Cxcl12 (C-X-C motif chemokine ligand 12) - Rat Genome Database

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Gene: Cxcl12 (C-X-C motif chemokine ligand 12) Rattus norvegicus
Analyze
Symbol: Cxcl12
Name: C-X-C motif chemokine ligand 12
RGD ID: 3651
Description: Predicted to enable CXCR chemokine receptor binding activity; chemokine activity; and integrin binding activity. Involved in several processes, including detection of stimulus involved in sensory perception of pain; nervous system development; and regulation of ion transport. Located in several cellular components, including extracellular space; nucleus; and plasma membrane. Used to study myocardial infarction. Biomarker of anti-basement membrane glomerulonephritis; brain ischemia; myocardial infarction; status epilepticus; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in breast carcinoma; diabetic angiopathy; human immunodeficiency virus infectious disease; and type 1 diabetes mellitus. Orthologous to human CXCL12 (C-X-C motif chemokine ligand 12); PARTICIPATES IN hypoxia inducible factor pathway; syndecan signaling pathway; chemokine mediated signaling pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: chemokine (C-X-C motif) ligand 12; chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1); SDF-1 gamma; Sdf1; Stromal cell-derived factor 1; stromal cell-derived factor-1 gamma
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Cxcl12_v3   Cxcl12_v1   Cxcl12_v2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24150,388,326 - 150,401,173 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4150,388,325 - 150,401,168 (+)Ensembl
Rnor_6.04149,261,044 - 149,273,891 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4149,261,044 - 149,273,891 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04215,195,689 - 215,208,536 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44153,503,576 - 153,516,423 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14153,748,473 - 153,755,186 (+)NCBI
Celera4139,267,343 - 139,280,188 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-schisandrin B  (EXP)
(25R)-cholest-5-ene-3beta,26-diol  (ISO)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-bromopropane  (ISO)
1-naphthyl isothiocyanate  (EXP)
1-octadec-9-enoylglycero-3-phosphate  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-hydroxyethyl methacrylate  (ISO)
26-hydroxycholesterol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
8'-apo-beta,psi-caroten-8'-al  (ISO)
8-Br-cAMP  (ISO)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
apigenin  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
asperentin  (ISO)
BAY 60-6583  (ISO)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[e]pyrene  (ISO)
beta-carotene  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
bucladesine  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcium atom  (ISO)
calcium phosphate  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
ceric oxide  (EXP)
cetrorelix  (ISO)
chlordecone  (ISO)
chloroprene  (ISO)
chloroquine  (ISO)
choline  (ISO)
ciguatoxin CTX1B  (ISO)
ciprofibrate  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibric acid  (EXP,ISO)
clomiphene  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
coumarin  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
daidzein  (ISO)
DDT  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
diethyl malate  (ISO)
diethyl maleate  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (EXP,ISO)
dipyridamole  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
edaravone  (EXP)
endosulfan  (EXP)
entinostat  (ISO)
estrone  (ISO)
ethanol  (EXP)
etoposide  (ISO)
fipronil  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gadodiamide hydrate  (ISO)
genistein  (ISO)
glafenine  (EXP)
glyceollin  (ISO)
glycidol  (EXP)
glyphosate  (ISO)
graphene oxide  (ISO)
GW 1929  (ISO)
heparin  (ISO)
hexestrol  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
indometacin  (EXP,ISO)
irinotecan  (ISO)
isotretinoin  (ISO)
leflunomide  (EXP)
linuron  (ISO)
lipopolysaccharide  (EXP)
liquiritigenin  (ISO)
luteolin  (EXP)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP)
melphalan  (ISO)
mestranol  (ISO)
methamphetamine  (EXP)
methapyrilene  (EXP,ISO)
methotrexate  (ISO)
methoxychlor  (ISO)
methylmercury chloride  (EXP)
mifepristone  (ISO)
ML-7  (ISO)
monodansylcadaverine  (ISO)
mycophenolic acid  (ISO)
mycotoxin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-Acetyl-S-(1,2-dichlorovinyl)-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
naringin  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (ISO)
nimesulide  (EXP)
nitric oxide  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
p-toluidine  (EXP)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
PCB138  (ISO)
perfluorooctanoic acid  (EXP,ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phytoestrogen  (ISO)
picene  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
plerixafor  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP,ISO)
propanal  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
ritonavir  (ISO)
rotenone  (ISO)
rutin  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
sterigmatocystin  (ISO)
streptozocin  (ISO)
tamoxifen  (ISO)
telmisartan  (ISO)
Tesaglitazar  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
toluene 2,4-diisocyanate  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
XL147  (ISO)
Y-27632  (ISO)
yohimbine  (ISO)
zalcitabine  (EXP)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (IMP)
ameboidal-type cell migration  (ISO)
animal organ regeneration  (IMP)
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
axon guidance  (IBA)
brain development  (IEP,ISO)
branching involved in blood vessel morphogenesis  (ISO)
cell chemotaxis  (IBA,ISO)
cell migration  (TAS)
cell-cell adhesion  (ISO)
cellular response to chemokine  (ISO)
chemokine (C-X-C motif) ligand 12 signaling pathway  (ISO)
chemokine-mediated signaling pathway  (IBA,ISO)
defense response  (IEA)
detection of mechanical stimulus involved in sensory perception of pain  (IMP)
detection of temperature stimulus involved in sensory perception of pain  (IMP)
dopaminergic neuron differentiation  (ISO)
germ cell development  (ISO)
germ cell migration  (ISO)
immune response  (IEA)
induction of positive chemotaxis  (IBA,ISO)
integrin activation  (ISO)
killing of cells of other organism  (ISO)
motor neuron axon guidance  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of dendritic cell apoptotic process  (ISO)
negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage  (ISO)
negative regulation of leukocyte tethering or rolling  (ISO)
neuron migration  (IDA)
positive regulation of axon extension involved in axon guidance  (IMP)
positive regulation of calcium ion import  (ISO)
positive regulation of cell adhesion  (ISO)
positive regulation of cell migration  (IBA,IMP,ISO)
positive regulation of cell population proliferation  (IMP)
positive regulation of chemotaxis  (ISO)
positive regulation of dopamine secretion  (IDA)
positive regulation of endothelial cell proliferation  (IMP)
positive regulation of ERK1 and ERK2 cascade  (ISO)
positive regulation of monocyte chemotaxis  (ISO)
positive regulation of myoblast fusion  (ISO)
positive regulation of neuron differentiation  (IMP)
positive regulation of protein kinase B signaling  (ISO)
positive regulation of T cell migration  (ISO)
regulation of calcium ion transport  (IDA)
regulation of cell migration  (ISO)
response to heat  (IEP)
response to hypoxia  (IEP)
response to mechanical stimulus  (IEP)
response to peptide hormone  (IEP)
response to radiation  (IEP)
response to ultrasound  (IEP)
T cell chemotaxis  (ISO)
T cell proliferation  (ISO)
telencephalon cell migration  (IMP)

