Ybx1 (Y box binding protein 1) - Rat Genome Database

Name: Ybx1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Ybx1 (Y box binding protein 1) Rattus norvegicus

Analyze

Symbol:

Ybx1

Name:

Y box binding protein 1

RGD ID:

61843

Description:

Enables nucleic acid binding activity and p53 binding activity. Involved in several processes, including negative regulation of apoptotic process; negative regulation of insulin receptor signaling pathway; and regulation of transcription by RNA polymerase II. Located in several cellular components, including dendrite; neuronal cell body; and perinuclear region of cytoplasm. Part of messenger ribonucleoprotein complex. Biomarker of myocardial infarction. Orthologous to human YBX1 (Y-box binding protein 1); PARTICIPATES IN cisplatin drug pathway; p53 signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

Byb1; CBF-A; Cbfa; CCAAT-binding transcription factor 1 subunit A; CCAAT-binding transcription factor I subunit A; Dbpb; DNA binding protein B; DNA-binding protein B; Ef1a; EFI-A; enhancer factor 1 alpha; enhancer factor 1 subunit A; enhancer factor I subunit A; Msy1; Nsep1; nuclease sensitive element binding protein 1; nuclease-sensitive element-binding protein 1; Y box protein 1; Y box transcription factor; Y-box transcription factor; Y-box-binding protein 1; YB-1; Yb1

RGD Orthologs

Human

Mouse

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	YBX1 (Y-box binding protein 1)	HGNC	Ensembl, HomoloGene, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Ybx1 (Y box protein 1)	RGD	RGD
Sus scrofa (pig):	YBX1 (Y-box binding protein 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	YBX1 (Y-box binding protein 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ybx1 (Y-box binding protein 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	YBX1 (Y-box binding protein 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Ybx1 (Y box protein 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	ybx1 (Y box binding protein 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	cey-1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	yps	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	cey-4	Alliance	DIOPT (Ensembl Compara\|InParanoid\|PANTHER)

Related Pseudogenes:

Ybx1-ps1 Ybx1-ps18 Ybx1-ps20 Ybx1-ps21 Ybx1-ps22 Ybx1-ps23 Ybx1-ps24 Ybx1-ps3

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	132,882,137 - 132,899,108 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	132,882,145 - 132,898,862 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	135,609,596 - 135,626,412 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	5	137,366,056 - 137,382,871 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	5	137,386,642 - 137,403,467 (-)	NCBI	Rnor_WKY
Rnor_6.0	5	138,319,754 - 138,336,721 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	138,319,762 - 138,336,475 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	142,132,028 - 142,152,551 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	139,859,176 - 139,875,840 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	139,864,480 - 139,881,067 (-)	NCBI
Celera	5	131,407,618 - 131,424,346 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Breast Neoplasms (ISO)

Charcot-Marie-Tooth disease dominant intermediate C (ISO)

Colonic Neoplasms (ISO)

Experimental Liver Cirrhosis (ISO)

myocardial infarction (IEP)

Neoplasm Recurrence, Local (ISO)

Refractory Anemia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(Z)-3-butylidenephthalide (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

2,4,6-tribromophenol (ISO)

3',5'-cyclic UMP (ISO)

3-chloropropane-1,2-diol (EXP)

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

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

4,4'-sulfonyldiphenol (ISO)

5-fluorouracil (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (EXP)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

beauvericin (ISO)

Benzo[k]fluoranthene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

caffeine (ISO)

calcidiol (EXP)

chloropicrin (ISO)

chromium(6+) (ISO)

chrysene (ISO)

cisplatin (EXP,ISO)

cocaine (EXP)

copper atom (ISO)

copper(0) (ISO)

coumarin (ISO)

coumestrol (ISO)

CU-O LINKAGE (ISO)

Cuprizon (EXP)

cypermethrin (EXP)

dexamethasone (ISO)

dibutyl phthalate (ISO)

doxorubicin (ISO)

folic acid (ISO)

indometacin (ISO)

ivermectin (ISO)

lead(0) (ISO)

lead(2+) (ISO)

lithium chloride (ISO)

mercury atom (ISO)

mercury(0) (ISO)

methamphetamine (EXP)

miconazole (ISO)

Monobutylphthalate (ISO)

ozone (EXP)

p-toluidine (EXP)

paracetamol (EXP,ISO)

quinoline (ISO)

resveratrol (ISO)

rotenone (EXP)

