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: Exhibits single-stranded DNA binding activity. Involved in animal organ regeneration; negative regulation of transcription by RNA polymerase II; and spermatogenesis. Localizes to gap junction and nucleus. Orthologous to human YBX3 (Y-box binding protein 3); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24165,129,747 - 165,153,101 (-)NCBI
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04165,606,819 - 165,630,041 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04228,170,272 - 228,193,525 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44169,076,517 - 169,099,849 (-)NCBIRGSC3.4rn4RGSC3.4
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)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (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)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
atrazine  (EXP)
beauvericin  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium dichloride  (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)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
flutamide  (EXP)
fructose  (EXP)
griseofulvin  (ISO)
indometacin  (ISO)
ketamine  (EXP)
methotrexate  (EXP)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (EXP)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenol red  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
propiconazole  (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)
trimellitic anhydride  (ISO)
urethane  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)

References

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  


Genomics

Comparative Map Data
Ybx3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24165,129,747 - 165,153,101 (-)NCBI
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04165,606,819 - 165,630,041 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04228,170,272 - 228,193,525 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44169,076,517 - 169,099,849 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl1210,699,089 - 10,723,323 (-)EnsemblGRCh38hg38GRCh38
GRCh381210,699,084 - 10,723,442 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371210,851,688 - 10,875,922 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361210,742,955 - 10,767,171 (-)NCBINCBI36hg18NCBI36
Build 341210,742,955 - 10,767,171NCBI
Celera1216,000,000 - 16,024,276 (-)NCBI
Cytogenetic Map12p13.2NCBI
HuRef1210,580,443 - 10,604,713 (-)NCBIHuRef
CHM1_11210,821,053 - 10,845,329 (-)NCBICHM1_1
Ybx3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396131,341,821 - 131,365,413 (-)NCBIGRCm39mm39
GRCm39 Ensembl6131,341,818 - 131,365,439 (-)Ensembl
GRCm386131,364,858 - 131,388,450 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6131,364,855 - 131,388,476 (-)EnsemblGRCm38mm10GRCm38
MGSCv376131,314,876 - 131,338,468 (-)NCBIGRCm37mm9NCBIm37
MGSCv366131,330,551 - 131,354,143 (-)NCBImm8
Celera6136,414,596 - 136,438,226 (-)NCBICelera
Cytogenetic Map6F3NCBI
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
PanPan1.11210,994,177 - 11,018,504 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1210,996,380 - 11,018,172 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01210,728,049 - 10,752,267 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.02735,383,798 - 35,411,218 (+)NCBI
UMICH_Zoey_3.12735,266,703 - 35,294,044 (+)NCBI
UNSW_CanFamBas_1.02735,211,037 - 35,238,385 (+)NCBI
UU_Cfam_GSD_1.02711,081,610 - 11,108,979 (-)NCBI
YBX3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl561,337,863 - 61,361,280 (+)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 (-)NCBI
ChlSab1.1 Ensembl1110,500,361 - 10,522,226 (-)Ensembl
Vero_WHO_p1.0NW_0236660892,576,328 - 2,600,838 (-)NCBI

Position Markers
RH136939  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2483,535,605 - 83,535,785 (+)MAPPER
mRatBN7.24165,129,895 - 165,130,076 (+)MAPPER
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 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4146942075168998263Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157423126184226339Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4134917642179917642Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
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)4145547014184226339Rat
6478720Alc23Alcohol consumption QTL 230.00509drinking behavior trait (VT:0001422)ethanol drink intake rate to body weight ratio (CMO:0001616)4155386197184226339Rat
6478728Anxrr36Anxiety related response QTL 360.01061locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478733Anxrr37Anxiety related response QTL 370.00095locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478737Anxrr38Anxiety related response QTL 380.00159locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
6478757Anxrr44Anxiety related response QTL 440.01087locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
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)4123587009168587009Rat
6478782Anxrr52Anxiety related response QTL 520.02091locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
6478785Anxrr53Anxiety related response QTL 530.01397locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4155386197184226339Rat
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)4145547014184226339Rat
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)4145547014184226339Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4156855449184226339Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
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)4146086918168047091Rat

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007427   ⟹   ENSRNOP00000007427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4165,606,819 - 165,630,118 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000068185   ⟹   ENSRNOP00000059241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24165,129,747 - 165,153,101 (-)NCBI
RefSeq Acc Id: XM_039108451   ⟹   XP_038964379
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24165,129,747 - 165,150,165 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_114185   ⟸   NM_031979
- UniProtKB: 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
RefSeq Acc Id: XP_038964379   ⟸   XM_039108451
- Peptide Label: isoform X2
Protein Domains
CSD

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621056 AgrOrtholog
Ensembl Genes ENSRNOG00000005480 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007427 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000059241 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007427 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000068185 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
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
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, 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