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Gene: Ybx3 (Y box binding protein 3) Rattus norvegicus

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Symbol:

Ybx3

Name:

Y box binding protein 3

RGD ID:

621056

Description:

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); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

cold shock domain protein A; cold shock domain-containing protein A; Csda; Dbpa; DNA-binding protein A; MGC124554; muscle Y-box protein YB2; RYB-A; Y-box-binding protein 3; Y-box-binding protein A; Yb2

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	YBX3 (Y-box binding protein 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Ybx3 (Y box protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ybx3 (Y-box binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	YBX3 (Y-box binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	YBX3 (Y-box binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	YBX3 (Y-box binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	YBX3 (Y-box binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Ybx3 (Y-box binding protein 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	TYR (tyrosinase)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	YBX3 (Y-box binding protein 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ybx3 (Y box protein 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	ybx1 (Y box binding protein 1)	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	cey-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	cey-1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	yps	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	yps	Alliance	DIOPT (InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	ybx3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	ybx3	Alliance	DIOPT (Ensembl Compara\|OMA\|PANTHER\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	166,861,180 - 166,884,532 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	166,861,181 - 166,884,691 (-)	Ensembl				GRCr8
mRatBN7.2	4	165,129,747 - 165,153,101 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	165,129,758 - 165,153,161 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	171,414,533 - 171,437,843 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	167,197,552 - 167,220,862 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	165,831,596 - 165,854,906 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	165,606,819 - 165,630,041 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	165,606,819 - 165,630,118 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	228,170,272 - 228,193,525 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	169,076,517 - 169,099,849 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	153,733,515 - 153,756,519 (-)	NCBI		Celera
RGSC_v3.1	4	169,321,476 - 169,344,762 (-)	NCBI
Cytogenetic Map	4	q42	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Optic Nerve Injuries (IEP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(1->4)-beta-D-glucan (ISO)

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP,ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,6-dimethoxyphenol (ISO)

2,6-dinitrotoluene (EXP)

2-butoxyethanol (ISO)

2-hydroxypropanoic acid (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3H-1,2-dithiole-3-thione (EXP)

4,4'-sulfonyldiphenol (ISO)

4-hydroxynon-2-enal (ISO)

6-propyl-2-thiouracil (EXP)

7,12-dimethyltetraphene (ISO)

acrolein (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

atrazine (EXP)

beauvericin (ISO)

benzo[a]pyrene (ISO)

beta-lapachone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol AF (ISO)

buspirone (EXP)

Butylbenzyl phthalate (ISO)

cadmium dichloride (ISO)

caffeine (ISO)

candesartan (EXP)

carbon nanotube (ISO)

chloropicrin (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

cocaine (EXP)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumarin (ISO)

Cuprizon (EXP)

cyclophosphamide (EXP)

cyclosporin A (ISO)

deoxynivalenol (ISO)

dexamethasone (ISO)

Dibutyl phosphate (ISO)

dibutyl phthalate (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

elemental selenium (ISO)

endosulfan (EXP)

fenthion (ISO)

flutamide (EXP)

FR900359 (ISO)

fructose (EXP)

furfural (ISO)

griseofulvin (ISO)

indometacin (ISO)

ivermectin (ISO)

ketamine (EXP)

methidathion (ISO)

methotrexate (EXP)

methylmercury chloride (ISO)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (EXP)

Nivalenol (ISO)

ozone (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (EXP,ISO)

phenethyl caffeate (EXP)

phenobarbital (ISO)

phenol red (ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

propiconazole (ISO)

quercetin (ISO)

rac-lactic acid (ISO)

raloxifene (EXP)

resveratrol (ISO)

SB 431542 (ISO)

selenium atom (ISO)

sodium arsenite (ISO)

sodium chloride (ISO)

sodium fluoride (ISO)

tamoxifen (ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

urethane (ISO)

vinclozolin (EXP)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ regeneration (IEP)

cellular hyperosmotic response (IEA,ISO)

cellular response to tumor necrosis factor (IEA,ISO)

DNA-templated transcription (IEA)

fertilization (ISO)

in utero embryonic development (ISO)

male gonad development (ISO)

negative regulation of apoptotic process (ISO)

negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (ISO)

negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (IEA,ISO)

negative regulation of necroptotic process (IEA,ISO)

negative regulation of skeletal muscle tissue development (ISO)

negative regulation of transcription by RNA polymerase II (IMP,ISO)

positive regulation of cytoplasmic translation (ISO)

positive regulation of organ growth (ISO)

regulation of gene expression (IBA)

spermatogenesis (IEP,ISO)