SCH 23390 (EXP)

silicon dioxide (ISO)

sodium arsenite (EXP,ISO)

sodium dichromate (EXP,ISO)

T-2 toxin (ISO)

tetrachloromethane (ISO)

tetraphene (ISO)

thioacetamide (EXP)

trichloroethene (EXP)

trimellitic anhydride (ISO)

triptonide (ISO)

urethane (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to interleukin-7 (ISO)

CRD-mediated mRNA stabilization (ISO,ISS)

embryonic morphogenesis (ISS)

epidermis development (ISO,ISS)

in utero embryonic development (ISO)

miRNA transport (ISO,ISS)

mRNA processing (IEA)

mRNA stabilization (ISO,ISS)

negative regulation of apoptotic process (IDA)

negative regulation of cellular senescence (ISO,ISS)

negative regulation of insulin receptor signaling pathway (IMP)

negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (ISO)

negative regulation of striated muscle cell differentiation (ISO)

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

negative regulation of translation (ISS)

positive regulation of cell division (IEA)

positive regulation of cell population proliferation (IMP)

positive regulation of cytoplasmic translation (ISO)

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

protein localization to cytoplasmic stress granule (ISO)

regulation of DNA-templated transcription (ISO)

regulation of gene expression (IBA)

RNA splicing (IEA)

RNA transport (ISO,ISS)

tRNA transport (ISO,ISS)

Cellular Component

CRD-mediated mRNA stability complex (ISO)

cytoplasm (IDA,ISO)

cytoplasmic stress granule (ISO,ISS)

cytosol (ISO)

dendrite (IDA)

endoplasmic reticulum (ISO)

extracellular exosome (ISO,ISS)

histone pre-mRNA 3'end processing complex (ISO,ISS)

intracellular membrane-bounded organelle (ISO)

messenger ribonucleoprotein complex (IBA,IDA)

neuronal cell body (IDA)

nuclear membrane (ISO)

nucleus (IBA,IDA,ISO)

perinuclear region of cytoplasm (IDA)

plasma membrane (ISO)

ribonucleoprotein complex (ISO,ISS)

synapse (ISO)

U12-type spliceosomal complex (ISO)

Molecular Function

C5-methylcytidine-containing RNA binding (ISO,ISS)

chromatin binding (ISO)

GTPase binding (ISO)

miRNA binding (ISO,ISS)

mRNA binding (IPI,ISO)

nucleic acid binding (IBA,IEA)

p53 binding (IMP)

protein binding (IPI,ISO)

RNA binding (IDA,ISO,ISS)

sequence-specific DNA binding (IDA)

sequence-specific double-stranded DNA binding (ISO)

single-stranded DNA binding (IDA,ISO)

transcription factor binding (IPI)

Molecular Pathway Annotations Click to see Annotation Detail View

cisplatin drug pathway (ISO)

