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 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 ...
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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25132,882,137 - 132,899,108 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5135,609,596 - 135,626,412 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.05137,366,056 - 137,382,871 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.05137,386,642 - 137,403,467 (-)NCBIRnor_WKY
Rnor_6.05138,319,754 - 138,336,721 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,319,762 - 138,336,475 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05142,132,028 - 142,152,551 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45139,859,176 - 139,875,840 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15139,864,480 - 139,881,067 (-)NCBI
Celera5131,407,618 - 131,424,346 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

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  


Genomics

Comparative Map Data
Ybx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25132,882,137 - 132,899,108 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx5135,609,596 - 135,626,412 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.05137,366,056 - 137,382,871 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.05137,386,642 - 137,403,467 (-)NCBIRnor_WKY
Rnor_6.05138,319,754 - 138,336,721 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5138,319,762 - 138,336,475 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05142,132,028 - 142,152,551 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45139,859,176 - 139,875,840 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15139,864,480 - 139,881,067 (-)NCBI
Celera5131,407,618 - 131,424,346 (-)NCBICelera
Cytogenetic Map5q36NCBI
YBX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38142,682,418 - 42,703,805 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl142,682,418 - 42,703,805 (+)EnsemblGRCh38hg38GRCh38
GRCh37143,148,089 - 43,169,476 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36142,920,653 - 42,940,607 (+)NCBINCBI36Build 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 Ensembl
GRCm384119,277,327 - 119,296,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4119,277,981 - 119,294,604 (-)EnsemblGRCm38mm10GRCm38
MGSCv374118,949,932 - 118,967,118 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 Ensembl6168,716,789 - 168,736,604 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248921,939,641 - 1,957,621 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
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)546711509161317411Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)590450144135450144Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)594858972143070159Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)597570330136479578Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
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)5111416838156416838Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5120740824143608494Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
7394710Emca12Estrogen-induced mammary cancer QTL 12mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5124160767133749643Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
1300122Wbc1White blood cell count QTL 12.75leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)5125392826139989768Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
1581505Rf54Renal function QTL 54kidney physiology trait (VT:0002136)kidney 20-HETE level (CMO:0001854)5128033842133011550Rat
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)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1331803Rf32Renal function QTL 322.798kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)5129132428143070159Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat

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
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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000015875   ⟹   ENSRNOP00000015875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)Ensembl
Rnor_6.0 Ensembl5138,319,762 - 138,336,475 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118144   ⟹   ENSRNOP00000093960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5132,882,145 - 132,898,862 (-)Ensembl
RefSeq Acc Id: NM_031563   ⟹   NP_113751
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25132,882,137 - 132,898,868 (-)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_008764058   ⟹   XP_008762280
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25132,882,137 - 132,899,080 (-)NCBI
Rnor_6.05138,319,754 - 138,336,677 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008764059   ⟹   XP_008762281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25132,882,137 - 132,899,108 (-)NCBI
Rnor_6.05138,319,754 - 138,336,721 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113751   ⟸   NM_031563
- UniProtKB: Q4KMA4 (UniProtKB/Swiss-Prot),   P62961 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008762281   ⟸   XM_008764059
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008762280   ⟸   XM_008764058
- Peptide Label: isoform X1
- UniProtKB: Q3ZAV2 (UniProtKB/TrEMBL),   E9PTV8 (UniProtKB/TrEMBL)
- 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 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, 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