Cd47 (Cd47 molecule) - Rat Genome Database

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Gene: Cd47 (Cd47 molecule) Rattus norvegicus
Analyze
Symbol: Cd47
Name: Cd47 molecule
RGD ID: 2308
Description: Enables protein binding activity involved in heterotypic cell-cell adhesion. Involved in several processes, including cellular response to cytokine stimulus; monocyte extravasation; and regulation of phagocytosis. Located in cell surface. Orthologous to human CD47 (CD47 molecule); PARTICIPATES IN cell-extracellular matrix signaling pathway; INTERACTS WITH (+)-schisandrin B; 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CD47 antigen (Rh-related antigen, integrin-associated signal transducer); IAP; integrin-associated protein; Itgp; leukocyte surface antigen CD47; MGC93490
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21150,906,052 - 50,970,000 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1150,906,177 - 50,969,425 (-)Ensembl
Rnor_6.01153,511,485 - 53,575,754 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1153,514,595 - 53,575,175 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01156,677,247 - 56,739,505 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41152,098,355 - 52,158,169 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11152,155,955 - 52,215,758 (-)NCBI
Celera1150,551,511 - 50,611,556 (-)NCBICelera
Cytogenetic Map11q21NCBI
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)
1,2,4-trimethylbenzene  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,4-methylenedioxymethamphetamine  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxynon-2-enal  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetazolamide  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
beauvericin  (ISO)
benzene  (EXP)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
chrysene  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP)
disodium selenite  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
enniatin  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
hypochlorous acid  (ISO)
irinotecan  (ISO)
iron(III) nitrilotriacetate  (EXP)
ivermectin  (ISO)
lead diacetate  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (EXP)
methylparaben  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nonanoic acid  (ISO)
NSC 23766  (ISO)
ozone  (EXP,ISO)
p-toluidine  (EXP)
paclitaxel  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parathion  (ISO)
pentachlorophenol  (ISO)
phenobarbital  (EXP)
phenytoin  (EXP)
pirinixic acid  (EXP)
propanal  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sunitinib  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
toluene 2,4-diisocyanate  (ISO)
torcetrapib  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
Triptolide  (EXP)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
venlafaxine hydrochloride  (EXP)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9592107   PMID:10816079   PMID:11509594   PMID:12477932   PMID:14634079   PMID:15297459   PMID:15383453   PMID:15489334   PMID:15700281   PMID:19205621   PMID:19505377   PMID:19724054  
PMID:20554646   PMID:22193512   PMID:22215724   PMID:22871113   PMID:23087362   PMID:23376485   PMID:23472187   PMID:23799952   PMID:23990210   PMID:25482981   PMID:25706387   PMID:26617765  
PMID:27960187   PMID:28228282   PMID:29476059   PMID:30720765   PMID:31059044   PMID:31377653  


Genomics

Comparative Map Data
Cd47
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21150,906,052 - 50,970,000 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1150,906,177 - 50,969,425 (-)Ensembl
Rnor_6.01153,511,485 - 53,575,754 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1153,514,595 - 53,575,175 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01156,677,247 - 56,739,505 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41152,098,355 - 52,158,169 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11152,155,955 - 52,215,758 (-)NCBI
Celera1150,551,511 - 50,611,556 (-)NCBICelera
Cytogenetic Map11q21NCBI
CD47
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3108,043,091 - 108,091,862 (-)EnsemblGRCh38hg38GRCh38
GRCh383108,043,091 - 108,094,200 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373107,761,938 - 107,809,878 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363109,244,631 - 109,292,625 (-)NCBINCBI36hg18NCBI36
Build 343109,244,836 - 109,292,592NCBI
Celera3106,158,598 - 106,206,555 (-)NCBI
Cytogenetic Map3q13.12NCBI
HuRef3105,135,236 - 105,183,196 (-)NCBIHuRef
CHM1_13107,726,104 - 107,774,070 (-)NCBICHM1_1
Cd47
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391649,671,691 - 49,732,799 (+)NCBIGRCm39mm39
GRCm39 Ensembl1649,620,896 - 49,735,373 (+)Ensembl
GRCm381649,851,328 - 49,912,503 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1649,800,533 - 49,915,010 (+)EnsemblGRCm38mm10GRCm38
MGSCv371649,855,767 - 49,911,801 (+)NCBIGRCm37mm9NCBIm37
MGSCv361649,775,280 - 49,831,314 (+)NCBImm8
Celera1650,198,659 - 50,254,756 (+)NCBICelera
Cytogenetic Map16B5NCBI
Cd47
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554278,704,519 - 8,740,962 (-)NCBIChiLan1.0ChiLan1.0
CD47
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13112,104,037 - 112,140,818 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3112,104,037 - 112,143,522 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03105,170,246 - 105,217,603 (-)NCBIMhudiblu_PPA_v0panPan3
CD47
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13313,315,984 - 13,362,971 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3313,319,266 - 13,363,580 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3313,425,087 - 13,468,588 (-)NCBI
ROS_Cfam_1.03313,485,123 - 13,528,697 (-)NCBI
UMICH_Zoey_3.13313,354,729 - 13,398,227 (-)NCBI
UNSW_CanFamBas_1.03313,420,284 - 13,463,780 (-)NCBI
UU_Cfam_GSD_1.03313,832,991 - 13,876,700 (-)NCBI
LOC101967799
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602141,436,987 - 141,483,915 (+)NCBI
SpeTri2.0NW_0049366451,363,406 - 1,408,624 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD47
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13151,429,288 - 151,502,164 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113151,427,933 - 151,488,064 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213160,472,681 - 160,518,106 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CD47
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12272,702,236 - 72,749,344 (+)NCBI
ChlSab1.1 Ensembl2272,702,324 - 72,751,887 (+)Ensembl
Vero_WHO_p1.0NW_02366604193,741,579 - 93,790,134 (-)NCBI

Position Markers
AI071341  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21150,968,148 - 50,968,366 (+)MAPPERmRatBN7.2
Rnor_6.01153,573,899 - 53,574,116NCBIRnor6.0
Rnor_5.01156,737,649 - 56,737,866UniSTSRnor5.0
RGSC_v3.41152,156,893 - 52,157,110UniSTSRGSC3.4
Celera1150,610,280 - 50,610,497UniSTS
Cytogenetic Map11q21UniSTS
AB012693  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21150,909,961 - 50,910,063 (+)MAPPERmRatBN7.2
Rnor_6.01153,515,395 - 53,515,496NCBIRnor6.0
Rnor_5.01156,680,537 - 56,680,638UniSTSRnor5.0
RGSC_v3.41152,099,170 - 52,099,271UniSTSRGSC3.4
Celera1150,552,326 - 50,552,427UniSTS
Cytogenetic Map11q21UniSTS
AW108519  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21150,909,339 - 50,909,466 (+)MAPPERmRatBN7.2
Rnor_6.01153,514,773 - 53,514,899NCBIRnor6.0
Rnor_5.01156,679,915 - 56,680,041UniSTSRnor5.0
RGSC_v3.41152,098,548 - 52,098,674UniSTSRGSC3.4
Celera1150,551,704 - 50,551,830UniSTS
Cytogenetic Map11q21UniSTS
Z25524  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21150,909,257 - 50,909,458 (+)MAPPERmRatBN7.2
Rnor_6.01153,514,691 - 53,514,891NCBIRnor6.0
Rnor_5.01156,679,833 - 56,680,033UniSTSRnor5.0
RGSC_v3.41152,098,466 - 52,098,666UniSTSRGSC3.4
Celera1150,551,622 - 50,551,822UniSTS
Cytogenetic Map11q21UniSTS
RH138892  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21150,914,483 - 50,914,603 (+)MAPPERmRatBN7.2
Rnor_6.01153,519,908 - 53,520,027NCBIRnor6.0
Rnor_5.01156,685,050 - 56,685,169UniSTSRnor5.0
RGSC_v3.41152,103,692 - 52,103,811UniSTSRGSC3.4
Celera1150,556,848 - 50,556,967UniSTS
Cytogenetic Map11q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:52
Interacting mature miRNAs:57
Transcripts:ENSRNOT00000050142
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
Medium 3 43 57 41 19 41 4 6 74 35 34 11 4
Low 4 5 7 4
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248262 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248267 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001840415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_358250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF017437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085740 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D87659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232318 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000050142   ⟹   ENSRNOP00000050938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1150,909,841 - 50,969,388 (-)Ensembl
Rnor_6.0 Ensembl1153,518,726 - 53,575,060 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078221   ⟹   ENSRNOP00000068714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1150,909,850 - 50,969,425 (-)Ensembl
Rnor_6.0 Ensembl1153,515,343 - 53,575,161 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078434   ⟹   ENSRNOP00000071430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1150,909,847 - 50,969,409 (-)Ensembl
Rnor_6.0 Ensembl1153,514,595 - 53,575,175 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098840   ⟹   ENSRNOP00000082971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1150,906,177 - 50,969,385 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099732   ⟹   ENSRNOP00000097243
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1150,906,177 - 50,958,470 (-)Ensembl
RefSeq Acc Id: NM_019195   ⟹   NP_062068
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21150,909,147 - 50,969,425 (-)NCBI
Rnor_6.01153,514,580 - 53,575,175 (-)NCBI
Rnor_5.01156,677,247 - 56,739,505 (-)NCBI
RGSC_v3.41152,098,355 - 52,158,169 (-)RGD
Celera1150,551,511 - 50,611,556 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248262   ⟹   XP_006248324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21150,909,843 - 50,970,000 (-)NCBI
Rnor_6.01153,511,485 - 53,575,754 (-)NCBI
Rnor_5.01156,677,247 - 56,739,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248263   ⟹   XP_006248325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21150,909,843 - 50,970,000 (-)NCBI
Rnor_6.01153,511,485 - 53,575,754 (-)NCBI
Rnor_5.01156,677,247 - 56,739,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248264   ⟹   XP_006248326
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21150,906,052 - 50,970,000 (-)NCBI
Rnor_6.01153,511,485 - 53,575,754 (-)NCBI
Rnor_5.01156,677,247 - 56,739,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248266   ⟹   XP_006248328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21150,909,843 - 50,970,000 (-)NCBI
Rnor_6.01153,511,485 - 53,575,754 (-)NCBI
Rnor_5.01156,677,247 - 56,739,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248267   ⟹   XP_006248329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21150,909,843 - 50,970,000 (-)NCBI
Rnor_6.01153,511,485 - 53,575,754 (-)NCBI
Rnor_5.01156,677,247 - 56,739,505 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062068   ⟸   NM_019195
- Peptide Label: precursor
- UniProtKB: P97829 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006248329   ⟸   XM_006248267
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006248326   ⟸   XM_006248264
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006248325   ⟸   XM_006248263
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006248324   ⟸   XM_006248262
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JTH4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248328   ⟸   XM_006248266
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000071430   ⟸   ENSRNOT00000078434
RefSeq Acc Id: ENSRNOP00000068714   ⟸   ENSRNOT00000078221
RefSeq Acc Id: ENSRNOP00000050938   ⟸   ENSRNOT00000050142
RefSeq Acc Id: ENSRNOP00000097243   ⟸   ENSRNOT00000099732
RefSeq Acc Id: ENSRNOP00000082971   ⟸   ENSRNOT00000098840
Protein Domains
Ig-like   Ig-like V-type

Transcriptome

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

Promoters
RGD ID:13698121
Promoter ID:EPDNEW_R8646
Type:initiation region
Name:Cd47_1
Description:Cd47 molecule
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_6.01153,575,178 - 53,575,238EPDNEW

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)
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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)
ACI/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
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/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
F344/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
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
F344/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/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
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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (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
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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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)
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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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (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: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (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: 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)
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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
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
M520/NRrrcMcwi (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
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)
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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
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)
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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
PVG/Seac (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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)
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)
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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/OlalpcvMcwi (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
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)
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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: 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)
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/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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2308 AgrOrtholog
Ensembl Genes ENSRNOG00000001964 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000050938 UniProtKB/Swiss-Prot
  ENSRNOP00000068714 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071430 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000050142 UniProtKB/Swiss-Prot
  ENSRNOT00000078221 UniProtKB/TrEMBL
  ENSRNOT00000078434 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7189894 IMAGE-MGC_LOAD
InterPro CD47 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CD47_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CD47_Vset UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IgV_CD47 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29364 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93490 IMAGE-MGC_LOAD
NCBI Gene 29364 ENTREZGENE
PANTHER PTHR10613 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CD47 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V-set_CD47 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cd47 PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217664
UniProt A0A0G2JTH4 ENTREZGENE, UniProtKB/TrEMBL
  CD47_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35294 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-29 Cd47  Cd47 molecule  Cd47  CD47 antigen (Rh-related antigen, integrin-associated signal transducer)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Cd47  CD47 antigen (Rh-related antigen, integrin-associated signal transducer)    integrin-associated protein  Name updated 1299863 APPROVED
2002-06-10 Cd47  integrin-associated protein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in renal cells 69802
gene_mutations_overexpression overexpression may be associated with Fe-NTA-induced renal cortical tubular damage and with tumor progression and metastasis 69802
gene_process may be involved in regulating renal cell growth 69802