p53 signaling pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transcriptional regulation by p53.	Beckerman R and Prives C, Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000935. doi: 10.1101/cshperspect.a000935. Epub 2010 Apr 28.
2.	Tumour metastasis suppressor, nm23-beta, inhibits gelatinase A transcription by interference with transactivator Y-box protein-1 (YB-1).	Cheng S, etal., Biochem J 2002 Sep 15;366(Pt 3):807-16.
3.	Identification in the rat brain of a set of nuclear proteins interacting with H1 degrees mRNA.	Di Liegro CM, etal., Neuroscience. 2013 Jan 15;229:71-6. doi: 10.1016/j.neuroscience.2012.10.072. Epub 2012 Nov 14.
4.	Y-box protein-1 is the crucial mediator of antifibrotic interferon-gamma effects.	Dooley S, etal., J Biol Chem. 2006 Jan 20;281(3):1784-95. Epub 2005 Nov 8.
5.	Transcription factor YB-1 mediates DNA polymerase alpha gene expression.	En-Nia A, etal., J Biol Chem. 2005 Mar 4;280(9):7702-11. Epub 2004 Dec 21.
6.	Identification of YB-1 as a regulator of PTP1B expression: implications for regulation of insulin and cytokine signaling.	Fukada T and Tonks NK, EMBO J 2003 Feb 3;22(3):479-93.
7.	Isolation and characterization of brain Y-box protein: developmentally regulated expression, polyribosomal association and dendritic localization.	Funakoshi T, etal., Brain Res Mol Brain Res. 2003 Oct 21;118(1-2):1-9.
8.	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.
9.	Y-box factor YB1 controls p53 apoptotic function.	Homer C, etal., Oncogene. 2005 Dec 15;24(56):8314-25.
10.	Expression of the multifunctional Y-box protein, YB-1, in myofibroblasts of the infarcted rat heart.	Kamalov G, etal., Biochem Biophys Res Commun. 2005 Aug 19;334(1):239-44.
11.	Y-box binding protein-1 controls CC chemokine ligand-5 (CCL5) expression in smooth muscle cells and contributes to neointima formation in atherosclerosis-prone mice.	Krohn R, etal., Circulation. 2007 Oct 16;116(16):1812-20. Epub 2007 Sep 24.
12.	The Y-box-binding protein, YB1, is a potential negative regulator of the p53 tumor suppressor.	Lasham A, etal., J Biol Chem. 2003 Sep 12;278(37):35516-23. Epub 2003 Jun 30.
13.	Molecular composition of staufen2-containing ribonucleoproteins in embryonic rat brain.	Maher-Laporte M, etal., PLoS One. 2010 Jun 28;5(6):e11350. doi: 10.1371/journal.pone.0011350.
14.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
15.	Diurnal variation of the serine dehydratase mRNA level in rat liver.	Ogawa H, etal., Arch Biochem Biophys 1994 Jan;308(1):285-91.
16.	Isolation and characterization of a cDNA clone for the CCAAT transcription factor EFIA reveals a novel structural motif.	Ozer J, etal., J Biol Chem 1990 Dec 25;265(36):22143-52.
17.	GOA pipeline	RGD automated data pipeline
18.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
19.	Nuclease sensitive element binding protein 1 associates with the selenocysteine insertion sequence and functions in mammalian selenoprotein translation.	Shen Q, etal., J Cell Physiol. 2006 Jun;207(3):775-83.
20.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
21.	Inhibition of transcription by platinum antitumor compounds.	Todd RC and Lippard SJ, Metallomics. 2009;1(4):280-91. doi: 10.1039/b907567d.
22.	High expression of YB-1 gene in erythroid cells in patients with refractory anemia.	Yokoyama H, etal., Int J Hematol. 2003 Oct;78(3):213-8.
23.	CARP, a cardiac ankyrin repeat protein, is downstream in the Nkx2-5 homeobox gene pathway.	Zou Y, etal., Development. 1997 Feb;124(4):793-804.

Additional References at PubMed

PMID:15146077	PMID:15489334	PMID:16641100	PMID:17289661	PMID:18335541	PMID:18809583	PMID:19029303	PMID:19323802	PMID:19561594	PMID:19590238	PMID:19640841	PMID:22337869
PMID:22361279	PMID:22801372	PMID:24337748	PMID:24625528	PMID:24965446	PMID:26102006	PMID:27080258	PMID:27559612	PMID:28341602	PMID:28755400	PMID:29073095	PMID:31358969
PMID:31967332	PMID:35151240	PMID:35255737

Genomics

Comparative Map Data

Ybx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	132,882,137 - 132,899,108 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	132,882,145 - 132,898,862 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	135,609,596 - 135,626,412 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	5	137,366,056 - 137,382,871 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	5	137,386,642 - 137,403,467 (-)	NCBI	Rnor_WKY
Rnor_6.0	5	138,319,754 - 138,336,721 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	138,319,762 - 138,336,475 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	142,132,028 - 142,152,551 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	139,859,176 - 139,875,840 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	139,864,480 - 139,881,067 (-)	NCBI
Celera	5	131,407,618 - 131,424,346 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

YBX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	42,682,418 - 42,703,805 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	1	42,682,418 - 42,703,805 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	43,148,089 - 43,169,476 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	42,920,653 - 42,940,607 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	42,817,216 - 42,837,113	NCBI
Celera	1	41,429,993 - 41,449,949 (+)	NCBI		Celera
Cytogenetic Map	1	p34.2	NCBI
HuRef	1	41,269,041 - 41,287,988 (+)	NCBI		HuRef
HuRef	1	41,268,237 - 41,268,497 (+)	NCBI		HuRef
CHM1_1	1	43,264,924 - 43,284,881 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	1	42,552,913 - 42,574,300 (+)	NCBI		T2T-CHM13v2.0

