Wnt5a (Wnt family member 5A) - Rat Genome Database

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Gene: Wnt5a (Wnt family member 5A) Rattus norvegicus
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Symbol: Wnt5a
Name: Wnt family member 5A
RGD ID: 69250
Description: Predicted to enable protein domain specific binding activity and signaling receptor binding activity. Involved in several processes, including estrous cycle; positive regulation of neuron projection arborization; and response to testosterone. Acts upstream of or within Wnt signaling pathway, planar cell polarity pathway. Located in cytoplasm and extracellular space. Human ortholog(s) of this gene implicated in autosomal dominant Robinow syndrome 1. Orthologous to human WNT5A (Wnt family member 5A); PARTICIPATES IN Wnt signaling pathway; Wnt signaling, canonical pathway; Wnt signaling, non-canonical pathway; INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: protein Wnt-5a; wingless-related MMTV integration site 5A; wingless-type MMTV integration site 5A; wingless-type MMTV integration site family, member 5A; Wnt-5a protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2163,695,667 - 3,718,234 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl163,697,032 - 3,718,234 (+)Ensembl
Rnor_6.0164,469,451 - 4,490,271 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl164,469,468 - 4,489,860 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0164,414,512 - 4,433,990 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4163,782,025 - 3,799,625 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1163,782,022 - 3,799,623 (+)NCBI
Celera163,644,605 - 3,665,720 (+)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(-)-gambogic acid  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetaldehyde  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
atrazine  (EXP)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
cadmium atom  (ISO)
calciol  (ISO)
calcitriol  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
casticin  (ISO)
CHIR 99021  (ISO)
chlorpyrifos  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
cyclosporin A  (ISO)
cyfluthrin  (ISO)
cypermethrin  (ISO)
D-glucose  (EXP,ISO)
decabromodiphenyl ether  (EXP)
Deguelin  (ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP,ISO)
dieldrin  (EXP)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
fluoranthene  (ISO)
flusilazole  (EXP,ISO)
folic acid  (ISO)
fulvestrant  (ISO)
gemcitabine  (ISO)
genistein  (EXP,ISO)
glucose  (EXP,ISO)
glyphosate  (EXP,ISO)
homocysteine  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
isotretinoin  (ISO)
lipopolysaccharide  (ISO)
maneb  (EXP)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (ISO)
mitomycin C  (ISO)
N-methyl-N-nitrosourea  (EXP)
nickel atom  (EXP)
nickel sulfate  (ISO)
nitrofen  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paraquat  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phenytoin  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP)
tributylstannane  (ISO)
trichostatin A  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of GTPase activity  (IEA,ISO)
activation of protein kinase B activity  (IEA,ISO)
ameboidal-type cell migration  (ISO)
anterior/posterior axis specification, embryo  (IEA,ISO)
anterior/posterior pattern specification  (ISO)
atrial septum development  (IEA,ISO)
axis elongation  (ISO)
axon guidance  (ISO)
axonogenesis  (ISO)
canonical Wnt signaling pathway  (IBA,IEA,ISO)
cartilage development  (IEA)
cell differentiation  (IEP)
cell fate commitment  (IBA)
cell migration  (ISO)
cellular protein localization  (IEA,ISO)
cellular response to calcium ion  (IEA,ISO)
cellular response to interferon-gamma  (IEA,ISO)
cellular response to lipopolysaccharide  (IEA,ISO)
cellular response to molecule of bacterial origin  (ISO)
cellular response to transforming growth factor beta stimulus  (IEA,ISO)
cervix development  (IEA,ISO)
chemoattraction of serotonergic neuron axon  (IEA,ISO)
chemorepulsion of dopaminergic neuron axon  (IEA,ISO)
cochlea morphogenesis  (IEA,ISO)
convergent extension  (ISO)
convergent extension involved in axis elongation  (IEA,ISO)
convergent extension involved in organogenesis  (IEA,ISO)
determination of left/right symmetry  (ISO)
development of primary male sexual characteristics  (ISO)
digestive tract morphogenesis  (ISO)
dopaminergic neuron differentiation  (ISO)
embryonic digit morphogenesis  (IEA,ISO)
embryonic limb morphogenesis  (ISO)
embryonic skeletal system development  (IEA,ISO)
epithelial cell proliferation involved in mammary gland duct elongation  (IEA,ISO)
epithelial to mesenchymal transition  (ISO)
