Ybx1 MGI Mouse Gene Detail - MGI:99146

Symbol

Ybx1
Name

Y box protein 1
Synonyms

dbpB, DNA binding protein B, EF1A, MSY1, Nsep1, YB-1

Feature Type

protein coding gene
IDs

MGI:99146
NCBI Gene: 22608
Alliance

genome feature page
Transcription Start Sites

9 TSS

Sequence Map

Chr4:119135178-119151801 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 55.34 cM, cytoband D1
Mapping Data

3 experiments

SNPs within 2kb

407 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_99146	protein coding gene	Chr4:119134524-119153462 (-)
129S1/SvImJ	ENSMUSG00200011216	protein coding gene	Chr4:113039572-113056192 (-)
A/J	ENSMUSG00195030206	protein coding gene	Chr4:114285645-114302343 (-)
AKR/J	ENSMUSG00220020660	protein coding gene	Chr4:113646805-113663433 (-)
BALB/cJ	ENSMUSG00180040777	protein coding gene	Chr4:112348915-112365634 (-)
C3H/HeJ	ENSMUSG00175022087	protein coding gene	Chr4:113362093-113378813 (-)
C57BL/6NJ	ENSMUSG00215031647	protein coding gene	Chr4:114473148-114489773 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026396	protein coding gene	Chr4:109834148-109850703 (-)
CAST/EiJ	ENSTCUG00005042266	protein coding gene	Chr4:113169034-113185533 (-)
CBA/J	ENSMUSG00210052021	protein coding gene	Chr4:112968583-112985303 (-)
DBA/2J	ENSMUSG00185044765	protein coding gene	Chr4:114520639-114537335 (-)
FVB/NJ	ENSMUSG00205018646	protein coding gene	Chr4:112444510-112461229 (-)
JF1/MsJ	ENSUMUG00000012627	protein coding gene	Chr4:114427726-114444383 (-)
LP/J	ENSMUSG00230042412	protein coding gene	Chr4:117857343-117873963 (-)
NOD/ShiLtJ	ENSMUSG00190037694	protein coding gene	Chr4:112351192-112367815 (-)
NZO/HlLtJ	ENSMUSG00225014846	protein coding gene	Chr4:123404248-123420871 (-)
PWK/PhJ	ENSLUMG00010039885	protein coding gene	Chr4:111845763-111862227 (-)
SPRET/EiJ	ENSMSPG00010034746	protein coding gene	Chr4:113928929-113944097 (-)
WSB/EiJ	ENSIUOG00005036688	protein coding gene	Chr4:112660916-112677568 (-)

Human Ortholog

YBX1, Y-box binding protein 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

YBX1, Y-box binding protein 1
Synonyms

BP-8, CBF-A, CSDA2, CSDB, DBPB, EFI-A, MDR-NF1, NSEP-1, NSEP1, YB-1, YB1
Links

HGNC:8014

NCBI Gene ID: 4904

UniProt: P67809
Chr Location

1p34.2; chr1:42682408-42703805 (+) GRCh38

MGI Vertebrate Homology

Ybx1 stringent orthology
1 human;1 mouse;2 rat;1 zebrafish
HCOP

vertebrate homology predictions: YBX1
Gene Tree

Ybx1

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Phenotype Summary

27 phenotypes from 3 alleles in 4 genetic backgrounds
5 phenotypes from multigenic genotypes
2 images
28 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

27
Chemically induced (other)

2
Endonuclease-mediated

5
Gene trapped

14
Radiation induced

1
Targeted

5
Genomic Mutations

4 involving Ybx1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

21 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous null mice exhibit embryonic and perinatal lethality and are severely growth retarded. Some mice exhibit craniofacial defects and respiratory failure. MEFs are more sensitive to oxidative stress resulting in premature senescence.

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All GO Annotations

106
GO References

23

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

782
Tissues

103
cDNA Data

516
Literature Summary

22

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA YBX1

Xenbase ybx1

ZFIN ybx1

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All Sequences

101
RefSeq

8
UniProt

8
CCDS

CCDS18579.1

Ensembl

ENSMUSG00000028639 (Evidence)
NCBI Gene

22608

			Length	Strain/Species	Flank
genomic	ENSMUSG00000028639	Ensembl Gene Model \| MGI Sequence Detail	16624	C57BL/6J	± kb
transcript	ENSMUST00000079644	Ensembl \| MGI Sequence Detail	1628	Not Applicable
polypeptide	ENSMUSP00000078589	Ensembl \| MGI Sequence Detail	322	Not Applicable

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UniProt

8 Sequences
Protein Ontology

PR:000017525 Y-box-binding protein 1

(term hierarchy)
InterPro Domains

IPR011129 Cold-shock domain

IPR019844 Cold-shock domain, conserved site

IPR050181 Cold shock domain-containing protein

IPR002059 Cold-shock domain, DNA-binding

IPR012340 Nucleic acid-binding, OB-fold
GlyGen

P62960 1 site, 1 O-linked glycan (1 site)

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All nucleic 530

cDNA 518

Primer pair 8

Other 4

Antibodies 5

Microarray probesets 6

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MGD-MRK-15843, MGI:2140677

Summaries

All 143

Developmental Gene Expression 22

Gene Ontology 23

Phenotypes 28
Earliest

J:1387 Shaughnessy M, et al., Absence of MHC gene expression in lens and cloning of dbpB/YB-1, a DNA-binding protein expressed in mouse lens. Curr Eye Res. 1992 Feb;11(2):175-81
Latest

J:391318 Ikeda S, et al., Deletion of Ybx1 results in germ cell hypoplasia in mouse embryos. J Reprod Dev. 2026 Aug 1;72(4):700-709

TSS for Ybx1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr43106	Chr4:119151941-119151950 (-)	-145 bp
Tssr43105	Chr4:119151911-119151922 (-)	-116 bp
Tssr43104	Chr4:119151717-119151735 (-)	75 bp
Tssr43103	Chr4:119151697-119151715 (-)	95 bp
Tssr43102	Chr4:119151644-119151667 (-)	145 bp
Tssr43101	Chr4:119151597-119151642 (-)	181 bp
Tssr43100	Chr4:119151435-119151507 (-)	330 bp
Tssr43099	Chr4:119139450-119139477 (-)	12,337 bp
Tssr43098	Chr4:119136303-119136317 (-)	15,491 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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