Cellular Component

Molecular Function

References

References - curated
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3. Aicher A, etal., Circulation. 2006 Dec 19;114(25):2823-30. Epub 2006 Dec 4.
4. Badillo AT, etal., J Surg Res. 2007 Nov;143(1):35-42.
5. Butler JM, etal., J Clin Invest. 2005 Jan;115(1):86-93.
6. Dubois-Laforgue D, etal., Diabetes. 2001 May;50(5):1211-3.
7. Fujinaka H, etal., J Nephrol. 2007 May-Jun;20(3):357-63.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Gleichmann M, etal., Eur J Neurosci. 2000 Jun;12(6):1857-66.
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11. Hassanshahi G, etal., Iran J Allergy Asthma Immunol. 2008 Jun;7(2):61-8.
12. Havens AM, etal., J Periodontol. 2008 May;79(5):845-53.
13. Hu XM, etal., Sci Rep. 2017 Jun 21;7(1):4005. doi: 10.1038/s41598-017-04198-3.
14. Humpert PM, etal., Clin Chem. 2006 Jun;52(6):1206-8.
15. Ide A, etal., Hum Immunol. 2003 Oct;64(10):973-8.
16. Ilhan A, etal., Mol Cell Endocrinol. 2009 Jan 27;298(1-2):1-10. Epub 2008 Oct 22.
17. Jung KH, etal., Epilepsia. 2009 Mar;50(3):537-49. Epub 2008 Nov 20.
18. Lai P, etal., Graefes Arch Clin Exp Ophthalmol. 2008 Dec;246(12):1707-13. Epub 2008 Aug 16.
19. Lei Y, etal., Dig Dis Sci. 2009 Mar 18.
20. Leng Q, etal., BMC Immunol. 2008 Sep 15;9:51.
21. Li XQ, etal., PLoS One. 2016 Oct 19;11(10):e0163807. doi: 10.1371/journal.pone.0163807. eCollection 2016.
22. Lin Y, etal., Fertil Steril. 2008 Apr 1.
23. Loader B, etal., Otol Neurotol. 2008 Sep;29(6):739-44.
24. Matin K, etal., Immunology. 2002 Oct;107(2):222-32.
25. MGD data from the GO Consortium
26. NCBI rat LocusLink and RefSeq merged data July 26, 2002
27. Oh SB, etal., J Neurosci. 2001 Jul 15;21(14):5027-35.
28. Ohshima Y, etal., J Neurosci. 2008 Aug 13;28(33):8344-53.
29. OMIM Disease Annotation Pipeline
30. Paredes MF, etal., J Neurosci. 2006 Sep 13;26(37):9404-12.
31. Pillarisetti K and Gupta SK, Inflammation 2001 Oct;25(5):293-300.
32. Pipeline to import KEGG annotations from KEGG into RGD
33. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
34. Pritchett J, etal., BMC Dev Biol. 2007 Apr 10;7:31.
35. Razmkhah M, etal., Cancer Lett. 2005 Jul 28;225(2):261-6. Epub 2004 Dec 13.
36. Reiss K, etal., Neuroscience 2002;115(1):295-305.
37. Reiss K, etal., Neuroscience 2002;115(1):295-305.
38. RGD automated data pipeline
39. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
40. RGD automated import pipeline for gene-chemical interactions
41. Roy I, etal., Cancer Res. 2015 Sep 1;75(17):3529-42. doi: 10.1158/0008-5472.CAN-14-2645.
42. Segret A, etal., J Histochem Cytochem. 2007 Feb;55(2):141-50. Epub 2006 Oct 16.
43. Shigihara T, etal., Ann N Y Acad Sci. 2003 Nov;1005:328-31.
44. Shimode K, etal., Tissue Eng Part A. 2009 Feb 27.
45. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
46. Sun YX, etal., J Cell Biochem. 2003 Jun 1;89(3):462-73.
47. Trecki J and Unterwald EM, Neuroscience. 2009 Mar 20.
48. Wang Y, etal., Brain Res. 2008 Feb 21;1195:104-12. Epub 2007 Dec 14.
49. Wang Y, etal., Brain Res. 2014 Aug 5;1575:78-86. doi: 10.1016/j.brainres.2014.05.035. Epub 2014 Jun 9.