establishment of epithelial cell apical/basal polarity  (IEA,ISO)
establishment of planar polarity  (IEA,ISO)
estrous cycle  (IEP)
face development  (IEA,ISO)
genitalia development  (ISO)
heart looping  (IEA,ISO)
hematopoietic stem cell proliferation  (IEA,ISO)
hindgut morphogenesis  (IEA,ISO)
hypophysis morphogenesis  (IEA,ISO)
inner ear morphogenesis  (ISO)
JNK cascade  (IEA,ISO)
keratinocyte differentiation  (IEA,ISO)
kidney development  (IEA,ISO)
lateral sprouting involved in mammary gland duct morphogenesis  (IEA,ISO)
limb morphogenesis  (ISO)
lung alveolus development  (IEP)
lung development  (IEA,ISO)
male gonad development  (IEA,ISO)
mammary gland branching involved in thelarche  (IEA,ISO)
melanocyte proliferation  (IEA,ISO)
mesenchymal-epithelial cell signaling  (IEA,ISO)
mesodermal to mesenchymal transition involved in gastrulation  (IEA,ISO)
midbrain development  (ISO)
midbrain dopaminergic neuron differentiation  (ISO)
midgut development  (IEA,ISO)
morphogenesis of an epithelium  (ISO)
negative chemotaxis  (ISO)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of axon extension involved in axon guidance  (IEA,ISO)
negative regulation of BMP signaling pathway  (IEA,ISO)
negative regulation of canonical Wnt signaling pathway  (ISO)
negative regulation of cell proliferation in midbrain  (IEA,ISO)
negative regulation of epithelial cell proliferation  (IEA,ISO)
negative regulation of fat cell differentiation  (IEA,ISO)
negative regulation of fibroblast growth factor receptor signaling pathway  (IEA,ISO)
negative regulation of melanin biosynthetic process  (IEA,ISO)
negative regulation of mesenchymal cell proliferation  (IEA,ISO)
negative regulation of prostatic bud formation  (IEA,ISO)
negative regulation of synapse assembly  (IEA,ISO)
negative regulation of transcription, DNA-templated  (IEA,ISO)
neural tube closure  (ISO)
neural tube development  (ISO)
neurogenesis  (ISO)
neuron differentiation  (IBA,IEP)
neuron projection morphogenesis  (ISO)
non-canonical Wnt signaling pathway  (ISO)
non-canonical Wnt signaling pathway via JNK cascade  (IEA,ISO)
notochord morphogenesis  (IEA,ISO)
olfactory bulb interneuron development  (IEA,ISO)
paraxial mesoderm formation  (IEA,ISO)
pericardium morphogenesis  (ISO)
planar cell polarity pathway involved in axis elongation  (IEA,ISO)
planar cell polarity pathway involved in axon guidance  (IEA,ISO)
planar cell polarity pathway involved in cardiac muscle tissue morphogenesis  (IEA,ISO)
planar cell polarity pathway involved in cardiac right atrium morphogenesis  (IEA,ISO)
planar cell polarity pathway involved in gastrula mediolateral intercalation  (IEA,ISO)
planar cell polarity pathway involved in neural tube closure  (IEA,ISO)
planar cell polarity pathway involved in outflow tract morphogenesis  (IEA,ISO)
planar cell polarity pathway involved in pericardium morphogenesis  (IEA,ISO)
planar cell polarity pathway involved in ventricular septum morphogenesis  (IEA,ISO)
positive regulation of angiogenesis  (IEA,ISO)
positive regulation of cartilage development  (IEA,ISO)
positive regulation of cell population proliferation  (ISO)
positive regulation of cell-cell adhesion  (IMP)
positive regulation of cell-cell adhesion mediated by cadherin  (IEA,ISO)
positive regulation of chemokine production  (IEA,ISO)
positive regulation of cytokine production  (ISO)
positive regulation of cytokine production involved in immune response  (ISO)
positive regulation of endocytosis  (IEA,ISO)
positive regulation of endothelial cell migration  (IEA,ISO)
positive regulation of endothelial cell proliferation  (IEA,ISO)
positive regulation of epithelial cell proliferation  (ISO)
positive regulation of fibroblast proliferation  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of GTPase activity  (ISO)
positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway  (IEA,ISO)
positive regulation of inflammatory response  (IEA,ISO)
positive regulation of interferon-gamma production  (IEA,ISO)
positive regulation of interleukin-1 beta production  (IEA,ISO)
positive regulation of interleukin-6 production  (IEA,ISO)
positive regulation of interleukin-8 production  (IEA,ISO)
positive regulation of JNK cascade  (IEA,ISO)
positive regulation of JUN kinase activity  (IEA,ISO)
positive regulation of macrophage activation  (IEA,ISO)
positive regulation of macrophage cytokine production  (IEA,ISO)
positive regulation of meiotic nuclear division  (IEA,ISO)
positive regulation of mesenchymal cell proliferation  (IEA,ISO)
positive regulation of neuron death  (IEA,ISO)
positive regulation of neuron projection arborization  (IEA,IGI,ISO)
positive regulation of neuron projection development  (IEA,ISO)
