Sfrp1 (secreted frizzled-related protein 1) - Rat Genome Database

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Gene: Sfrp1 (secreted frizzled-related protein 1) Rattus norvegicus
Analyze
Symbol: Sfrp1
Name: secreted frizzled-related protein 1
RGD ID: 621074
Description: Predicted to enable several functions, including Wnt-protein binding activity; frizzled binding activity; and heparin binding activity. Involved in several processes, including cellular response to prostaglandin E stimulus; negative regulation of osteoclast differentiation; and osteoblast differentiation. Predicted to be located in cell surface; collagen-containing extracellular matrix; and cytosol. Predicted to be active in extracellular space. Orthologous to human SFRP1 (secreted frizzled related protein 1); PARTICIPATES IN Wnt signaling, canonical pathway; Wnt signaling pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 3-aminobenzamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: sFRP-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21668,575,763 - 68,613,905 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1668,575,763 - 68,614,286 (-)Ensembl
Rnor_6.01673,372,007 - 73,410,777 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1673,372,007 - 73,410,777 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01673,006,739 - 73,045,509 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41673,030,458 - 73,067,304 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11673,031,966 - 73,066,892 (-)NCBI
Celera1666,467,691 - 66,505,810 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3-aminobenzamide  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-formyltetrahydrofolic acid  (EXP)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
aflatoxin B1  (EXP)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP,ISO)
biguanides  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
boron nitride  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP)
calciol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
CU-O LINKAGE  (ISO)
Cuprizon  (EXP)
cytarabine  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
ethanol  (ISO)
folic acid  (ISO)
glyphosate  (EXP)
heparin  (EXP)
hydroquinone  (ISO)
lead diacetate  (EXP)
mercury atom  (ISO)
mercury dibromide  (ISO)
mercury(0)  (ISO)
methotrexate  (EXP)
methylmercury chloride  (ISO)
mifepristone  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
naphthalene  (ISO)
nickel atom  (ISO)
oxaliplatin  (EXP)
p-chloromercuribenzoic acid  (ISO)
p-menthan-3-ol  (ISO)
panobinostat  (ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
pravastatin  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
Soman  (EXP)
Sporidesmin  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
theaflavin  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vorinostat  (ISO)
XL147  (ISO)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior/posterior pattern specification  (ISO)
bone trabecula formation  (IEA,ISO)
canonical Wnt signaling pathway  (IBA,IEA,ISO)
cellular response to BMP stimulus  (IEA,ISO)
cellular response to estradiol stimulus  (IEA,ISO)
cellular response to estrogen stimulus  (IEA,ISO)
cellular response to fibroblast growth factor stimulus  (IEA,ISO)
cellular response to growth factor stimulus  (ISO)
cellular response to heparin  (IEA,ISO)
cellular response to hypoxia  (IEA,ISO)
cellular response to interleukin-1  (IEA,ISO)
cellular response to prostaglandin E stimulus  (IEA,IEP,ISO)
cellular response to starvation  (IEA,ISO)
cellular response to transforming growth factor beta stimulus  (IEA,ISO)
cellular response to tumor necrosis factor  (IEA,ISO)
cellular response to vitamin D  (IEA,ISO)
cellular response to X-ray  (IEA,ISO)
convergent extension involved in somitogenesis  (IEA,ISO)
development of primary male sexual characteristics  (ISO)
digestive tract morphogenesis  (IEA,ISO)
dopaminergic neuron differentiation  (IEA,ISO)
dorsal/ventral axis specification  (IEA,ISO)
female gonad development  (IEA,ISO)
hematopoietic progenitor cell differentiation  (ISO)
hematopoietic stem cell differentiation  (IEA,ISO)
hemopoiesis  (ISO)
male gonad development  (IEA,ISO)
negative regulation of androgen receptor signaling pathway  (IEA,ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of B cell differentiation  (IEA,ISO)
negative regulation of BMP signaling pathway  (IEA,ISO)