Cellular Component

bicellular tight junction (ISO)

cytoplasm (IEA,ISO)

cytosol (IEA,ISO)

gap junction (IDA)

nucleus (IBA,IEA,ISO)

perinuclear region of cytoplasm (ISO)

synapse (ISO)

Molecular Function

DNA binding (IEA,ISO)

mRNA 3'-UTR binding (ISO)

nucleic acid binding (IBA,IEA)

protein binding (ISO)

ribonucleoprotein complex binding (ISO)

RNA binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

single-stranded DNA binding (IDA,IEA,ISO)

small GTPase binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Association of connexin36 and zonula occludens-1 with zonula occludens-2 and the transcription factor zonula occludens-1-associated nucleic acid-binding protein at neuronal gap junctions in rodent retina.	Ciolofan C, etal., Neuroscience. 2006 Jun 30;140(2):433-51. Epub 2006 May 2.
2.	Screening for differentially expressed genes in the rat inner retina and optic nerve after optic nerve crush.	Dieterich DC, etal., Neurosci Lett. 2002 Jan 4;317(1):29-32.
3.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
5.	A novel growth-inducible gene that encodes a protein with a conserved cold-shock domain.	Ito K, etal., Nucleic Acids Res 1994 Jun 11;22(11):2036-41.
6.	Expression of a Y-box protein, YB2/RYB-a, precedes protamine 2 expression during spermatogenesis in rodents.	Iuchi Y, etal., Mol Hum Reprod. 2001 Nov;7(11):1023-31.
7.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
8.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
10.	Cloning and characterization of a novel transcriptional repressor of the nicotinic acetylcholine receptor delta-subunit gene.	Sapru MK, etal., J Biol Chem 1996 Mar 22;271(12):7203-11.

Additional References at PubMed

PMID:10772793	PMID:12117816	PMID:12433987	PMID:12477932	PMID:15592429	PMID:16954378	PMID:17934523	PMID:18676817	PMID:22658674	PMID:22681889	PMID:22711822	PMID:29393348
PMID:35352799

Genomics

Comparative Map Data

Ybx3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	166,861,180 - 166,884,532 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	166,861,181 - 166,884,691 (-)	Ensembl				GRCr8
mRatBN7.2	4	165,129,747 - 165,153,101 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	165,129,758 - 165,153,161 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	171,414,533 - 171,437,843 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	167,197,552 - 167,220,862 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	165,831,596 - 165,854,906 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	165,606,819 - 165,630,041 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	165,606,819 - 165,630,118 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	228,170,272 - 228,193,525 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	169,076,517 - 169,099,849 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	153,733,515 - 153,756,519 (-)	NCBI		Celera
RGSC_v3.1	4	169,321,476 - 169,344,762 (-)	NCBI
Cytogenetic Map	4	q42	NCBI

YBX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	10,699,089 - 10,723,323 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	10,699,077 - 10,723,388 (-)	Ensembl			hg38	GRCh38
GRCh37	12	10,851,688 - 10,875,922 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	10,742,955 - 10,767,171 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	12	10,742,955 - 10,767,171	NCBI
Celera	12	16,000,000 - 16,024,276 (-)	NCBI		Celera
Cytogenetic Map	12	p13.2	NCBI
HuRef	12	10,580,443 - 10,604,713 (-)	NCBI		HuRef
CHM1_1	12	10,821,053 - 10,845,329 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	10,572,193 - 10,596,426 (-)	NCBI		T2T-CHM13v2.0

Ybx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	131,341,821 - 131,365,413 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	131,341,818 - 131,365,439 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	131,364,858 - 131,388,450 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	131,364,855 - 131,388,476 (-)	Ensembl			mm10	GRCm38
MGSCv37	6	131,314,876 - 131,338,468 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	131,330,551 - 131,354,143 (-)	NCBI		MGSCv36	mm8
Celera	6	136,414,596 - 136,438,226 (-)	NCBI		Celera
Cytogenetic Map	6	F3	NCBI
cM Map	6	63.44	NCBI

