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

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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 DNA binding activity; mRNA 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 dendrite; neuronal cell body; and perinuclear region of cytoplasm. Part of protein-containing 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: VALIDATED
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
Black Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Ybx1-ps1   Ybx1-ps10   Ybx1-ps11   Ybx1-ps15   Ybx1-ps18   Ybx1-ps2   Ybx1-ps20   Ybx1-ps21   Ybx1-ps23   Ybx1-ps24   Ybx1-ps3   Ybx1-ps5   Ybx1-ps6   Ybx1-ps7   Ybx1-ps8   Ybx1-ps9  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85138,167,444 - 138,188,155 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5138,167,444 - 138,184,188 (-)EnsemblGRCr8
mRatBN7.25132,882,137 - 132,898,885 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5135,609,596 - 135,626,412 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05137,366,056 - 137,382,871 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05137,386,642 - 137,403,467 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05138,319,754 - 138,336,721 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,319,762 - 138,336,475 (-)Ensemblrn6Rnor6.0
Rnor_5.05142,132,028 - 142,152,551 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45139,859,176 - 139,875,840 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5131,407,618 - 131,424,346 (-)NCBICelera
RGSC_v3.15139,864,480 - 139,881,067 (-)NCBI
Cytogenetic Map5q36NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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)
amitrole  (EXP)
ammonium chloride  (EXP)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
beauvericin  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-lapachone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
Bisphenol B  (ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (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)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
doxorubicin  (ISO)
folic acid  (ISO)
FR900359  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
lead(0)  (ISO)
lipopolysaccharide  (ISO)
lithium chloride  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
Mesaconitine  (EXP)
methamphetamine  (EXP)
methimazole  (EXP)
miconazole  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
Monobutylphthalate  (ISO)
monoethyl phthalate  (ISO)
nitrates  (ISO)
Nivalenol  (ISO)
ozone  (EXP)
p-toluidine  (EXP)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
quinoline  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
SCH 23390  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
sulfadimethoxine  (EXP)
T-2 toxin  (ISO)
tetrachloromethane  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
triptonide  (ISO)
urethane  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
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   PMID:35352799   PMID:38700571  


Genomics

Comparative Map Data
Ybx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85138,167,444 - 138,188,155 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl5138,167,444 - 138,184,188 (-)EnsemblGRCr8
mRatBN7.25132,882,137 - 132,898,885 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx5135,609,596 - 135,626,412 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05137,366,056 - 137,382,871 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05137,386,642 - 137,403,467 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.05138,319,754 - 138,336,721 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,319,762 - 138,336,475 (-)Ensemblrn6Rnor6.0
Rnor_5.05142,132,028 - 142,152,551 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.45139,859,176 - 139,875,840 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera5131,407,618 - 131,424,346 (-)NCBICelera
RGSC_v3.15139,864,480 - 139,881,067 (-)NCBI
Cytogenetic Map5q36NCBI
YBX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38142,682,418 - 42,703,805 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl142,682,408 - 42,703,805 (+)Ensemblhg38GRCh38
GRCh37143,148,089 - 43,169,476 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36142,920,653 - 42,940,607 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34142,817,216 - 42,837,113NCBI
Celera141,429,993 - 41,449,949 (+)NCBICelera
Cytogenetic Map1p34.2NCBI
HuRef141,269,041 - 41,287,988 (+)NCBIHuRef
HuRef141,268,237 - 41,268,497 (+)NCBIHuRef
CHM1_1143,264,924 - 43,284,881 (+)NCBICHM1_1
T2T-CHM13v2.0142,552,913 - 42,574,300 (+)NCBIT2T-CHM13v2.0
Ybx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394119,134,524 - 119,153,462 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl4119,135,178 - 119,151,801 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm384119,277,327 - 119,296,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4119,277,981 - 119,294,604 (-)Ensemblmm10GRCm38
MGSCv374118,949,932 - 118,967,118 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv364118,776,166 - 118,792,322 (-)NCBIMGSCv36mm8
Celera4118,005,093 - 118,022,345 (-)NCBICelera
Cytogenetic Map4D2.1NCBI
YBX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6168,716,772 - 168,736,604 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.16168,716,782 - 168,736,475 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26156,189,780 - 156,217,499 (-)NCBISscrofa10.2Sscrofa10.2susScr3
YBX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12090,229,927 - 90,250,213 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603326,660,015 - 26,680,491 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ybx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248921,939,098 - 1,957,623 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248921,939,641 - 1,957,621 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ybx1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1137,666,574 - 37,683,076 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ybx1
308 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5102105698152749382Rat
2303586Gluco52Glucose level QTL 522blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)5100826632145826632Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5130249266172190305Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116702075161702075Rat
1354583Despr3Despair related QTL34.980.0002locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)5132930505172190305Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5130678987145274255Rat
7365049Bp359Blood pressure QTL 359arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133308734140009902Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)599905133172190305Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5134369218156289444Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5133789363172190305Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5134369199172190305Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5136631198172190305Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112142946157142946Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112142946157142946Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5110770739155770739Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5133081618172190305Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)551657967166600247Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5138002522170842766Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112142946157142946Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5133270647172190305Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5133789363172190305Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)598972960143972960Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125969677172190305Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
2303618Vencon1Ventilatory control QTL 13.8respiration trait (VT:0001943)oxygen consumption (CMO:0002169)5100826632145826632Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111236572156236572Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)594034903139034903Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5131708216172190305Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114131300159131300Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125969677156302135Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112142946157142946Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116702075161702075Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112142946157142946Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116702075161702075Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)574335621156302135Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116702075161702075Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114131300159131300Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5133081618172190305Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5104262817153890625Rat

Markers in Region
PMC140751P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q36UniSTS
RH128187  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10q22UniSTS
Cytogenetic Map5q36UniSTS
BF396960  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25132,890,613 - 132,890,796 (+)MAPPERmRatBN7.2
Rnor_6.05138,328,230 - 138,328,412NCBIRnor6.0
Rnor_5.05142,144,300 - 142,144,482UniSTSRnor5.0
RGSC_v3.45139,867,589 - 139,867,771UniSTSRGSC3.4
Celera5131,416,094 - 131,416,276UniSTS
RH 3.4 Map5868.5UniSTS
Cytogenetic Map5q36UniSTS
UniSTS:265529  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21039,161,708 - 39,162,139 (+)MAPPERmRatBN7.2
mRatBN7.21171,305,106 - 171,305,537 (+)MAPPERmRatBN7.2
Rnor_6.01186,640,518 - 186,640,948NCBIRnor6.0
Rnor_6.01040,380,888 - 40,381,318NCBIRnor6.0
Rnor_5.01193,602,676 - 193,603,106UniSTSRnor5.0
Rnor_5.01040,220,375 - 40,220,805UniSTSRnor5.0
RGSC_v3.41175,179,533 - 175,179,963UniSTSRGSC3.4
RGSC_v3.41040,444,669 - 40,445,099UniSTSRGSC3.4
Celera1038,499,026 - 38,499,456UniSTS
Cytogenetic Map1q35UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map10q22UniSTS


Expression

RNA-SEQ Expression

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


Ensembl Acc Id: ENSRNOT00000015875   ⟹   ENSRNOP00000015875
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5138,167,444 - 138,184,188 (-)Ensembl
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)Ensembl
Rnor_6.0 Ensembl5138,319,762 - 138,336,475 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118144   ⟹   ENSRNOP00000093960
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5138,167,444 - 138,184,188 (-)Ensembl
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000162514   ⟹   ENSRNOP00000103798
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl5138,167,444 - 138,184,188 (-)Ensembl
RefSeq Acc Id: NM_001416726   ⟹   NP_001403655
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85138,167,444 - 138,184,188 (-)NCBI
mRatBN7.25132,882,137 - 132,898,885 (-)NCBI
RefSeq Acc Id: NM_001416727   ⟹   NP_001403656
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85138,167,444 - 138,184,188 (-)NCBI
mRatBN7.25132,882,137 - 132,898,885 (-)NCBI
RefSeq Acc Id: NM_031563   ⟹   NP_113751
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85138,167,444 - 138,184,188 (-)NCBI
mRatBN7.25132,882,137 - 132,898,885 (-)NCBI
Rnor_6.05138,319,754 - 138,336,481 (-)NCBI
Rnor_5.05142,132,028 - 142,152,551 (-)NCBI
RGSC_v3.45139,859,176 - 139,875,840 (-)RGD
Celera5131,407,618 - 131,424,346 (-)RGD
Sequence:
RefSeq Acc Id: XM_063288254   ⟹   XP_063144324
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr85138,167,444 - 138,188,155 (-)NCBI
RefSeq Acc Id: NP_113751   ⟸   NM_031563
- Peptide Label: isoform 2
- UniProtKB: Q4KMA4 (UniProtKB/Swiss-Prot),   P62961 (UniProtKB/Swiss-Prot),   A6JZM8 (UniProtKB/TrEMBL),   Q76MJ6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015875   ⟸   ENSRNOT00000015875
Ensembl Acc Id: ENSRNOP00000093960   ⟸   ENSRNOT00000118144
RefSeq Acc Id: NP_001403656   ⟸   NM_001416727
- Peptide Label: isoform 3
- UniProtKB: A0A8I6AJV4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001403655   ⟸   NM_001416726
- Peptide Label: isoform 1
- UniProtKB: Q76MJ6 (UniProtKB/TrEMBL),   E9PTV8 (UniProtKB/TrEMBL),   Q3ZAV2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063144324   ⟸   XM_063288254
- Peptide Label: isoform X1
- UniProtKB: Q76MJ6 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000103798   ⟸   ENSRNOT00000162514
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 AssemblyChrPosition (strand)Source
Rnor_6.05138,336,494 - 138,336,554EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61843 AgrOrtholog
BioCyc Gene G2FUF-40091 BioCyc
Ensembl Genes ENSRNOG00000023786 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000015875 ENTREZGENE
  ENSRNOT00000118144 ENTREZGENE
  ENSRNOT00000162514 ENTREZGENE
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7105037 IMAGE-MGC_LOAD
  IMAGE:7107271 IMAGE-MGC_LOAD
  IMAGE:7124218 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: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
PANTHER COLD SHOCK DOMAIN CONTAINING PROTEINS UniProtKB/Swiss-Prot
Pfam CSD UniProtKB/Swiss-Prot
PhenoGen Ybx1 PhenoGen
PRINTS COLDSHOCK UniProtKB/Swiss-Prot
PROSITE CSD_1 UniProtKB/Swiss-Prot
  CSD_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000023786 RatGTEx
SMART CSP UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot
UniProt A0A8I6AJV4 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L3F8_RAT UniProtKB/TrEMBL
  A6JZM8 ENTREZGENE, UniProtKB/TrEMBL
  E9PTV8 ENTREZGENE
  P62961 ENTREZGENE
  Q3ZAV2 ENTREZGENE, UniProtKB/TrEMBL
  Q4KMA4 ENTREZGENE
  Q76MJ6 ENTREZGENE, UniProtKB/TrEMBL
  YBOX1_RAT UniProtKB/Swiss-Prot
UniProt Secondary 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