negative regulation of bone remodeling  (IEA,ISO)
negative regulation of canonical Wnt signaling pathway  (IBA,IDA,ISO)
negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation  (IEA,ISO)
negative regulation of cell growth  (IEA,ISO)
negative regulation of cell migration  (IEA,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of epithelial cell proliferation  (IEA,ISO)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of fibroblast apoptotic process  (IEA,ISO)
negative regulation of fibroblast proliferation  (IEA,ISO)
negative regulation of gene expression  (IEA,ISO)
negative regulation of insulin secretion  (IEA,ISO)
negative regulation of JUN kinase activity  (IEA,ISO)
negative regulation of ossification  (IEA,ISO)
negative regulation of osteoblast differentiation  (IEA,ISO)
negative regulation of osteoblast proliferation  (IEA,ISO)
negative regulation of osteoclast differentiation  (IEA,IMP,ISO)
negative regulation of peptidyl-tyrosine phosphorylation  (IEA,ISO)
negative regulation of planar cell polarity pathway involved in axis elongation  (IEA,ISO)
negative regulation of transcription, DNA-templated  (IEA,ISO)
negative regulation of Wnt signaling pathway  (IDA,ISO,TAS)
negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification  (IEA,ISO)
neural crest cell fate commitment  (IEA,ISO)
neural tube closure  (ISO)
neural tube development  (ISO)
osteoblast differentiation  (IEA,IEP,ISO)
planar cell polarity pathway involved in neural tube closure  (IEA,ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of canonical Wnt signaling pathway  (IEA,ISO)
positive regulation of cell growth  (IEA,ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of epithelial cell proliferation  (IEA,ISO)
positive regulation of extrinsic apoptotic signaling pathway  (ISO)
positive regulation of extrinsic apoptotic signaling pathway via death domain receptors  (IEA,ISO)
positive regulation of fat cell differentiation  (IEA,ISO)
positive regulation of fibroblast apoptotic process  (IEA,ISO)
positive regulation of non-canonical Wnt signaling pathway  (IEA,ISO)
positive regulation of smoothened signaling pathway  (IEA,ISO)
positive regulation of transcription, DNA-templated  (IEA,ISO)
positive regulation of Wnt signaling pathway  (ISO)
prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis  (IEA,ISO)
proteolysis  (IEA)
regulation of branching involved in prostate gland morphogenesis  (IEA,ISO)
regulation of cell cycle process  (IEA,ISO)
regulation of establishment of planar polarity  (ISO)
regulation of midbrain dopaminergic neuron differentiation  (IEA,ISO)
regulation of neuron projection development  (IEA,ISO)
regulation of ossification  (IMP)
response to organic cyclic compound  (ISO)
response to xenobiotic stimulus  (IEA,ISO)
somatic stem cell population maintenance  (IEA,ISO)
somitogenesis  (ISO)
stromal-epithelial cell signaling involved in prostate gland development  (IEA,ISO)
ureteric bud development  (IEA,ISO)
Wnt signaling pathway involved in somitogenesis  (IEA,ISO)
Wnt signaling pathway, planar cell polarity pathway  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1927703   PMID:9192640   PMID:9391078   PMID:9724099   PMID:10347172   PMID:10654605   PMID:10660608   PMID:10980594   PMID:11287180   PMID:11741940   PMID:11932307   PMID:12055200  
PMID:14581477   PMID:14976225   PMID:15886250   PMID:16077939   PMID:16288033   PMID:16467359   PMID:16532032   PMID:16545622   PMID:17035233   PMID:17443492   PMID:17462603   PMID:17471511  
PMID:17500071   PMID:17994217   PMID:18257070   PMID:18371946   PMID:18787224   PMID:18941195   PMID:19072540   PMID:19095296   PMID:19100252   PMID:19199708   PMID:19254787   PMID:19277043  
PMID:19300477   PMID:19569235   PMID:19664990   PMID:19723665   PMID:19734317   PMID:19778523   PMID:19850029   PMID:19896444   PMID:20033841   PMID:20130188   PMID:20208569   PMID:20234818  
PMID:20551380   PMID:22206666   PMID:22290867   PMID:22313323   PMID:22535492   PMID:23073828   PMID:23376485   PMID:24006456   PMID:24080158   PMID:25046226   PMID:26282432   PMID:27048460  
PMID:27559042   PMID:29319176   PMID:31799642   PMID:32238888  


Genomics

Comparative Map Data
Sfrp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21668,575,763 - 68,613,905 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1668,575,763 - 68,614,286 (-)Ensembl
Rnor_6.01673,372,007 - 73,410,777 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1673,372,007 - 73,410,777 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01673,006,739 - 73,045,509 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41673,030,458 - 73,067,304 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11673,031,966 - 73,066,892 (-)NCBI
Celera1666,467,691 - 66,505,810 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
SFRP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl841,261,962 - 41,309,473 (-)EnsemblGRCh38hg38GRCh38
GRCh38841,261,962 - 41,309,473 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37841,119,481 - 41,166,992 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36841,238,635 - 41,286,137 (-)NCBINCBI36hg18NCBI36
Build 34841,238,635 - 41,286,137NCBI
Celera840,068,517 - 40,116,053 (-)NCBI
Cytogenetic Map8p11.21NCBI
HuRef839,647,919 - 39,695,566 (-)NCBIHuRef
CHM1_1841,167,412 - 41,215,102 (-)NCBICHM1_1
Sfrp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39823,901,401 - 23,939,648 (+)NCBIGRCm39mm39
GRCm39 Ensembl823,901,518 - 23,939,648 (+)Ensembl
GRCm38823,411,383 - 23,449,632 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl823,411,502 - 23,449,632 (+)EnsemblGRCm38mm10GRCm38
MGSCv37824,521,974 - 24,560,104 (+)NCBIGRCm37mm9NCBIm37
MGSCv36824,877,063 - 24,915,177 (+)NCBImm8
Celera824,905,624 - 24,944,019 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map811.48NCBI
Sfrp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555361,663,344 - 1,703,514 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555361,663,721 - 1,702,678 (+)NCBIChiLan1.0ChiLan1.0
SFRP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1837,956,423 - 38,001,865 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0840,507,027 - 40,555,053 (-)NCBIMhudiblu_PPA_v0panPan3
SFRP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11624,262,451 - 24,306,162 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1624,261,946 - 24,302,964 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1624,766,734 - 24,810,532 (+)NCBI
ROS_Cfam_1.01626,010,215 - 26,053,984 (+)NCBI
UMICH_Zoey_3.11624,382,043 - 24,425,801 (+)NCBI
UNSW_CanFamBas_1.01624,943,898 - 24,987,804 (+)NCBI
UU_Cfam_GSD_1.01624,995,596 - 25,039,359 (+)NCBI
Sfrp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494347,320,083 - 47,364,001 (+)NCBI
SpeTri2.0NW_0049367851,276,478 - 1,320,397 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SFRP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1710,436,426 - 10,489,748 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11710,436,414 - 10,489,773 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21711,790,230 - 11,878,539 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SFRP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1839,243,775 - 39,289,050 (-)NCBI
ChlSab1.1 Ensembl839,243,780 - 39,288,984 (-)Ensembl
Vero_WHO_p1.0NW_0236660522,558,131 - 2,612,751 (+)NCBI
Sfrp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247802,133,105 - 2,172,301 (+)NCBI

Position Markers
RH135173  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,579,854 - 68,580,064 (+)MAPPERmRatBN7.2
Rnor_6.01673,376,095 - 73,376,304NCBIRnor6.0
Rnor_5.01673,010,827 - 73,011,036UniSTSRnor5.0
RGSC_v3.41673,032,774 - 73,032,983UniSTSRGSC3.4
Celera1666,471,780 - 66,471,989UniSTS
RH 3.4 Map16635.6UniSTS
Cytogenetic Map16q12.5UniSTS
RH135431  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,577,534 - 68,577,728 (+)MAPPERmRatBN7.2
Rnor_6.01673,373,779 - 73,373,972NCBIRnor6.0
Rnor_5.01673,008,511 - 73,008,704UniSTSRnor5.0
RGSC_v3.41673,030,458 - 73,030,651UniSTSRGSC3.4
Celera1666,469,463 - 66,469,656UniSTS
RH 3.4 Map16660.2UniSTS
Cytogenetic Map16q12.5UniSTS
RH137493  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,578,149 - 68,578,349 (+)MAPPERmRatBN7.2
Rnor_6.01673,374,394 - 73,374,593NCBIRnor6.0
Rnor_5.01673,009,126 - 73,009,325UniSTSRnor5.0
RGSC_v3.41673,031,073 - 73,031,272UniSTSRGSC3.4
Celera1666,470,078 - 66,470,275UniSTS
Cytogenetic Map16q12.5UniSTS
RH141094  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,577,204 - 68,577,385 (+)MAPPERmRatBN7.2
Rnor_6.01673,373,449 - 73,373,629NCBIRnor6.0
Rnor_5.01673,008,181 - 73,008,361UniSTSRnor5.0
RGSC_v3.41673,030,128 - 73,030,308UniSTSRGSC3.4
Celera1666,469,133 - 66,469,313UniSTS
RH 3.4 Map16659.7UniSTS
Cytogenetic Map16q12.5UniSTS
RH141243  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,575,913 - 68,576,115 (+)MAPPERmRatBN7.2
Rnor_6.01673,372,158 - 73,372,359NCBIRnor6.0
Rnor_5.01673,006,890 - 73,007,091UniSTSRnor5.0
RGSC_v3.41673,028,256 - 73,028,457UniSTSRGSC3.4
Celera1666,467,842 - 66,468,043UniSTS
RH 3.4 Map16570.32UniSTS
Cytogenetic Map16q12.5UniSTS
Sfrp1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,578,094 - 68,578,875 (+)MAPPERmRatBN7.2
Rnor_6.01673,374,339 - 73,375,119NCBIRnor6.0
Rnor_5.01673,009,071 - 73,009,851UniSTSRnor5.0
RGSC_v3.41673,031,018 - 73,031,798UniSTSRGSC3.4
Celera1666,470,023 - 66,470,801UniSTS
Cytogenetic Map16q12.5UniSTS
Sfrp1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21668,578,094 - 68,578,873 (+)MAPPERmRatBN7.2
Rnor_6.01673,374,339 - 73,375,117NCBIRnor6.0
Rnor_5.01673,009,071 - 73,009,849UniSTSRnor5.0
RGSC_v3.41673,031,018 - 73,031,796UniSTSRGSC3.4
Celera1666,470,023 - 66,470,799UniSTS
Cytogenetic Map16q12.5UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:41
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000024128
Prediction methods: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
Medium 1 30 13 6 11 6 57 35 32
Low 2 13 40 31 8 31 8 11 17 9 11 8
Below cutoff 4 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024128   ⟹   ENSRNOP00000024128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1668,575,763 - 68,614,286 (-)Ensembl
Rnor_6.0 Ensembl1673,372,007 - 73,410,777 (-)Ensembl
RefSeq Acc Id: NM_001276712   ⟹   NP_001263641
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21668,575,763 - 68,613,905 (-)NCBI
Rnor_6.01673,372,007 - 73,410,777 (-)NCBI
Rnor_5.01673,006,739 - 73,045,509 (-)NCBI
Celera1666,467,691 - 66,505,810 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001263641 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD49337 (Get FASTA)   NCBI Sequence Viewer  
  EDM09033 (Get FASTA)   NCBI Sequence Viewer  
  Q9R168 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001263641   ⟸   NM_001276712
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000024128   ⟸   ENSRNOT00000024128
Protein Domains
FZ   NTR

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (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
F344/NRrrc (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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/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)
FHH/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
FHL/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)
FHL/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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:621074 AgrOrtholog
Ensembl Genes ENSRNOG00000017783 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024128 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024128 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.2000.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.40.50.120 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Frizzled/SFRP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Frizzled_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Frizzled_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Netrin_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Netrin_module_non-TIMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SFRP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SFRP1_CRD UniProtKB/TrEMBL
  TIMP-like_OB-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84402 UniProtKB/TrEMBL
NCBI Gene 84402 ENTREZGENE
PANTHER PTHR11309 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11309:SF87 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF01392 UniProtKB/TrEMBL
PhenoGen Sfrp1 PhenoGen
PROSITE NTR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PS50038 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART C345C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FRI UniProtKB/TrEMBL
Superfamily-SCOP SSF50242 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF63501 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1LLX7_RAT UniProtKB/TrEMBL
  Q9R168 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-12-14 Sfrp1  secreted frizzled-related protein 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Sfrp1  secreted frizzled-related protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation promoter activity is induced by phosphorylated CREB and the adaptor protein CBP 724587
gene_transcript region -202 to -144 contains the transcriptional activation domain 724587