Csf1 (colony stimulating factor 1) - Rat Genome Database

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Gene: Csf1 (colony stimulating factor 1) Rattus norvegicus
Analyze
Symbol: Csf1
Name: colony stimulating factor 1
RGD ID: 621063
Description: Enables identical protein binding activity. Involved in several processes, including myeloid leukocyte differentiation; odontogenesis; and ossification. Located in extracellular space. Used to study anti-basement membrane glomerulonephritis; high grade glioma; and osteopetrosis. Biomarker of systemic scleroderma. Human ortholog(s) of this gene implicated in interstitial cystitis. Orthologous to human CSF1 (colony stimulating factor 1); PARTICIPATES IN cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: colony stimulating factor 1 (macrophage); colony stimulating factor 1(macrophage); CSF-1; macrophage colony-stimulating factor 1; MCSF
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Csf1tl  
Genetic Models: F344tl
Is Marker For: Strains:   LEW-tl   LEW-tl.BN-(D2Arb16-D2Wox8)  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22195,377,215 - 195,396,608 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl2210,522,375 - 210,550,560 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02210,522,370 - 210,550,546 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02229,989,430 - 230,017,945 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42203,292,765 - 203,307,968 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12203,255,518 - 203,270,701 (-)NCBI
Celera2188,024,644 - 188,043,645 (-)NCBICelera
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-amphetamine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-tert-butylhydroquinone  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
5-azacytidine  (EXP)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B2  (ISO)
aldehydo-D-glucosamine  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
aripiprazole  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
asbestos  (ISO)
aspartame  (ISO)
atazanavir sulfate  (ISO)
benzalkonium chloride  (ISO)
benzamide  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzoates  (ISO)
beta-D-glucosamine  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
C.I. Natural Red 20  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
cholesterol  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
DAPT  (EXP)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
diclofenac  (ISO)
dioxygen  (EXP,ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenamidone  (ISO)
fenvalerate  (EXP)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
graphite  (EXP)
GTP  (ISO)
GW 4064  (ISO)
histamine  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (EXP,ISO)
LY294002  (ISO)
methamphetamine  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
monosodium L-glutamate  (ISO)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP,ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
niclosamide  (ISO)
nitric oxide  (ISO)
o-anisidine  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
Risedronate sodium  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
succimer  (ISO)
sulindac  (EXP)
T-2 toxin  (EXP)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetracycline  (ISO)
thymidine  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triadimefon  (ISO)
trichloroethene  (ISO)
triclosan  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
urethane  (ISO)
zinc atom  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
branching involved in mammary gland duct morphogenesis  (ISO)
cell population proliferation  (IDA)
developmental process involved in reproduction  (ISO)
homeostasis of number of cells within a tissue  (ISO)
inflammatory response  (IEA)
innate immune response  (IEA)
macrophage colony-stimulating factor signaling pathway  (ISO)
macrophage differentiation  (IDA,IEP)
mammary duct terminal end bud growth  (ISO)
mammary gland fat development  (ISO)
microglial cell proliferation  (ISO)
negative regulation of neuron death  (IEA,ISO)
odontogenesis  (IMP)
ossification  (IMP)
osteoclast differentiation  (IBA,IEA,IMP,ISO)
osteoclast proliferation  (ISO)
positive regulation of cell migration  (ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell-matrix adhesion  (ISO)
positive regulation of cellular protein metabolic process  (IEA,ISO)
positive regulation of gene expression  (IEA,ISO)
positive regulation of macrophage chemotaxis  (IEA,ISO)
positive regulation of macrophage colony-stimulating factor signaling pathway  (IEA,ISO)
positive regulation of macrophage derived foam cell differentiation  (IEA,ISO)
positive regulation of macrophage differentiation  (IBA,IEA,ISO)