Ybx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	119,134,524 - 119,153,462 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	119,135,178 - 119,151,801 (-)	Ensembl		GRCm39 Ensembl
GRCm38	4	119,277,327 - 119,296,265 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	119,277,981 - 119,294,604 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	118,949,932 - 118,967,118 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	118,776,166 - 118,792,322 (-)	NCBI		MGSCv36	mm8
Celera	4	118,005,093 - 118,022,345 (-)	NCBI		Celera
Cytogenetic Map	4	D2.1	NCBI

YBX1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	168,716,789 - 168,736,604 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	168,716,782 - 168,736,475 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	156,189,780 - 156,217,499 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

YBX1
(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	20	90,229,927 - 90,250,213 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666033	26,660,015 - 26,680,491 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ybx1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624892	1,939,098 - 1,957,623 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624892	1,939,641 - 1,957,621 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Ybx1
73 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	234
Count of miRNA genes:	154
Interacting mature miRNAs:	163
Transcripts:	ENSRNOT00000015875, ENSRNOT00000050213, ENSRNOT00000058700
Prediction methods:	Microtar, Miranda, Rnahybrid
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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35189153	141643988	Rat
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	46711509	161317411	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	50328551	141643988	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	59793399	143070159	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	60293434	161481680	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	69540295	151018848	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	82394392	166664054	Rat
631527	Tls1	T-lymphoma susceptibility QTL 1	0	0.001	thymus integrity trait (VT:0010555)	post-insult time to onset of T-cell lymphoma (CMO:0001907)	5	90450144	135450144	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	94858972	143070159	Rat
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	97059760	147465714	Rat
2317753	Glom24	Glomerulus QTL 24	3.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	5	97570330	136479578	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	99216724	148607142	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	103689353	148689353	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	105999803	150999803	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	106906205	151906205	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	106906205	151906205	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	106906205	151906205	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	106906205	151906205	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	106906205	151906205	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	108845856	153845856	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	108845856	153845856	Rat
8657050	Bw146	Body weight QTL 146	19.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	108938288	153938288	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	111416838	156416838	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	111416838	156416838	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	111416838	156416838	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	111416838	156416838	Rat
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	120740824	143608494	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	120740824	151018848	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	121846814	166846814	Rat
7394710	Emca12	Estrogen-induced mammary cancer QTL 12			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	124160767	133749643	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	124965598	166875058	Rat
1300122	Wbc1	White blood cell count QTL 1	2.75		leukocyte quantity (VT:0000217)	total white blood cell count (CMO:0000365)	5	125392826	139989768	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	126424772	166875058	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	127798274	166875058	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	127798274	166875058	Rat
1581505	Rf54	Renal function QTL 54			kidney physiology trait (VT:0002136)	kidney 20-HETE level (CMO:0001854)	5	128033842	133011550	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	128506074	166875058	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	128506074	166875058	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	128924607	166875058	Rat
1331803	Rf32	Renal function QTL 32	2.798		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	129132428	143070159	Rat
70156	Niddm30	Non-insulin dependent diabetes mellitus QTL 30	3.98		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	5	129132447	151006154	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	130130159	166875058	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	131345754	166875058	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132717196	165560427	Rat

Markers in Region

PMC140751P1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	5	q36	UniSTS

RH128187

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Cytogenetic Map	10	q22	UniSTS
Cytogenetic Map	5	q36	UniSTS

BF396960

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	132,890,613 - 132,890,796 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	138,328,230 - 138,328,412	NCBI	Rnor6.0
Rnor_5.0	5	142,144,300 - 142,144,482	UniSTS	Rnor5.0
RGSC_v3.4	5	139,867,589 - 139,867,771	UniSTS	RGSC3.4
Celera	5	131,416,094 - 131,416,276	UniSTS
RH 3.4 Map	5	868.5	UniSTS
Cytogenetic Map	5	q36	UniSTS

