Ybx3 Y box protein 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ybx3provided by MGI
Official Full Name: Y box protein 3provided by MGI
Primary source: MGI:MGI:2137670
See related: Ensembl:ENSMUSG00000030189 AllianceGenome:MGI:2137670
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: Yb2; Csda; Dpba; MSY3; MSY4; dbpA; oxyR
Summary: Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; mRNA 3'-UTR binding activity; and ribonucleoprotein complex binding activity. Involved in negative regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including male gonad development; negative regulation of skeletal muscle tissue development; and positive regulation of organ growth. Located in cytoplasm and nucleus. Is active in synapse. Is expressed in several structures, including brain; branchial arch; jaw; limb bud; and sensory organ. Orthologous to human YBX3 (Y-box binding protein 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in testis adult (RPKM 404.0), liver E14 (RPKM 96.6) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 F3; 6 63.44 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (131341821..131365413, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (131364858..131388450, complement)

Chromosome 6 - NC_000072.7 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?

DNA-binding protein-A: a multitool in tubular epithelial cells.
Title: DNA-binding protein-A: a multitool in tubular epithelial cells.
DNA-binding protein-A promotes kidney ischemia/reperfusion injury and participates in mitochondrial function.
Title: DNA-binding protein-A promotes kidney ischemia/reperfusion injury and participates in mitochondrial function.
The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells.
Title: The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells.
Cold Shock Domain Protein DbpA Orchestrates Tubular Cell Damage and Interstitial Fibrosis in Inflammatory Kidney Disease.
Title: Cold Shock Domain Protein DbpA Orchestrates Tubular Cell Damage and Interstitial Fibrosis in Inflammatory Kidney Disease.
homozygous double mutants could not be generated as haploinsufficiency of both Ybx2 and Ybx3 caused sterility characterized by extensive defects in spermatid differentiation.
Title: Compound Heterozygosity for Y Box Proteins Causes Sterility Due to Loss of Translational Repression.
In a hindlimb ischemia model, transfer of short-hairpin RNA targeting CSDA ameliorated ischemia without direct transfer of angiogenic factors.
Title: Critical roles of cold shock domain protein A as an endogenous angiogenesis inhibitor in skeletal muscle.
ZO-1 and ZONAB are critical for differentiation and homeostasis of the RPE monolayer and may be involved in RPE disorders such as proliferative vitroretinopathy and atrophic age-related macular degeneration
Title: The tight junction associated signalling proteins ZO-1 and ZONAB regulate retinal pigment epithelium homeostasis in mice.
results indicated CD133(+) subpopulation of SW480 SCPs bear heterogeneous invasive and metastatic ability, and CRC-CSCs might be a heterogeous subpopulation
Title: Cold shock domain protein A (CSDA) overexpression inhibits tumor growth and lymph node metastasis in a mouse model of squamous cell carcinoma.
MSY4 is an important component of the mechanisms that sense epithelial density and participates in the complex transcriptional networks that regulate the switch between proliferation and differentiation
Title: ZONAB promotes proliferation and represses differentiation of proximal tubule epithelial cells.
Loss of Cold shock domain protein A leads to angiogenesis and lymphangiogenesis
Title: Cold shock domain protein A represses angiogenesis and lymphangiogenesis via inhibition of serum response element.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

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

Endonuclease-mediated (4)
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

Csda (e-PCR), detects polymorphism
- UniSTS:498754

RH136939 (e-PCR)
- UniSTS:219028

G61989 (e-PCR)
- UniSTS:139208

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonucleoprotein complex 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
acts_upstream_of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular hyperosmotic response	IEA Inferred from Electronic Annotation more info
involved_in cellular hyperosmotic response	ISO Inferred from Sequence Orthology more info
involved_in cellular response to tumor necrosis factor	IEA Inferred from Electronic Annotation more info
involved_in cellular response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of ectopic germ cell programmed cell death	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fertilization	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 male gonad development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of developmental process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of necroptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of necroptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of reproductive process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of skeletal muscle tissue development	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of organ growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in gap junction	ISO Inferred from Sequence Orthology more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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 3

Names: DNA-binding protein A; cold shock domain protein A; cold shock domain-containing protein A

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_011733.2 → NP_035863.1 Y-box-binding protein 3 short isoform

See identical proteins and their annotated locations for NP_035863.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame segment in the coding region, compared to variant 1. The resulting protein, known as the short isoform, is shorter than the long isoform.

Source sequence(s)

BC027785, BC048242

Consensus CDS

CCDS20605.1

UniProtKB/TrEMBL

Q68G78

Related

ENSMUSP00000085172.3, ENSMUST00000087865.4

Conserved Domains (1) summary

pfam00313
Location:83 → 152

CSD; 'Cold-shock' DNA-binding domain
NM_139117.2 → NP_620817.2 Y-box-binding protein 3 long isoform

See identical proteins and their annotated locations for NP_620817.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and it encodes the long isoform.

Source sequence(s)

BC027785, BC048242

Consensus CDS

CCDS20606.1

UniProtKB/Swiss-Prot

Q80WG4, Q9EQF7, Q9EQF8, Q9JKB3

UniProtKB/TrEMBL

Q8BPG0

Related

ENSMUSP00000032309.7, ENSMUST00000032309.13

Conserved Domains (1) summary

pfam00313
Location:83 → 152

CSD; 'Cold-shock' DNA-binding domain