50. Wei FY, etal., PLoS One. 2014 Sep 2;9(9):e106722. doi: 10.1371/journal.pone.0106722. eCollection 2014.
51. Wragg A, etal., J Mol Med. 2008 Nov;86(11):1221-32. Epub 2008 Aug 9.
52. Xu Q, etal., Clin Exp Pharmacol Physiol. 2007 Jul;34(7):624-31.
53. Yano T, etal., Diabetes. 2007 Dec;56(12):2946-57. Epub 2007 Sep 18.
54. Yuan YZ, etal., Zhonghua Yan Ke Za Zhi. 2007 Oct;43(10):912-6.
55. Zheng D, etal., Am J Pathol. 2006 Dec;169(6):2066-74.
56. Zhu Y, etal., Nat Neurosci 2002 Aug;5(8):719-20.
57. Zhuang Y, etal., Chin Med J (Engl). 2009 Jan 20;122(2):183-7.
58. Zong ZW, etal., Radiat Res. 2008 Oct;170(4):444-50.
Additional References at PubMed
PMID:8962122   PMID:12183377   PMID:12707343   PMID:12900445   PMID:12949249   PMID:15048928   PMID:15059845   PMID:15626744   PMID:15731012   PMID:15754085   PMID:16129397   PMID:16476083  
PMID:16630729   PMID:16702540   PMID:16837851   PMID:17088326   PMID:17148615   PMID:17275519   PMID:17496162   PMID:17520275   PMID:17572689   PMID:17875967   PMID:17901225   PMID:18029549  
PMID:18073458   PMID:18075260   PMID:18293886   PMID:18308860   PMID:18583990   PMID:18589171   PMID:18606818   PMID:18615560   PMID:18753332   PMID:18802065   PMID:18978811   PMID:19008373  
PMID:19064997   PMID:19181961   PMID:19228460   PMID:19340530   PMID:19647005   PMID:19737463   PMID:19788842   PMID:19937807   PMID:20032115   PMID:20045921   PMID:20127490   PMID:20348095  
PMID:20388803   PMID:20586815   PMID:20617464   PMID:20629320   PMID:20847314   PMID:20889568   PMID:21043834   PMID:21345805   PMID:21388641   PMID:21507304   PMID:21601937   PMID:21706136  
PMID:22006493   PMID:22058039   PMID:22323084   PMID:22330724   PMID:22355073   PMID:22457824   PMID:22493069   PMID:22535492   PMID:22549778   PMID:22575885   PMID:22694179   PMID:22845908  
PMID:22884805   PMID:22978573   PMID:23148226   PMID:23178697   PMID:23193174   PMID:23376485   PMID:23393395   PMID:23439595   PMID:23460790   PMID:23533145   PMID:23555743   PMID:23576796  
PMID:23620790   PMID:23651977   PMID:23732617   PMID:23844157   PMID:23917520   PMID:23969990   PMID:23984821   PMID:24312447   PMID:24557113   PMID:24581269   PMID:24626964   PMID:24637920  
PMID:24661402   PMID:24824367   PMID:24876262   PMID:24955809   PMID:24973214   PMID:24988468   PMID:25241080   PMID:25251779   PMID:25260613   PMID:25453873   PMID:25604551   PMID:25636237  
PMID:26002466   PMID:26164455   PMID:26392311   PMID:26398409   PMID:26444377   PMID:26597700   PMID:26781879   PMID:26818151   PMID:26886751   PMID:26939868   PMID:26974138   PMID:27011380  
PMID:27237374   PMID:27251706   PMID:27400149   PMID:27614125   PMID:27979472   PMID:27982773   PMID:28412763   PMID:28701189   PMID:28734802   PMID:28855566   PMID:29114002   PMID:29130552  
PMID:29166835   PMID:29207050   PMID:29236198   PMID:29301984   PMID:29348441   PMID:29568770   PMID:29568895   PMID:29693117   PMID:29715476   PMID:30120960   PMID:30221695   PMID:30362535  
PMID:30391592   PMID:30541517   PMID:30955244   PMID:31400639   PMID:31652450   PMID:31894855   PMID:32006698   PMID:32165091   PMID:32198816   PMID:32449535   PMID:32751701   PMID:33079278  