Ybx3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955413	7,089,719 - 7,108,473 (+)	Ensembl
ChiLan1.0	NW_004955413	7,090,085 - 7,111,542 (+)	NCBI	ChiLan1.0	ChiLan1.0

YBX3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	16,170,908 - 16,195,183 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	16,167,659 - 16,191,821 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	10,728,049 - 10,752,267 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	10,994,177 - 11,018,504 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	10,996,380 - 11,018,172 (-)	Ensembl			panPan2	panpan1.1

YBX3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	35,043,756 - 35,066,230 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	35,043,699 - 35,066,227 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	11,465,924 - 11,493,283 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	35,383,798 - 35,411,218 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	27	35,383,839 - 35,411,207 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	27	35,266,703 - 35,294,044 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	35,211,037 - 35,238,385 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	11,081,610 - 11,108,979 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

YBX3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	61,337,862 - 61,361,279 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	5	61,337,868 - 61,361,269 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	64,060,833 - 64,084,239 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

YBX3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	10,498,162 - 10,522,432 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	10,500,361 - 10,522,226 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666089	2,576,328 - 2,600,838 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ybx3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	6	16,830,287 - 16,853,589 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Ybx3
88 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	488
Count of miRNA genes:	165
Interacting mature miRNAs:	181
Transcripts:	ENSRNOT00000007427, ENSRNOT00000068185
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
6478754	Anxrr43	Anxiety related response QTL 43		0.14035	locomotor behavior trait (VT:0001392)	distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)	4	146370897	184426481	Rat
724558	Plsm2	Polydactyly-luxate syndrome (PLS) morphotypes QTL 2		0.0003	hindlimb integrity trait (VT:0010563)	hind foot phalanges count (CMO:0001949)	4	134095016	179095016	Rat
1582237	Kidm34	Kidney mass QTL 34	4	0.0001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	4	149763204	169799698	Rat
6478693	Anxrr32	Anxiety related response QTL 32		0.00092	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	146370897	184426481	Rat
6478757	Anxrr44	Anxiety related response QTL 44		0.01087	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
1358364	Sradr4	Stress Responsive Adrenal Weight QTL 4	4.92		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	131384565	176384565	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	27730518	170099664	Rat
61451	Ciaa4	CIA Autoantibody QTL 4	3.1		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	4	123870974	168870974	Rat
1331738	Bp209	Blood pressure QTL 209	2.979		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	140059299	181024663	Rat
6478700	Anxrr33	Anxiety related response QTL 33		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146370897	184426481	Rat
1298524	Oia8	Oil induced arthritis QTL 8			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	140059299	184426481	Rat
10053718	Scort25	Serum corticosterone level QTL 25	2.15	0.0097	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	157292416	184426481	Rat
738009	Sach4	Saccharine consumption QTL 4	4.9	0.000016	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	60916264	184426481	Rat
634335	Anxrr16	Anxiety related response QTL 16	7.22		locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	4	94638356	168870820	Rat
737821	Hcar9	Hepatocarcinoma resistance QTL 9	3.7		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	4	106848959	168870974	Rat
7411558	Bw133	Body weight QTL 133	13.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	4	127263297	172263297	Rat
6478778	Anxrr51	Anxiety related response QTL 51		0.25384	locomotor behavior trait (VT:0001392)	measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)	4	126334185	171334185	Rat
10401796	Kidm48	Kidney mass QTL 48			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	147299608	184426481	Rat
6478718	Anxrr34	Anxiety related response QTL 34		0.00896	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146370897	184426481	Rat
6478782	Anxrr52	Anxiety related response QTL 52		0.02091	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
631511	Pia7	Pristane induced arthritis QTL 7	4.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	123870974	168870974	Rat
634347	Hcar8	Hepatocarcinoma resistance QTL 8	5.8		liver integrity trait (VT:0010547)	liver tumorous lesion area to total liver area ratio (CMO:0001075)	4	124700988	169700988	Rat
6478720	Alc23	Alcohol consumption QTL 23		0.00509	drinking behavior trait (VT:0001422)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	155834926	184426481	Rat
6478785	Anxrr53	Anxiety related response QTL 53		0.01397	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
738031	Alc14	Alcohol consumption QTL 14	7.6	0.00003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	60916264	174095838	Rat
1576316	Ept5	Estrogen-induced pituitary tumorigenesis QTL 5	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	4	100752691	179366077	Rat
1581566	Eae21	Experimental allergic encephalomyelitis QTL 21	6.2		body mass (VT:0001259)	maximum body weight loss to initial body weight ratio (CMO:0001400)	4	137447185	182447185	Rat
1578674	Bmd12	Bone mineral density QTL 12	3.8		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	4	137430611	182430611	Rat
6478728	Anxrr36	Anxiety related response QTL 36		0.01061	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
738016	Alc16	Alcohol consumption QTL 16	3.6	0.00015	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	4	60916264	184426481	Rat
1358202	Gluco11	Glucose level QTL 11	2.4	0.02	adipocyte glucose uptake trait (VT:0004185)	absolute change in adipocyte glucose uptake (CMO:0000873)	4	86709649	168870974	Rat
61422	Cia13	Collagen induced arthritis QTL 13	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	134199006	168870974	Rat
634342	Cia24	Collagen induced arthritis QTL 24	4.5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	148121375	176967367	Rat
6478733	Anxrr37	Anxiety related response QTL 37		0.00095	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
737978	Pia23	Pristane induced arthritis QTL 23	5.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	123870974	168870974	Rat
61362	Oia2	Oil induced arthritis QTL 2		0.001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	140059299	184426481	Rat
6478737	Anxrr38	Anxiety related response QTL 38		0.00159	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	155834926	184426481	Rat
2293659	Bmd35	Bone mineral density QTL 35	4.5	0.0001	femur strength trait (VT:0010010)	femoral neck ultimate force (CMO:0001703)	4	160623982	184426481	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	12212457	182430611	Rat
6478748	Anxrr42	Anxiety related response QTL 42		0.28008	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	146370897	184426481	Rat
12798525	Anxrr57	Anxiety related response QTL 57	3.21	0.05	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	4	148834094	168870974	Rat