positive regulation of macrophage migration  (ISO)
positive regulation of microglial cell migration  (IEA,ISO)
positive regulation of monocyte differentiation  (ISO)
positive regulation of mononuclear cell proliferation  (IEA,ISO)
positive regulation of multicellular organism growth  (ISO)
positive regulation of odontogenesis of dentin-containing tooth  (ISO)
positive regulation of osteoclast differentiation  (IEA,ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of Ras protein signal transduction  (ISO)
regulation of ossification  (ISO)
response to ischemia  (IEA,ISO)
transmembrane receptor protein tyrosine kinase signaling pathway  (IEA,ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Borycki A, etal., Biochim Biophys Acta 1993 Aug 19;1174(2):143-52.
2. Budrys NM, etal., Fertil Steril. 2012 May;97(5):1129-35.e1. doi: 10.1016/j.fertnstert.2012.02.007. Epub 2012 Feb 24.
3. Corcoran AT, etal., World J Urol. 2013 Feb;31(1):241-6. doi: 10.1007/s00345-012-0852-y. Epub 2012 Mar 24.
4. Dobbins DE, etal., Biochem Biophys Res Commun 2002 Jun 28;294(5):1114-20.
5. Fraser DD, etal., Crit Care Explor. 2020 Jun 22;2(6):e0144. doi: 10.1097/CCE.0000000000000144. eCollection 2020 Jun.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Gerdprasert O, etal., Mol Hum Reprod 2002 Jun;8(6):518-24.
8. Haraguchi K, etal., Nephron Clin Pract. 2006;102(1):c14-20. Epub 2005 Sep 13.
9. Isbel NM, etal., Nephrol Dial Transplant. 2001 Aug;16(8):1638-47.
10. Iyoda M, etal., Kidney Int. 2009 May;75(10):1060-70. doi: 10.1038/ki.2009.43. Epub 2009 Feb 25.
11. Jang MH, etal., J Immunol. 2006 Sep 15;177(6):4055-63.
12. Jeffes EW, etal., J Immunol. 2005 Mar 1;174(5):2533-43.
13. Jin Y, etal., Lab Invest. 2013 Jul;93(7):801-11. doi: 10.1038/labinvest.2013.64. Epub 2013 Apr 29.
14. Juniantito V, etal., Vet Pathol. 2013 Jan;50(1):76-85. doi: 10.1177/0300985812450718. Epub 2012 Jun 13.
15. Kirma N, etal., Cancer Res. 2004 Jun 15;64(12):4162-70.
16. Le Meur Y, etal., Transplantation. 2002 Apr 27;73(8):1318-24.
17. Lenda DM, etal., J Immunol. 2004 Oct 1;173(7):4744-54.
18. Liu F, etal., Arthritis Rheumatol. 2020 Oct;72(10):1668-1678. doi: 10.1002/art.41386. Epub 2020 Sep 6.
19. Menke J, etal., Cancer Res. 2012 Jan 1;72(1):187-200. doi: 10.1158/0008-5472.CAN-11-1232. Epub 2011 Nov 3.
20. Menke J, etal., J Am Soc Nephrol. 2011 Oct;22(10):1821-33. doi: 10.1681/ASN.2011010038. Epub 2011 Sep 1.
21. Menke J, etal., J Immunol. 2008 Nov 15;181(10):7367-79.
22. MGD data from the GO Consortium
23. Miyazaki K, etal., Clin Exp Immunol. 1997 May;108(2):318-23.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Paulus P, etal., Cancer Res. 2006 Apr 15;66(8):4349-56.
26. Pipeline to import KEGG annotations from KEGG into RGD
27. Rajavashisth T, etal., J Clin Invest 1998 Jun 15;101(12):2702-10.
28. RGD automated data pipeline
29. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
30. RGD automated import pipeline for gene-chemical interactions
31. Richardsen E, etal., Histopathology. 2008 May 28;.
32. Rolle U, etal., Kidney Int. 2002 Aug;62(2):507-13.
33. Rysava R, etal., Cas Lek Cesk. 2002 Apr 26;141(8):244-7.
34. Saionji K and Ohsaka A, Acta Haematol. 2001;105(1):21-6.
35. Sajja VS, etal., Biomed Sci Instrum. 2012;48:374-9.
36. Singh KA, etal., Transpl Int. 2009 Jul;22(7):730-7. doi: 10.1111/j.1432-2277.2009.00840.x. Epub 2009 Jan 29.
37. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
38. Tamimi RM, etal., Cancer Res. 2008 Jan 1;68(1):18-21.
39. Tian S, etal., Inflamm Res. 2007 Jul;56(7):304-10.
40. Utsunomiya K, etal., J Diabetes Complications. 1995 Oct-Dec;9(4):292-5.
41. Van Wesenbeeck L, etal., Proc Natl Acad Sci U S A 2002 Oct 29;99(22):14303-8.
42. Yamamoto S, etal., J Neurochem. 2010 Nov;115(4):1057-67. doi: 10.1111/j.1471-4159.2010.06996.x. Epub 2010 Oct 12.
43. Yang Y, etal., J Allergy Clin Immunol. 2020 Apr 29. pii: S0091-6749(20)30576-5. doi: 10.1016/j.jaci.2020.04.027.
44. Zhang MZ, etal., J Clin Invest. 2012 Dec 3;122(12):4519-32. doi: 10.1172/JCI60363. Epub 2012 Nov 12.
45. Zorzi P, etal., J Leukoc Biol. 2010 Nov;88(5):1051-9. Epub 2010 Jul 13.
Additional References at PubMed
PMID:1739124   PMID:2408759   PMID:2460758   PMID:3264878   PMID:8922060   PMID:9215625   PMID:10652277   PMID:10666185   PMID:10804170   PMID:12865350   PMID:14696961   PMID:15203935  
PMID:15304486   PMID:15657444   PMID:16237150   PMID:16304045   PMID:16883060   PMID:17053831   PMID:17068143   PMID:17244792   PMID:17442941   PMID:18606301   PMID:19017797   PMID:19100238  
PMID:19219684   PMID:19893052   PMID:21048959   PMID:21176538   PMID:22153499   PMID:22451653   PMID:22902366   PMID:23376485   PMID:23392676   PMID:23443487   PMID:23711477   PMID:24006456  
PMID:30687013  