Genomics

Comparative Map Data
Cxcl12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24150,388,326 - 150,401,173 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4150,388,325 - 150,401,168 (+)Ensembl
Rnor_6.04149,261,044 - 149,273,891 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4149,261,044 - 149,273,891 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04215,195,689 - 215,208,536 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44153,503,576 - 153,516,423 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14153,748,473 - 153,755,186 (+)NCBI
Celera4139,267,343 - 139,280,188 (+)NCBICelera
Cytogenetic Map4q42NCBI
CXCL12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1044,370,165 - 44,386,493 (-)EnsemblGRCh38hg38GRCh38
GRCh381044,292,088 - 44,385,097 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371044,865,613 - 44,880,545 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361044,185,611 - 44,200,548 (-)NCBINCBI36hg18NCBI36
Build 341044,192,516 - 44,200,551NCBI
Celera1040,869,153 - 40,884,099 (-)NCBI
Cytogenetic Map10q11.21NCBI
HuRef1041,391,945 - 41,406,899 (-)NCBIHuRef
CHM1_11044,904,782 - 44,919,728 (-)NCBICHM1_1
Cxcl12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396117,145,496 - 117,158,329 (+)NCBIGRCm39mm39
GRCm39 Ensembl6117,145,496 - 117,158,328 (+)Ensembl
GRCm386117,168,535 - 117,181,368 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6117,168,535 - 117,181,367 (+)EnsemblGRCm38mm10GRCm38
MGSCv376117,118,553 - 117,131,386 (+)NCBIGRCm37mm9NCBIm37
MGSCv366117,134,182 - 117,146,986 (+)NCBImm8
Celera6118,991,272 - 119,004,105 (+)NCBICelera
Cytogenetic Map6F1NCBI
cM Map654.81NCBI
Cxcl12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555461,929,269 - 1,941,690 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555461,929,269 - 1,941,690 (-)NCBIChiLan1.0ChiLan1.0
CXCL12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11044,476,962 - 44,564,231 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1044,552,480 - 44,564,231 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01041,296,975 - 41,384,864 (-)NCBIMhudiblu_PPA_v0panPan3
CXCL12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1282,895,916 - 2,903,543 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha283,126,200 - 3,137,772 (+)NCBI
ROS_Cfam_1.0283,070,799 - 3,082,409 (+)NCBI
UMICH_Zoey_3.1282,868,050 - 2,879,621 (+)NCBI
UNSW_CanFamBas_1.0282,906,153 - 2,917,718 (+)NCBI
UU_Cfam_GSD_1.0283,043,671 - 3,055,243 (+)NCBI
Cxcl12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721382,545,003 - 82,559,854 (+)NCBI
SpeTri2.0NW_0049366174,224,131 - 4,239,080 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CXCL12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1491,516,429 - 91,552,766 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11491,516,383 - 91,543,857 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21499,990,204 - 100,017,171 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CXCL12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1940,005,580 - 40,020,513 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl940,011,439 - 40,020,494 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605646,393,964 - 46,408,906 (+)NCBIVero_WHO_p1.0
Cxcl12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249221,261,228 - 1,273,755 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D4Wox52  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24150,397,157 - 150,397,328 (+)MAPPERmRatBN7.2