UniSTS:265529

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	39,161,708 - 39,162,139 (+)	MAPPER	mRatBN7.2
mRatBN7.2	1	171,305,106 - 171,305,537 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	186,640,518 - 186,640,948	NCBI	Rnor6.0
Rnor_6.0	10	40,380,888 - 40,381,318	NCBI	Rnor6.0
Rnor_5.0	1	193,602,676 - 193,603,106	UniSTS	Rnor5.0
Rnor_5.0	10	40,220,375 - 40,220,805	UniSTS	Rnor5.0
RGSC_v3.4	1	175,179,533 - 175,179,963	UniSTS	RGSC3.4
RGSC_v3.4	10	40,444,669 - 40,445,099	UniSTS	RGSC3.4
Celera	10	38,499,026 - 38,499,456	UniSTS
Cytogenetic Map	1	q35	UniSTS
Cytogenetic Map	5	q36	UniSTS
Cytogenetic Map	10	q22	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031563	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008764058	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008764059	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC098918	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC072486	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC098672	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC103637	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D13309	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ224204	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ232156	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M69138	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000015875 ⟹ ENSRNOP00000015875

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	132,882,145 - 132,898,862 (-)	Ensembl
Rnor_6.0 Ensembl	5	138,319,762 - 138,336,475 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000118144 ⟹ ENSRNOP00000093960

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	132,882,145 - 132,898,862 (-)	Ensembl

RefSeq Acc Id:

NM_031563 ⟹ NP_113751

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	132,882,137 - 132,898,868 (-)	NCBI
Rnor_6.0	5	138,319,754 - 138,336,481 (-)	NCBI
Rnor_5.0	5	142,132,028 - 142,152,551 (-)	NCBI
RGSC_v3.4	5	139,859,176 - 139,875,840 (-)	RGD
Celera	5	131,407,618 - 131,424,346 (-)	RGD

Sequence:

show sequence

CGGGAGCGGAGAGCGGACCCCAGAGAGCCCTGAGAGCCCCACCGCCGCCGCCGGCCTAGTCACC
ATCACACCCGGGAGGAGCCGCAGCCGTCGCCGCCGGCCCCAGTCACCATCACCGCAACCATGAG
CAGCGAGGCCGAGACCCAGCAGCCGCCCGCCGCCCCCGCCGCCGCCCTCAGCGCCGCCGACACC
AAGCCCGGCTCCACGGGCAGCGGCGCGGGTAGTGGCGGCCCGGGCGGCCTCACATCGGCGGCGC
CCGCCGGCGGGGACAAGAAGGTCATCGCAACGAAGGTTTTGGGAACAGTAAAATGGTTCAATGT
AAGGAACGGATACGGTTTCATCAACAGGAATGACACCAAGGAAGACGTATTTGTACACCAGACG
GCCATAAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGAGATGGAGAGACTGTGGAGT
TTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCTAATGTTACAGGCCCTGGTGGAGTTCC
AGTTCAAGGCAGTAAATACGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCGTAGGGGT
CCTCCACGCAATTACCAGCAAAATTACCAGAATAGTGAGAGTGGGGAAAAGAATGAAGGATCGG
AAAGCGCTCCTGAAGGCCAGGCCCAACAACGCCGGCCCTATCGCAGGCGAAGGTTCCCACCTTA
CTACATGCGGAGACCCTATGCGCGTCGACCACAGTATTCCAACCCCCCTGTGCAAGGAGAAGTG
ATGGAGGGTGCTGACAACCAGGGTGCAGGAGAGCAAGGTAGACCAGTGAGACAGAATATGTATC
GGGGTTACAGACCACGATTCCGCAGGGGCCCTCCTCGCCAAAGACAGCCTAGAGAGGATGGCAA
TGAAGAGGACAAAGAAAATCAAGGAGATGAGACCCAAGGTCAGCAGCCACCTCAACGTCGGTAT
CGCCGCAACTTCAATTACCGACGCAGACGCCCAGAGAACCCTAAACCACAAGATGGCAAAGAGA
CAAAAGCAGCCGATCCACCAGCTGAGAATTCGTCCGCTCCCGAGGCTGAGCAGGGCGGGGCTGA
GTAAATGCCGGCTTACCATCTCTACCATCATCCGGTTTGGTCATCCAACAAGAAGAAATGAATA
TGAAATTCCAGCAATAAGAAATGAACAAAGATTGGAGCTGAAGACCTTAAGTGCTTGCTTTTTG
CCCGTTGACCAGATCCACTAGAACTGTCTGCATTATCTATGCAGCATGGGGTTTTTATTATTTT
TACCTAAAGATGTCTCTTTTTGGTAATGACAAACGTGTTTTTTAAGAAAAAAAAAAAAAAGGCC
TGGTTTTTCTCAATACACCTTTAACGGTTTTTAAATTGTTTCATATCTGGTCAAGTTGAGATTT
TTAAGAACTTCATTTTTAATTTGTAATAAAGTTTACAACTTGATTTTTTCAAAAAAGTCAACAA
ACTGCAAGCACCTGTTAATAAAGGTCTTAAATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008764058 ⟹ XP_008762280