Markers in Region

RH136939

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	83,535,605 - 83,535,785 (+)	MAPPER	mRatBN7.2
mRatBN7.2	4	165,129,895 - 165,130,076 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	165,606,957 - 165,607,137	NCBI	Rnor6.0
Rnor_6.0	4	84,582,471 - 84,582,650	NCBI	Rnor6.0
Rnor_5.0	4	228,170,410 - 228,170,590	UniSTS	Rnor5.0
Rnor_5.0	4	149,241,374 - 149,241,553	UniSTS	Rnor5.0
RGSC_v3.4	4	169,076,652 - 169,076,832	UniSTS	RGSC3.4
RGSC_v3.4	4	82,808,157 - 82,808,336	UniSTS	RGSC3.4
Celera	4	78,404,672 - 78,404,851	UniSTS
Celera	4	153,733,653 - 153,733,833	UniSTS
Cytogenetic Map	4	q42	UniSTS

AI549543

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	165,148,054 - 165,148,186 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	165,625,115 - 165,625,246	NCBI	Rnor6.0
Rnor_5.0	4	228,188,568 - 228,188,699	UniSTS	Rnor5.0
RGSC_v3.4	4	169,094,810 - 169,094,941	UniSTS	RGSC3.4
Celera	4	153,751,811 - 153,751,942	UniSTS
RH 3.4 Map	4	1014.9	UniSTS
Cytogenetic Map	4	q42	UniSTS

RH140312

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	4	q42	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039108450	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC105778	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473964	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D28557	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216542	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226232	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U22893	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000007427 ⟹ ENSRNOP00000007427

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	4	166,861,181 - 166,884,691 (-)	Ensembl
mRatBN7.2 Ensembl	4	165,129,758 - 165,153,161 (-)	Ensembl
Rnor_6.0 Ensembl	4	165,606,819 - 165,630,118 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000068185 ⟹ ENSRNOP00000059241

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	4	166,861,183 - 166,884,691 (-)	Ensembl
mRatBN7.2 Ensembl	4	165,129,760 - 165,153,161 (-)	Ensembl
Rnor_6.0 Ensembl	4	165,606,821 - 165,629,996 (-)	Ensembl

RefSeq Acc Id:

NM_031979 ⟹ NP_114185

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	166,861,181 - 166,884,491 (-)	NCBI
mRatBN7.2	4	165,129,758 - 165,153,069 (-)	NCBI
Rnor_6.0	4	165,606,819 - 165,630,041 (-)	NCBI
Rnor_5.0	4	228,170,272 - 228,193,525 (-)	NCBI
RGSC_v3.4	4	169,076,517 - 169,099,849 (-)	RGD
Celera	4	153,733,515 - 153,756,519 (-)	NCBI