Rnor_6.04149,269,876 - 149,270,046NCBIRnor6.0
Rnor_5.04215,204,521 - 215,204,691UniSTSRnor5.0
RGSC_v3.44153,512,408 - 153,512,578UniSTSRGSC3.4
Celera4139,276,174 - 139,276,343UniSTS
Cytogenetic Map4q42.1UniSTS
RH127482  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24150,400,826 - 150,401,033 (+)MAPPERmRatBN7.2
Rnor_6.04149,273,545 - 149,273,751NCBIRnor6.0
Rnor_5.04215,208,190 - 215,208,396UniSTSRnor5.0
RGSC_v3.44153,516,077 - 153,516,283UniSTSRGSC3.4
Celera4139,279,842 - 139,280,048UniSTS
RH 3.4 Map4968.82UniSTS
Cytogenetic Map4q42.1UniSTS
RH138767  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24150,394,362 - 150,394,585 (+)MAPPERmRatBN7.2
Rnor_6.04149,267,081 - 149,267,303NCBIRnor6.0
Rnor_5.04215,201,726 - 215,201,948UniSTSRnor5.0
RGSC_v3.44153,509,613 - 153,509,835UniSTSRGSC3.4
Celera4139,273,379 - 139,273,601UniSTS
RH 3.4 Map4968.82UniSTS
Cytogenetic Map4q42.1UniSTS
Cxcl12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24150,393,531 - 150,394,650 (+)MAPPERmRatBN7.2
Rnor_6.04149,266,250 - 149,267,368NCBIRnor6.0
Rnor_5.04215,200,895 - 215,202,013UniSTSRnor5.0
RGSC_v3.44153,508,782 - 153,509,900UniSTSRGSC3.4
Celera4139,272,548 - 139,273,666UniSTS
Cytogenetic Map4q42.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4148423102157580971Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:711
Count of miRNA genes:288
Interacting mature miRNAs:378
Transcripts:ENSRNOT00000066670, ENSRNOT00000071175
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 2 43 50 41 19 41 6 8 62 35 31 11 6
Low 1 7 2 3 12 10 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066670   ⟹   ENSRNOP00000059574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4150,388,325 - 150,401,168 (+)Ensembl
Rnor_6.0 Ensembl4149,261,044 - 149,273,891 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098665   ⟹   ENSRNOP00000085514
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4150,390,767 - 150,395,094 (+)Ensembl
RefSeq Acc Id: NM_001033882   ⟹   NP_001029054
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24150,388,326 - 150,401,173 (+)NCBI
Rnor_6.04149,261,044 - 149,273,891 (+)NCBI
Rnor_5.04215,195,689 - 215,208,536 (+)NCBI
RGSC_v3.44153,503,576 - 153,516,423 (+)RGD
Celera4139,267,343 - 139,280,188 (+)RGD
Sequence:
RefSeq Acc Id: NM_001033883   ⟹   NP_001029055
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24150,388,326 - 150,401,173 (+)NCBI
Rnor_6.04149,261,044 - 149,273,891 (+)NCBI
Rnor_5.04215,195,689 - 215,208,536 (+)NCBI
RGSC_v3.44153,503,576 - 153,516,423 (+)RGD
Celera4139,267,343 - 139,280,188 (+)RGD
Sequence:
RefSeq Acc Id: NM_022177   ⟹   NP_071513
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24150,388,326 - 150,395,096 (+)NCBI
Rnor_6.04149,261,044 - 149,267,814 (+)NCBI
Rnor_5.04215,195,689 - 215,208,536 (+)NCBI
RGSC_v3.44153,503,576 - 153,516,423 (+)RGD
Celera4139,267,343 - 139,274,112 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001029054   ⟸   NM_001033882
- Peptide Label: isoform beta precursor
- Sequence:
RefSeq Acc Id: NP_001029055   ⟸   NM_001033883
- Peptide Label: isoform gamma precursor
- UniProtKB: Q80YV8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_071513   ⟸   NM_022177
- Peptide Label: isoform alpha precursor
- UniProtKB: Q9QZD1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059574   ⟸   ENSRNOT00000066670
RefSeq Acc Id: ENSRNOP00000085514   ⟸   ENSRNOT00000098665
Protein Domains
SCY