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	132,882,137 - 132,899,080 (-)	NCBI
Rnor_6.0	5	138,319,754 - 138,336,677 (-)	NCBI

Sequence:

show sequence

AGCTGTGGGTCGGGCGAATTAGTCGCTAAAGGTACCAATGAGAGCACAGGAGCCGCGCAGCGTG
AGCCAATAGGTGCTAGAGACCCGGTCAGGTGGTGAGATGGACAACGATGTAGGCCAATGGGAGA
GGACGAGGGCGGGTCTACCGCGGGGCTTATCCCGCCCGTCCCGCCATTCTCGCTAGTTCGATCG
GTAGCGGGAGCGGAGAGCGGACCCCAGAGAGCCCTGAGAGCCCCACCGCCGCCGCCGGCCTAGT
CACCATCACACCCGGGAGGAGCCGCAGCCGTCGCCGCCGGCCCCAGTCACCATCACCGCAACCA
TGAGCAGCGAGGCCGAGACCCAGCAGCCGCCCGCCGCCCCCGCCGCCGCCCTCAGCGCCGCCGA
CACCAAGCCCGGCTCCACGGGCAGCGGCGCGGGTAGTGGCGGCCCGGGCGGCCTCACATCGGCG
GCGCCCGCCGGCGGGGACAAGAAGGTCATCGCAACGAAGGTTTTGGGAACAGTAAAATGGTTCA
ATGTAAGGAACGGATACGGTTTCATCAACAGGAATGACACCAAGGAAGACGTATTTGTACACCA
GACGGCCATAAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGAGATGGAGAGACTGTG
GAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCTAATGTTACAGGCCCTGGTGGAG
TTCCAGTTCAAGGCAGTAAATACGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCGTAG
GGGTCCTCCACGCAATTACCAGCAAAATTACCAGAATAGTGAGAGTGGGGAAAAGAATGAAGGA
TCGGAAAGCGCTCCTGAAGGCCAGGCCCAACAACGCCGGCCCTATCGCAGGCGAAGGTTCCCAC
CTTACTACATGCGGAGACCCTATGCGCGTCGACCACAGTATTCCAACCCCCCTGTGCAAGGAGA
AGTGATGGAGGGTGCTGACAACCAGGGTGCAGGAGAGCAAGGTAGACCAGTGAGACAGAATATG
TATCGGGGTTACAGACCACGATTCCGCAGTGTTCATTTCAGGGGCCCTCCTCGCCAAAGACAGC
CTAGAGAGGATGGCAATGAAGAGGACAAAGAAAATCAAGGAGATGAGACCCAAGGTCAGCAGCC
ACCTCAACGTCGGTATCGCCGCAACTTCAATTACCGACGCAGACGCCCAGAGAACCCTAAACCA
CAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATTCGTCCGCTCCCGAGGCTG
AGCAGGGCGGGGCTGAGTAAATGCCGGCTTACCATCTCTACCATCATCCGGTTTGGTCATCCAA
CAAGAAGAAATGAATATGAAATTCCAGCAATAAGAAATGAACAAAGATTGGAGCTGAAGACCTT
AAGTGCTTGCTTTTTGCCCGTTGACCAGATCCACTAGAACTGTCTGCATTATCTATGCAGCATG
GGGTTTTTATTATTTTTACCTAAAGATGTCTCTTTTTGGTAATGACAAACGTGTTTTTTAAGAA
AAAAAAAAAAGGCCTGGTTTTTCTCAATACACCTTTAACGGTTTTTAAATTGTTTCATATCTGG
TCAAGTTGAGATTTTTAAGAACTTCATTTTTAATTTGTAATAAAGTTTACAACTTGATTTTTTC
AAAAAAGTCAACAAACTGCAAGCACCTGTTAATAAAGGTCTTAAATAATA

hide sequence

RefSeq Acc Id:

XM_008764059 ⟹ XP_008762281

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	132,882,137 - 132,899,108 (-)	NCBI
Rnor_6.0	5	138,319,754 - 138,336,721 (-)	NCBI

Sequence:

show sequence

GCTCTCATTCTAGTTCCGGTCTCTATGGCGGCGGAGGCCGGAGAAGCTGTGGGTCGGGCGAATT
AGTCGCTAAAGGTACCAATGAGAGCACAGGAGCCGCGCAGCGTGAGCCAATAGGTGCTAGAGAC
CCGGTCAGGTGGTGAGATGGACAACGATGTAGGCCAATGGGAGAGGACGAGGGCGGGTCTACCG
CGGGGCTTATCCCGCCCGTCCCGCCATTCTCGCTAGTTCGATCGGTAGCGGGAGCGGAGAGCGG
ACCCCAGAGAGCCCTGAGAGCCCCACCGCCGCCGCCGGCCTAGTCACCATCACACCCGGGAGGA
GCCGCAGCCGTCGCCGCCGGCCCCAGTCACCATCACCGCAACCATGAGCAGCGAGGCCGAGACC
CAGCAGCCGCCCGCCGCCCCCGCCGCCGCCCTCAGCGCCGCCGACACCAAGCCCGGCTCCACGG
GCAGCGGCGCGGGTAGTGGCGGCCCGGGCGGCCTCACATCGGCGGCGCCCGCCGGCGGGGACAA
GAAGGTCATCGCAACGAAGGTTTTGGGAACAGTAAAATGGTTCAATGTAAGGAACGGATACGGT
TTCATCAACAGGAATGACACCAAGGAAGACGTATTTGTACACCAGGGTGCGGAGGCAGCTAATG
TTACAGGCCCTGGTGGAGTTCCAGTTCAAGGCAGTAAATACGCAGCAGACCGTAACCATTATAG
ACGCTATCCACGTCGTAGGGGTCCTCCACGCAATTACCAGCAAAATTACCAGAATAGTGAGAGT
GGGGAAAAGAATGAAGGATCGGAAAGCGCTCCTGAAGGCCAGGCCCAACAACGCCGGCCCTATC
GCAGGCGAAGGTTCCCACCTTACTACATGCGGAGACCCTATGCGCGTCGACCACAGTATTCCAA
CCCCCCTGTGCAAGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTGCAGGAGAGCAAGGTAGA
CCAGTGAGACAGAATATGTATCGGGGTTACAGACCACGATTCCGCAGTGTTCATTTCAGGGGCC
CTCCTCGCCAAAGACAGCCTAGAGAGGATGGCAATGAAGAGGACAAAGAAAATCAAGGAGATGA
GACCCAAGGTCAGCAGCCACCTCAACGTCGGTATCGCCGCAACTTCAATTACCGACGCAGACGC
CCAGAGAACCCTAAACCACAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATT
CGTCCGCTCCCGAGGCTGAGCAGGGCGGGGCTGAGTAAATGCCGGCTTACCATCTCTACCATCA
TCCGGTTTGGTCATCCAACAAGAAGAAATGAATATGAAATTCCAGCAATAAGAAATGAACAAAG
ATTGGAGCTGAAGACCTTAAGTGCTTGCTTTTTGCCCGTTGACCAGATCCACTAGAACTGTCTG
CATTATCTATGCAGCATGGGGTTTTTATTATTTTTACCTAAAGATGTCTCTTTTTGGTAATGAC
AAACGTGTTTTTTAAGAAAAAAAAAAAAGGCCTGGTTTTTCTCAATACACCTTTAACGGTTTTT
AAATTGTTTCATATCTGGTCAAGTTGAGATTTTTAAGAACTTCATTTTTAATTTGTAATAAAGT
TTACAACTTGATTTTTTCAAAAAAGTCAACAAACTGCAAGCACCTGTTAATAAAGGTCTTAAAT
AATA

hide sequence

Protein Sequences


Protein RefSeqs	NP_113751	(Get FASTA)	NCBI Sequence Viewer
	XP_008762280	(Get FASTA)	NCBI Sequence Viewer
	XP_008762281	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40906	(Get FASTA)	NCBI Sequence Viewer
	AAH72486	(Get FASTA)	NCBI Sequence Viewer
	AAH98672	(Get FASTA)	NCBI Sequence Viewer
	AAI03638	(Get FASTA)	NCBI Sequence Viewer
	BAA02569	(Get FASTA)	NCBI Sequence Viewer
	EDL90125	(Get FASTA)	NCBI Sequence Viewer
	P62961	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_113751 ⟸ NM_031563