Genomics

Comparative Map Data
Csf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22195,377,215 - 195,396,608 (-)NCBImRatBN7.2
Rnor_6.0 Ensembl2210,522,375 - 210,550,560 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02210,522,370 - 210,550,546 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02229,989,430 - 230,017,945 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42203,292,765 - 203,307,968 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12203,255,518 - 203,270,701 (-)NCBI
Celera2188,024,644 - 188,043,645 (-)NCBICelera
Cytogenetic Map2q34NCBI
CSF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1109,910,242 - 109,930,992 (+)EnsemblGRCh38hg38GRCh38
GRCh381109,910,506 - 109,930,992 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371110,453,471 - 110,473,614 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361110,254,980 - 110,273,878 (+)NCBINCBI36hg18NCBI36
Build 341110,165,498 - 110,184,397NCBI
Celera1108,699,836 - 108,719,046 (+)NCBI
Cytogenetic Map1p13.3NCBI
HuRef1108,322,980 - 108,343,084 (+)NCBIHuRef
CHM1_11110,568,036 - 110,588,399 (+)NCBICHM1_1
Csf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393107,648,364 - 107,668,048 (-)NCBIGRCm39mm39
GRCm39 Ensembl3107,648,364 - 107,667,785 (-)Ensembl
GRCm383107,741,048 - 107,760,469 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3107,741,048 - 107,760,469 (-)EnsemblGRCm38mm10GRCm38
MGSCv373107,543,966 - 107,563,387 (-)NCBIGRCm37mm9NCBIm37
MGSCv363107,869,116 - 107,888,525 (-)NCBImm8
Celera3110,073,392 - 110,092,813 (-)NCBICelera
Cytogenetic Map3F2.3NCBI
cM Map346.83NCBI
Csf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543513,404,508 - 13,424,247 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543513,404,236 - 13,423,059 (+)NCBIChiLan1.0ChiLan1.0
CSF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11127,764,916 - 127,864,188 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1127,764,916 - 127,781,943 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01112,555,755 - 112,575,894 (+)NCBIMhudiblu_PPA_v0panPan3
CSF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1642,028,454 - 42,047,028 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl642,034,149 - 42,049,371 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha644,804,295 - 44,823,439 (-)NCBI
ROS_Cfam_1.0642,360,013 - 42,379,162 (-)NCBI
UMICH_Zoey_3.1642,092,785 - 42,111,910 (-)NCBI
UNSW_CanFamBas_1.0642,050,361 - 42,070,486 (-)NCBI
UU_Cfam_GSD_1.0642,485,555 - 42,505,704 (-)NCBI
Csf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505818,720,989 - 18,742,009 (-)NCBI
SpeTri2.0NW_0049367041,372,137 - 1,393,355 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4110,178,478 - 110,197,901 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14110,178,466 - 110,198,232 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24120,592,959 - 120,605,764 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CSF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12023,615,107 - 23,635,399 (-)NCBI
Vero_WHO_p1.0NW_02366603834,824,127 - 34,844,440 (+)NCBI
Csf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247725,663,374 - 5,705,965 (+)NCBI