Transcriptome

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

Promoters
RGD ID:13693339
Promoter ID:EPDNEW_R3863
Type:multiple initiation site
Name:Cxcl12_1
Description:C-X-C motif chemokine ligand 12
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_6.04149,261,043 - 149,261,103EPDNEW

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)
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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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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)
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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
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (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)
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)
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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)
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)
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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)
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)
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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)
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:3651 AgrOrtholog
Ensembl Genes ENSRNOG00000013589 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059574 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066670 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7128141 IMAGE-MGC_LOAD
InterPro Chemokine_IL8-like_dom UniProtKB/TrEMBL
  CXC_Chemokine_domain UniProtKB/TrEMBL
  CXCL12 UniProtKB/TrEMBL
  Interleukin_8-like_sf UniProtKB/TrEMBL
MGC_CLONE MGC:93191 IMAGE-MGC_LOAD
NCBI Gene 24772 ENTREZGENE
PANTHER PTHR18837 UniProtKB/TrEMBL
Pfam IL8 UniProtKB/TrEMBL
PhenoGen Cxcl12 PhenoGen
SMART SCY UniProtKB/TrEMBL
Superfamily-SCOP Chemokine_IL8 UniProtKB/TrEMBL
UniProt Q80YV8 ENTREZGENE, UniProtKB/TrEMBL
  Q9QZD1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-08 Cxcl12  C-X-C motif chemokine ligand 12  Cxcl12  chemokine (C-X-C motif) ligand 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Cxcl12  chemokine (C-X-C motif) ligand 12  Cxcl12  chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-26 Cxcl12  chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)  Cxcl12  chemokine (C-X-C motif) ligand 12   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Cxcl12  chemokine (C-X-C motif) ligand 12   Sdf1  Stromal cell-derived factor 1  Symbol and Name updated 629477 APPROVED
2002-06-10 Sdf1  Stromal cell-derived factor 1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in embryonic and postnatal cerebellar meninges 625546
gene_process may be directly or indirectly involved in positioning EGL cells 625546
gene_process acts as an attractive guidance cue for neuronal migration in cerebellum 625546
gene_process when secreted can control migration of embryonic external germinal layer (EGL) 625546
gene_process involved in haematopoietic precursor cell migration and neuronal cell migration 632502