- UniProtKB:

Q4KMA4 (UniProtKB/Swiss-Prot), P62961 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSSEAETQQPPAAPAAALSAADTKPGSTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWF
NVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGG
VPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFP
PYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPRED
GNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGG
AE

hide sequence

RefSeq Acc Id:

XP_008762281 ⟸ XM_008764059

- Peptide Label:

isoform X2

- Sequence:

show sequence

MSSEAETQQPPAAPAAALSAADTKPGSTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWF
NVRNGYGFINRNDTKEDVFVHQGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQ
NYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYARRPQYSNPPVQGEVMEGADNQ
GAGEQGRPVRQNMYRGYRPRFRSVHFRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRN
FNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE

hide sequence

RefSeq Acc Id:	XP_008762280 ⟸ XM_008764058
- Peptide Label:	isoform X1
- UniProtKB:	Q3ZAV2 (UniProtKB/TrEMBL), E9PTV8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSSEAETQQPPAAPAAALSAADTKPGSTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWF NVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGG VPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFP PYYMRRPYARRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRSVHFRGPPRQRQ PREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEA EQGGAE hide sequence

RefSeq Acc Id:

ENSRNOP00000015875 ⟸ ENSRNOT00000015875

RefSeq Acc Id:

ENSRNOP00000093960 ⟸ ENSRNOT00000118144

Protein Domains

CSD

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P62961-F1-model_v2	AlphaFold	P62961	1-322	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693980

Promoter ID:

EPDNEW_R4504

Type:

multiple initiation site

Name:

Ybx1_1

Description:

Y box binding protein 1

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	5	138,336,494 - 138,336,554	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:61843	AgrOrtholog
BioCyc Gene	G2FUF-40091	BioCyc
Ensembl Genes	ENSRNOG00000023786	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000015875	ENTREZGENE
	ENSRNOP00000015875.6	UniProtKB/TrEMBL
	ENSRNOP00000093960.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000015875	ENTREZGENE
	ENSRNOT00000015875.8	UniProtKB/TrEMBL
	ENSRNOT00000118144.1	UniProtKB/TrEMBL
Gene3D-CATH	2.40.50.140	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7105037	IMAGE-MGC_LOAD
	IMAGE:7107271	IMAGE-MGC_LOAD
	IMAGE:7124218	IMAGE-MGC_LOAD
InterPro	CSD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CSD_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CSP_DNA-bd	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	NA-bd_OB-fold	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:500538	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:112628	IMAGE-MGC_LOAD
	MGC:124971	IMAGE-MGC_LOAD
	MGC:91399	IMAGE-MGC_LOAD
NCBI Gene	500538	ENTREZGENE
Pfam	CSD	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Ybx1	PhenoGen
PRINTS	COLDSHOCK	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	CSD_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CSD_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	CSP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF50249	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6AJV4_RAT	UniProtKB/TrEMBL
	E9PTV8	ENTREZGENE
	P62961	ENTREZGENE
	Q3ZAV2	ENTREZGENE, UniProtKB/TrEMBL
	Q4KMA4	ENTREZGENE
	YBOX1_RAT	UniProtKB/Swiss-Prot
UniProt Secondary	E9PTV8	UniProtKB/TrEMBL
	P22568	UniProtKB/Swiss-Prot
	P27817	UniProtKB/Swiss-Prot
	P43482	UniProtKB/Swiss-Prot
	Q4KMA4	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-12-15	Ybx1	Y box binding protein 1	Ybx1	Y box protein 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-04-18	Ybx1	Y box protein 1	Nsep1	nuclease sensitive element binding protein 1	Symbol and Name updated to reflect Human and Mouse nomenclature	1299863	APPROVED
2001-12-10	Nsep1	nuclease sensitive element binding protein 1			Symbol and Name updated to reflect Human and Mouse nomenclature	69665	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_physical_interaction	interacts with repeat sequence, 5'-GGGTTT-3'	633207
gene_process	increases PTP1B expression	727501

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations