Ybx3 (Y box binding protein 3) - Rat Genome Database

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Gene: Ybx3 (Y box binding protein 3) Rattus norvegicus
Analyze
Symbol: Ybx3
Name: Y box binding protein 3
RGD ID: 621056
Description: Enables single-stranded DNA binding activity. Involved in animal organ regeneration; negative regulation of transcription by RNA polymerase II; and spermatogenesis. Located in gap junction. Orthologous to human YBX3 (Y-box binding protein 3); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cold shock domain protein A; cold shock domain-containing protein A; Csda; Dbpa; DNA-binding protein A; MGC124554; muscle Y-box protein YB2; RYB-A; Y-box-binding protein 3; Y-box-binding protein A; Yb2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84166,861,180 - 166,884,532 (-)NCBIGRCr8
mRatBN7.24165,129,747 - 165,153,101 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4165,129,758 - 165,153,161 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4171,414,533 - 171,437,843 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04167,197,552 - 167,220,862 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04165,831,596 - 165,854,906 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04165,606,819 - 165,630,041 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04228,170,272 - 228,193,525 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44169,076,517 - 169,099,849 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14169,321,476 - 169,344,762 (-)NCBI
Celera4153,733,515 - 153,756,519 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(1->4)-beta-D-glucan  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
atrazine  (EXP)
beauvericin  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
candesartan  (EXP)
carbon nanotube  (ISO)
chloropicrin  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
fenthion  (ISO)
flutamide  (EXP)
FR900359  (ISO)
fructose  (EXP)
griseofulvin  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
ketamine  (EXP)
methidathion  (ISO)
methotrexate  (EXP)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenol red  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
raloxifene  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
trimellitic anhydride  (ISO)
urethane  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Association of connexin36 and zonula occludens-1 with zonula occludens-2 and the transcription factor zonula occludens-1-associated nucleic acid-binding protein at neuronal gap junctions in rodent retina. Ciolofan C, etal., Neuroscience. 2006 Jun 30;140(2):433-51. Epub 2006 May 2.
2. Screening for differentially expressed genes in the rat inner retina and optic nerve after optic nerve crush. Dieterich DC, etal., Neurosci Lett. 2002 Jan 4;317(1):29-32.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. A novel growth-inducible gene that encodes a protein with a conserved cold-shock domain. Ito K, etal., Nucleic Acids Res 1994 Jun 11;22(11):2036-41.
6. Expression of a Y-box protein, YB2/RYB-a, precedes protamine 2 expression during spermatogenesis in rodents. Iuchi Y, etal., Mol Hum Reprod. 2001 Nov;7(11):1023-31.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Cloning and characterization of a novel transcriptional repressor of the nicotinic acetylcholine receptor delta-subunit gene. Sapru MK, etal., J Biol Chem 1996 Mar 22;271(12):7203-11.
Additional References at PubMed
PMID:10772793   PMID:12117816   PMID:12433987   PMID:12477932   PMID:15592429   PMID:16954378   PMID:17934523   PMID:18676817   PMID:22658674   PMID:22681889   PMID:22711822   PMID:29393348  
PMID:35352799  


Genomics

Comparative Map Data
Ybx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84166,861,180 - 166,884,532 (-)NCBIGRCr8
mRatBN7.24165,129,747 - 165,153,101 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4165,129,758 - 165,153,161 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4171,414,533 - 171,437,843 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04167,197,552 - 167,220,862 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04165,831,596 - 165,854,906 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04165,606,819 - 165,630,041 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04228,170,272 - 228,193,525 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44169,076,517 - 169,099,849 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14169,321,476 - 169,344,762 (-)NCBI
Celera4153,733,515 - 153,756,519 (-)NCBICelera
Cytogenetic Map4q42NCBI
YBX3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381210,699,089 - 10,723,323 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1210,699,089 - 10,723,323 (-)EnsemblGRCh38hg38GRCh38
GRCh371210,851,688 - 10,875,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361210,742,955 - 10,767,171 (-)NCBINCBI36Build 36hg18NCBI36
Build 341210,742,955 - 10,767,171NCBI
Celera1216,000,000 - 16,024,276 (-)NCBICelera
Cytogenetic Map12p13.2NCBI
HuRef1210,580,443 - 10,604,713 (-)NCBIHuRef
CHM1_11210,821,053 - 10,845,329 (-)NCBICHM1_1
T2T-CHM13v2.01210,572,193 - 10,596,426 (-)NCBIT2T-CHM13v2.0
Ybx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396131,341,821 - 131,365,413 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6131,341,818 - 131,365,439 (-)EnsemblGRCm39 Ensembl
GRCm386131,364,858 - 131,388,450 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6131,364,855 - 131,388,476 (-)EnsemblGRCm38mm10GRCm38
MGSCv376131,314,876 - 131,338,468 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366131,330,551 - 131,354,143 (-)NCBIMGSCv36mm8
Celera6136,414,596 - 136,438,226 (-)NCBICelera
Cytogenetic Map6F3NCBI
cM Map663.44NCBI
Ybx3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554137,089,719 - 7,108,473 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554137,090,085 - 7,111,542 (+)NCBIChiLan1.0ChiLan1.0
YBX3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21016,170,908 - 16,195,183 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11216,167,659 - 16,191,821 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01210,728,049 - 10,752,267 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11210,994,177 - 11,018,504 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1210,996,380 - 11,018,172 (-)Ensemblpanpan1.1panPan2
YBX3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12735,043,756 - 35,066,230 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2735,043,699 - 35,066,227 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2711,465,924 - 11,493,283 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02735,383,798 - 35,411,218 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2735,383,839 - 35,411,207 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12735,266,703 - 35,294,044 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02735,211,037 - 35,238,385 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02711,081,610 - 11,108,979 (-)NCBIUU_Cfam_GSD_1.0
YBX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl561,337,862 - 61,361,279 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1561,337,868 - 61,361,269 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2564,060,833 - 64,084,239 (+)NCBISscrofa10.2Sscrofa10.2susScr3
YBX3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11110,498,162 - 10,522,432 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1110,500,361 - 10,522,226 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660892,576,328 - 2,600,838 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Ybx3
28 total Variants
miRNA Target Status