Position Markers
D3Mit104.1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera2188,043,818 - 188,044,071UniSTS
Cytogenetic Map2q34UniSTS
AI547928  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22195,378,243 - 195,378,453 (+)MAPPERmRatBN7.2
Rnor_6.02210,537,681 - 210,537,890NCBIRnor6.0
Rnor_6.02210,523,399 - 210,523,608NCBIRnor6.0
Rnor_5.02230,004,741 - 230,004,950UniSTSRnor5.0
Rnor_5.02229,990,459 - 229,990,668UniSTSRnor5.0
RGSC_v3.42203,293,789 - 203,293,998UniSTSRGSC3.4
Celera2188,025,668 - 188,025,877UniSTS
RH 3.4 Map21387.9UniSTS
Cytogenetic Map2q34UniSTS
CSF1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22195,384,314 - 195,384,469 (+)MAPPERmRatBN7.2
mRatBN7.22195,384,314 - 195,384,547 (+)MAPPERmRatBN7.2
Rnor_6.02210,529,458 - 210,529,690NCBIRnor6.0
Rnor_6.02210,529,458 - 210,529,612NCBIRnor6.0
Rnor_5.02229,996,518 - 229,996,750UniSTSRnor5.0
Rnor_5.02229,996,518 - 229,996,672UniSTSRnor5.0
RGSC_v3.42203,299,856 - 203,300,010UniSTSRGSC3.4
RGSC_v3.42203,299,856 - 203,300,088UniSTSRGSC3.4
Celera2188,031,723 - 188,031,955UniSTS
Celera2188,031,723 - 188,031,877UniSTS
Cytogenetic Map2q34UniSTS
AI176011  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22195,377,718 - 195,377,873 (+)MAPPERmRatBN7.2
Rnor_6.02210,522,874 - 210,523,028NCBIRnor6.0
Rnor_5.02229,989,934 - 229,990,088UniSTSRnor5.0
RGSC_v3.42203,293,264 - 203,293,418UniSTSRGSC3.4
Celera2188,025,143 - 188,025,297UniSTS
RH 3.4 Map21388.4UniSTS
Cytogenetic Map2q34UniSTS
PMC101742P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22195,384,882 - 195,385,229 (+)MAPPERmRatBN7.2
Rnor_6.02210,530,026 - 210,530,372NCBIRnor6.0
Rnor_5.02229,997,086 - 229,997,432UniSTSRnor5.0
RGSC_v3.42203,300,424 - 203,300,770UniSTSRGSC3.4
Celera2188,032,291 - 188,032,637UniSTS
Cytogenetic Map2q34UniSTS
PMC137879P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera2188,043,448 - 188,043,639UniSTS
Cytogenetic Map2q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
61458Bp10Blood pressure QTL 103.42arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1331745Bp203Blood pressure QTL 2034.377arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2189599258218414891Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1298083Bp158Blood pressure QTL 1582.62arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189020722215287351Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2189599258226936289Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2184165752229165752Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2190613715226808892Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2179335906224335906Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2185876309219753474Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2185876309219753474Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
2293084Iddm26Insulin dependent diabetes mellitus QTL 262.9blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2174930955213594495Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2179946951224946951Rat
4889834Pur24Proteinuria QTL 245.80.014total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)2184114274202447032Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2182171407227171407Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2182171407227171407Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2182171407227171407Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2182171407227171407Rat


Related Rat Strains
The following Strains have been annotated to Csf1


Genetic Models
This gene Csf1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:558
Count of miRNA genes:248
Interacting mature miRNAs:305
Transcripts:ENSRNOT00000025222
Prediction methods:Microtar, Miranda
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 4 10 6 13 6 14 19 27 11
Low 2 39 47 35 6 35 8 11 60 16 14 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_023981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006233187 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761426 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039103174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF514355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF514356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF514357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF515736 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC074007 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231611 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000025222   ⟹   ENSRNOP00000025221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2210,522,375 - 210,550,546 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081835   ⟹   ENSRNOP00000073134
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2210,528,025 - 210,550,490 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086403   ⟹   ENSRNOP00000072096
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2210,547,076 - 210,550,560 (-)Ensembl
RefSeq Acc Id: NM_023981   ⟹   NP_076471
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,377,220 - 195,396,291 (-)NCBI
Rnor_6.02210,522,375 - 210,550,546 (-)NCBI
Rnor_5.02229,989,430 - 230,017,945 (-)NCBI
RGSC_v3.42203,292,765 - 203,307,968 (-)RGD
Celera2188,024,644 - 188,043,645 (-)RGD
Sequence:
RefSeq Acc Id: XM_006233187   ⟹   XP_006233249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,381,709 - 195,396,573 (-)NCBI
Rnor_6.02210,525,874 - 210,550,416 (-)NCBI
Rnor_5.02229,989,430 - 230,017,945 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761426   ⟹   XP_008759648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,377,215 - 195,396,585 (-)NCBI
Rnor_6.02210,522,370 - 210,550,416 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761428   ⟹   XP_008759650
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,377,215 - 195,396,572 (-)NCBI
Rnor_6.02210,522,370 - 210,550,416 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008761429   ⟹   XP_008759651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,381,709 - 195,396,592 (-)NCBI
Rnor_6.02210,525,874 - 210,550,416 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017591125   ⟹   XP_017446614
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,377,215 - 195,396,571 (-)NCBI
Rnor_6.02210,524,370 - 210,550,416 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039103173   ⟹   XP_038959101
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,377,215 - 195,396,608 (-)NCBI
RefSeq Acc Id: XM_039103174   ⟹   XP_038959102
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22195,379,164 - 195,396,598 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_076471   ⟸   NM_023981
- Peptide Label: precursor
- UniProtKB: Q6GMN4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233249   ⟸   XM_006233187
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K4Q6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759650   ⟸   XM_008761428
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008759648   ⟸   XM_008761426
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008759651   ⟸   XM_008761429
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017446614   ⟸   XM_017591125
- Peptide Label: isoform X4
- UniProtKB: A0A0G2K4Q6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073134   ⟸   ENSRNOT00000081835
RefSeq Acc Id: ENSRNOP00000072096   ⟸   ENSRNOT00000086403
RefSeq Acc Id: ENSRNOP00000025221   ⟸   ENSRNOT00000025222
RefSeq Acc Id: XP_038959101   ⟸   XM_039103173
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038959102   ⟸   XM_039103174
- Peptide Label: isoform X6

Transcriptome

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

Promoters
RGD ID:13691672
Promoter ID:EPDNEW_R2187
Type:single initiation site
Name:Csf1_1
Description:colony stimulating factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02210,550,565 - 210,550,625EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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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)
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
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/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
WKY/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
WKY/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
WKY/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
WKY/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
WN/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
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:621063 AgrOrtholog
Ensembl Genes ENSRNOG00000018659 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025221 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000072096 UniProtKB/TrEMBL
  ENSRNOP00000073134 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025222 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000081835 UniProtKB/TrEMBL
  ENSRNOT00000086403 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7099454 IMAGE-MGC_LOAD
InterPro 4_helix_cytokine-like_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MCSF-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:78965 UniProtKB/TrEMBL
MGC_CLONE MGC:91410 IMAGE-MGC_LOAD
NCBI Gene 78965 ENTREZGENE
PANTHER PTHR10058 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CSF-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Csf1 PhenoGen
PIRSF MCSF-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47266 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K241_RAT UniProtKB/TrEMBL
  A0A0G2K4Q6 ENTREZGENE, UniProtKB/TrEMBL
  CSF1_RAT UniProtKB/Swiss-Prot
  Q6GMN4 ENTREZGENE, UniProtKB/TrEMBL
  Q8JZQ0 ENTREZGENE
  Q8K408_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-20 Csf1  colony stimulating factor 1  Csf1  colony stimulating factor 1 (macrophage)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Csf1  colony stimulating factor 1 (macrophage)    colony stimulating factor 1(macrophage)  Name updated 1299863 APPROVED
2002-08-07 Csf1  colony stimulating factor 1(macrophage)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the gene causes the toothless (tl) rat mutant, which has severe osteopetrosis 628338
gene_mutations_overexpression loss-of-function frameshift mutation results in toothless (tl) mutation in the rat 628338
gene_transcript 15 kilobases in size 628338
gene_transcript consists of 8 exons split by 7 introns stop signal (TAG) is in exon 8 628338