Ybx3 Y box binding protein 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ybx3provided by RGD
Official Full Name: Y box binding protein 3provided by RGD
Primary source: RGD:621056
See related: AllianceGenome:RGD:621056
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Yb2; Csda; Dbpa
Summary: Enables single-stranded DNA binding activity. Involved in animal organ regeneration; negative regulation of transcription by RNA polymerase II; and spermatogenesis. Located in gap junction. Orthologous to human YBX3 (Y-box binding protein 3). [provided by Alliance of Genome Resources, May 2025]
Expression: Biased expression in Muscle (RPKM 1552.8), Spleen (RPKM 988.5) and 7 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q42

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (166861180..166884532, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (165129747..165153101, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (165606819..165630041, complement)

Chromosome 4 - NC_086022.1 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
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?

These results suggest that Csda expression in alveolar epithelial cells type II decreases under hyperoxia conditions, which promotes transdifferentiation and inhibits proliferation of alveolar epithelial cells.
Title: Decreased ZONAB expression promotes excessive transdifferentiation of alveolar epithelial cells in hyperoxia-induced bronchopulmonary dysplasia.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ha2919 (e-PCR)
- UniSTS:515610

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

RH136939 (e-PCR)
- UniSTS:219028

RH140312 (e-PCR)
- UniSTS:222389

AI549543 (e-PCR)
- UniSTS:244155

G61989 (e-PCR)
- UniSTS:139208

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables mRNA 3'-UTR binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables ribonucleoprotein complex binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables small GTPase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in animal organ regeneration	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of apoptotic process	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fertilization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male gonad development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of RNA metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of developmental process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	ISO Inferred from Sequence Orthology more info
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 macromolecule biosynthetic process	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cytoplasmic translation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of organ growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

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

Names: DNA-binding protein A; RYB-A; Y-box-binding protein A; cold shock domain protein A; cold shock domain-containing protein A; muscle Y-box protein YB2

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_031979.3 → NP_114185.3 Y-box-binding protein 3

See identical proteins and their annotated locations for NP_114185.3

Status: PROVISIONAL

Source sequence(s)

U22893

UniProtKB/Swiss-Prot

Q62764, Q63748

Conserved Domains (1) summary

pfam00313
Location:83 → 152

CSD; 'Cold-shock' DNA-binding domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

166861180..166884532 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108450.2 → XP_038964378.1 Y-box-binding protein 3 isoform X1

Conserved Domains (1) summary

pfam00313
Location:83 → 152

CSD; 'Cold-shock' DNA-binding domain