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

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

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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat

Markers in Region
RH136939  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2483,535,605 - 83,535,785 (+)MAPPERmRatBN7.2
mRatBN7.24165,129,895 - 165,130,076 (+)MAPPERmRatBN7.2
Rnor_6.04165,606,957 - 165,607,137NCBIRnor6.0
Rnor_6.0484,582,471 - 84,582,650NCBIRnor6.0
Rnor_5.04228,170,410 - 228,170,590UniSTSRnor5.0
Rnor_5.04149,241,374 - 149,241,553UniSTSRnor5.0
RGSC_v3.44169,076,652 - 169,076,832UniSTSRGSC3.4
RGSC_v3.4482,808,157 - 82,808,336UniSTSRGSC3.4
Celera478,404,672 - 78,404,851UniSTS
Celera4153,733,653 - 153,733,833UniSTS
Cytogenetic Map4q42UniSTS
AI549543  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24165,148,054 - 165,148,186 (+)MAPPERmRatBN7.2
Rnor_6.04165,625,115 - 165,625,246NCBIRnor6.0
Rnor_5.04228,188,568 - 228,188,699UniSTSRnor5.0
RGSC_v3.44169,094,810 - 169,094,941UniSTSRGSC3.4
Celera4153,751,811 - 153,751,942UniSTS
RH 3.4 Map41014.9UniSTS
Cytogenetic Map4q42UniSTS
RH140312  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4q42UniSTS


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 1 3
Medium 3 43 51 35 19 35 8 10 74 34 38 11 8
Low 6 6 6 1
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000007427   ⟹   ENSRNOP00000007427
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4165,129,758 - 165,153,161 (-)Ensembl
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000068185   ⟹   ENSRNOP00000059241
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4165,129,760 - 165,153,161 (-)Ensembl
Rnor_6.0 Ensembl4165,606,821 - 165,629,996 (-)Ensembl
RefSeq Acc Id: NM_031979   ⟹   NP_114185
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84166,861,181 - 166,884,491 (-)NCBI
mRatBN7.24165,129,758 - 165,153,069 (-)NCBI
Rnor_6.04165,606,819 - 165,630,041 (-)NCBI
Rnor_5.04228,170,272 - 228,193,525 (-)NCBI
RGSC_v3.44169,076,517 - 169,099,849 (-)RGD
Celera4153,733,515 - 153,756,519 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039108450   ⟹   XP_038964378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84166,861,180 - 166,884,532 (-)NCBI
mRatBN7.24165,129,747 - 165,153,101 (-)NCBI
RefSeq Acc Id: NP_114185   ⟸   NM_031979
- UniProtKB: Q63748 (UniProtKB/Swiss-Prot),   Q62764 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007427   ⟸   ENSRNOT00000007427
RefSeq Acc Id: ENSRNOP00000059241   ⟸   ENSRNOT00000068185
RefSeq Acc Id: XP_038964378   ⟸   XM_039108450
- Peptide Label: isoform X1
Protein Domains
CSD

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

Transcriptome

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

Promoters
RGD ID:13693452
Promoter ID:EPDNEW_R3970
Type:initiation region
Name:Ybx3_1
Description:Y box binding protein 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04165,630,030 - 165,630,090EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621056 AgrOrtholog
BioCyc Gene G2FUF-42725 BioCyc
Ensembl Genes ENSRNOG00000005480 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007427.9 UniProtKB/TrEMBL
  ENSRNOT00000068185.4 UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.140 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7932542 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:83807 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124554 IMAGE-MGC_LOAD
NCBI Gene 83807 ENTREZGENE
PANTHER COLD SHOCK DOMAIN CONTAINING PROTEINS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Y-BOX-BINDING PROTEIN 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CSD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ybx3 PhenoGen
PRINTS COLDSHOCK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CSD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CSD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005480 RatGTEx
SMART CSP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50249 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D4A0L4_RAT UniProtKB/TrEMBL
  F1MA18_RAT UniProtKB/TrEMBL
  Q62764 ENTREZGENE
  Q63748 ENTREZGENE
  YBOX3_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q63748 UniProtKB/Swiss-Prot


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

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