Sequence:

show sequence

CTTCGGGGCCGGGAGACCCAGCGAGACCGCGAGCGCGCGCGTCCCCCGCCCTCGAGCCGCCGCC
CGCCGCCGCGCCGCGCGATCCGCACCGGCCTCCCCGAGAGCGAGCCGGCCGCCGCGACCGCCAC
CGCGCTAACCGCCGCCAACCGCCACCGAGGTGCCCGGAGAGAGCGGAGAGGCGGCATGAGCGAG
GCGGGCGAGGCCACCACCGGCGGCACCACGCTCCCGCAGGCCGCGGCCGACGCGCCCGCCGCGG
CGCCCCCGGACCCCGCGCCTAAGAGCCCGGCGGCCAGCGGCGCGCCCCAGGCCCCGGCGCCCGC
CGCGCTGCTCGCGGGGAGCCCCGGCGGAGACGCAGCCCCCGGGCCCGCCCCGGCCTCATCAGCC
CCCGCGGGAAGCGAGGACGCGGAGAAGAAAGTTCTCGCCACCAAAGTCCTTGGCACTGTCAAAT
GGTTCAACGTCAGAAATGGATATGGATTTATAAACCGAAACGACACCAAAGAAGATGTGTTTGT
ACACCAGACTGCCATCAAGAAGAATAATCCACGCAAGTATCTGCGCAGTGTGGGGGATGGAGAA
ACTGTAGAGTTTGATGTGGTTGAAGGAGAAAAGGGTGCTGAAGCAGCAAATGTGACTGGCCCAG
ATGGAGTTCCTGTAGAAGGGAGTCGCTATGCTGCTGATCGGCGCCGGTACAGACGCGGCTACTA
TGGCAGGCGCCGAGGACCTCCCCGTAATTACGCTGGGGAGGAGGAGGAGGAAGGGAGCGGCAGC
AGTGAAGGATTTGAGCCCCCTGCCGCAGATGGGCAGTTCTCTGGGGCCAGGAATCAGCTGCGCC
GCCCCCAGTATCGCCCTCCGTACCGGCAGCGGCGTTTCCCGCCTTACCACGTGGGACAGACCTT
TGACCGTCGCTCACGGGTCTTTCCCCATCCCAACAGAATGCAGGCTGGTGAGATTGGAGAGATG
AAGGATGGAGTCCCCGAGGGAGCGCAGCTCCAGGTTCATCGGAATCCCACTTACCGCCCAAGGT
TCCGCAGGGGACCTGCTCGCCCACGACCTGCCCCTGCTATTGGAGAGGCTGAAGATAAAGAAAA
TCAGCAAGCGGCCAATGGTCCAAACCAGCCGTCTGCCCGCCGTGGATTCCGACGCCCCTACAAC
TACAGGCGCCGCCCCCGTCCCCTCAACGCTGTTTCACAAGATGGCAAAGAGACCAAGGCAGGTG
AAGCACCAACTGAGAACCCCGCTCCAGCCACCGAACAGAGCAGTGCCGAGTGACCCTGGCTCCC
AGGCACCTTCACCACCAGCAGGGTGACCTTAAGAATTAATGACCATTCAAAAACAAGGCAAAAA
GCACACCCACGACCTTACCAACACCAAAGAAACATCTAAGCAATAAAACGGAAGACTAACCAAG
ATTTGGACATTAGAATGTTTACTGCTATTCTCTACGAAACTAACAACTGCAAAGGGAAGGAGCC
CGCACTGTCCATCAAGCTGCGTCCCGGGAACCTGCACAGGCAGAGAGCAGCCTCCCCATTTCAG
CAACCTAGTGCTTTATATTTTTTTCCTGGTTTTTACTGTTTTGGTAATATGAATTAAAAGAAGA
AATATTAATACCACATGGGGATTGCCCCAACCAAAGAAATCTGAAATATATAGTAAATGCTCTT
TTTCCTTTGTTGTTCATTTTGGATGCTGGTGCTAAACTTCCAAGTGTCATGATTTAAGAAGAAA
TTTTATGCCCTTATTTATTCCTAGGATGAGGGGAGAACATTTTTGCTTTCTTACATAGCTCTCT
CTGAAATGTGCAGTAACAAGTTCCTCAAAAATAAAATTTTTACCTTCAAAGGA

hide sequence

RefSeq Acc Id:

XM_039108450 ⟹ XP_038964378

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	166,861,180 - 166,884,532 (-)	NCBI
mRatBN7.2	4	165,129,747 - 165,153,101 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_114185	(Get FASTA)	NCBI Sequence Viewer
	XP_038964378	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB60520	(Get FASTA)	NCBI Sequence Viewer
	AAI05779	(Get FASTA)	NCBI Sequence Viewer
	BAA05907	(Get FASTA)	NCBI Sequence Viewer
	EDM01692	(Get FASTA)	NCBI Sequence Viewer
	EDM01693	(Get FASTA)	NCBI Sequence Viewer
	Q62764	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_114185 ⟸ NM_031979

- UniProtKB:

Q63748 (UniProtKB/Swiss-Prot), Q62764 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSEAGEATTGGTTLPQAAADAPAAAPPDPAPKSPAASGAPQAPAPAALLAGSPGGDAAPGPAPA
SSAPAGSEDAEKKVLATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVG
DGETVEFDVVEGEKGAEAANVTGPDGVPVEGSRYAADRRRYRRGYYGRRRGPPRNYAGEEEEEG
SGSSEGFEPPAADGQFSGARNQLRRPQYRPPYRQRRFPPYHVGQTFDRRSRVFPHPNRMQAGEI
GEMKDGVPEGAQLQVHRNPTYRPRFRRGPARPRPAPAIGEAEDKENQQAANGPNQPSARRGFRR
PYNYRRRPRPLNAVSQDGKETKAGEAPTENPAPATEQSSAE

hide sequence

Ensembl Acc Id:

ENSRNOP00000007427 ⟸ ENSRNOT00000007427

Ensembl Acc Id:

ENSRNOP00000059241 ⟸ ENSRNOT00000068185

RefSeq Acc Id:	XP_038964378 ⟸ XM_039108450
- Peptide Label:	isoform X1

Protein Domains

CSD

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q62764-F1-model_v2	AlphaFold	Q62764	1-361	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13693452

Promoter ID:

EPDNEW_R3970

Type:

initiation region

Name:

Ybx3_1

Description:

Y box binding protein 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	4	165,630,030 - 165,630,090	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:621056	AgrOrtholog
BioCyc Gene	G2FUF-42725	BioCyc
Ensembl Genes	ENSRNOG00000005480	Ensembl
Gene3D-CATH	2.40.50.140	UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7932542	IMAGE-MGC_LOAD
InterPro	Cold_shock_domain	UniProtKB/Swiss-Prot
	CSD	UniProtKB/Swiss-Prot
	CSD_1	UniProtKB/Swiss-Prot
	CSP_DNA-bd	UniProtKB/Swiss-Prot
	NA-bd_OB-fold	UniProtKB/Swiss-Prot
KEGG Report	rno:83807	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:124554	IMAGE-MGC_LOAD
NCBI Gene	83807	ENTREZGENE
PANTHER	COLD SHOCK DOMAIN CONTAINING PROTEINS	UniProtKB/Swiss-Prot
Pfam	CSD	UniProtKB/Swiss-Prot
PhenoGen	Ybx3	PhenoGen
PRINTS	COLDSHOCK	UniProtKB/Swiss-Prot
PROSITE	CSD_1	UniProtKB/Swiss-Prot
	CSD_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000005480	RatGTEx
SMART	CSP	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF50249	UniProtKB/Swiss-Prot
UniProt	D4A0L4_RAT	UniProtKB/TrEMBL
	F1MA18_RAT	UniProtKB/TrEMBL
	Q62764	ENTREZGENE
	Q63748	ENTREZGENE
	YBOX3_RAT	UniProtKB/Swiss-Prot
UniProt Secondary	Q63748	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-03-20	Ybx3	Y box binding protein 3	Csda	cold shock domain protein A	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-26	Csda	cold shock domain protein A			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Csda	cold shock domain protein A			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_domains	contains a cold-shock domain and an amino acid alignment similar to those of charge zipper proteins	632638
gene_expression	abundant in the skeletal muscle, spleen, and fetal liver	632638
gene_product	member of the Y-box binding protein family	632638
gene_regulation	developmentally regulated, low expression in new-born and adult livers	632638

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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