P27817, P43482, P62960

UniProtKB/TrEMBL

Q3UBT1, Q810K5

Related

ENSMUSP00000078589.7, ENSMUST00000079644.13

Conserved Domains (1) summary

pfam00313
Location:57 → 126

CSD; 'Cold-shock' DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

119134524..119153462 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030253407.1 → XP_030109267.1 Y-box-binding protein 1 isoform X3

UniProtKB/TrEMBL

Q810K5

Conserved Domains (1) summary

cd04458
Location:59 → 88

CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...
XM_006502934.4 → XP_006502997.1 Y-box-binding protein 1 isoform X2

UniProtKB/TrEMBL

Q60951

Conserved Domains (1) summary

cd04458
Location:59 → 88

CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...
XM_006502933.4 → XP_006502996.1 Y-box-binding protein 1 isoform X1

UniProtKB/TrEMBL

Q60951

Conserved Domains (1) summary

pfam00313
Location:57 → 126

CSD; 'Cold-shock' DNA-binding domain