positive regulation of NF-kappaB transcription factor activity  (IEA,ISO)
positive regulation of non-canonical Wnt signaling pathway  (IEA,ISO)
positive regulation of ossification  (IEA,ISO)
positive regulation of peptidyl-serine phosphorylation  (IEA,ISO)
positive regulation of peptidyl-threonine phosphorylation  (IEA,ISO)
positive regulation of protein binding  (IEA,ISO)
positive regulation of protein catabolic process  (IEA,ISO)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein kinase C activity  (IEA,ISO)
positive regulation of protein kinase C signaling  (IEA,ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of response to cytokine stimulus  (ISO)
positive regulation of T cell chemotaxis  (IEA,ISO)
positive regulation of thymocyte apoptotic process  (IEA,ISO)
positive regulation of timing of anagen  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of tumor necrosis factor production  (IEA,ISO)
positive regulation of type I interferon-mediated signaling pathway  (IEA,ISO)
post-anal tail morphogenesis  (IEA,ISO)
primary heart field specification  (IEA,ISO)
primitive streak formation  (IEA,ISO)
prostate gland development  (IEP)
protein phosphorylation  (IEA,ISO)
regulation of branching involved in mammary gland duct morphogenesis  (IEA,ISO)
regulation of I-kappaB kinase/NF-kappaB signaling  (IEA,ISO)
regulation of postsynapse organization  (IEA,ISO)
regulation of postsynaptic cytosolic calcium ion concentration  (IEA,ISO)
regulation of protein localization  (IEA,ISO)
regulation of synapse organization  (ISO)
response to estradiol  (IEP)
response to glucocorticoid  (IEP)
response to hyperoxia  (IEP)
response to organic cyclic compound  (IEP)
response to organic substance  (IEP,ISO)
response to testosterone  (IEP)
secondary heart field specification  (IEA,ISO)
secondary palate development  (IEA,ISO)
somite development  (ISO)
somitogenesis  (IEA,ISO)
tube closure  (ISO)
type B pancreatic cell development  (IEA,ISO)
urinary bladder development  (IEA,ISO)
uterus development  (IEA,ISO)
vagina development  (IEA,ISO)
ventricular septum development  (ISO)
Wnt signaling pathway  (ISO)
Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation  (IEA,ISO)
Wnt signaling pathway, calcium modulating pathway  (IEA,ISO)
Wnt signaling pathway, planar cell polarity pathway  (IDA,ISO)
wound healing  (IEA,ISO)

Cellular Component
cell surface  (IEA,ISO)
cytoplasm  (IDA)
extracellular matrix  (IEA,ISO)
extracellular space  (IBA,IDA,IEA,ISO)
glutamatergic synapse  (IEA,ISO)
postsynapse  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bian WJ, etal., Dev Neurobiol. 2015 Aug;75(8):805-22. doi: 10.1002/dneu.22250. Epub 2014 Dec 1.
2. Boucherat O, etal., Physiol Genomics. 2007 Dec 19;32(1):128-41. Epub 2007 Oct 2.
3. Bui TD, etal., Br J Cancer. 1997;75(8):1131-6.
4. Castelo-Branco G, etal., Mol Cell Neurosci. 2006 Feb;31(2):251-62. Epub 2005 Oct 21.
5. Castelo-Branco G, etal., Proc Natl Acad Sci U S A 2003 Oct 28;100(22):12747-52. Epub 2003 Oct 13.
6. Doi T and Puri P, J Pediatr Surg. 2009 Dec;44(12):2302-6.
7. Fracalossi AC, etal., Exp Mol Pathol. 2010 Feb;88(1):176-83. Epub 2009 Nov 17.
8. Fujio Y, etal., FEBS Lett. 2004 Aug 27;573(1-3):202-6.
9. Fujise T, etal., Am J Physiol Gastrointest Liver Physiol. 2007 Apr;292(4):G1150-6. Epub 2006 Dec 28.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Huang L, etal., Dev Biol. 2009 Apr 15;328(2):188-99. Epub 2009 Jan 14.
12. Jiang F, etal., J Hepatol. 2006 Sep;45(3):401-9. Epub 2006 May 3.
13. Katayama S, etal., Toxicol Sci. 2006 Jun;91(2):419-30. Epub 2006 Mar 21.
14. Lange C, etal., Neurodegener Dis. 2006;3(1-2):76-86.
15. MGD data from the GO Consortium
16. Miyakoshi T, etal., Acta Histochem Cytochem. 2009 Dec 29;42(6):205-13. Epub 2009 Dec 22.
17. NCBI rat LocusLink and RefSeq merged data July 26, 2002
18. OMIM Disease Annotation Pipeline
19. Pipeline to import KEGG annotations from KEGG into RGD
20. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
21. Pu Y, etal., Endocrinology. 2007 Apr;148(4):1697-706. Epub 2007 Jan 11.
22. RGD automated data pipeline
23. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
24. RGD automated import pipeline for gene-chemical interactions
25. RGD comprehensive gene curation
26. Ricken A, etal., Endocrinology 2002 Jul;143(7):2741-9.
27. Roel Nusse - Howard Hughes Medical Institute and the Department of Developmental Biology at Stanford University, California, USA
28. Song HH, etal., J Biol Chem. 2005 Jan 21;280(3):2116-25. Epub 2004 Nov 10.
29. van Amerongen R, etal., Sci Signal. 2008 Sep 2;1(35):re9.
30. Yang Y, etal., Development 2003 Mar;130(5):1003-15.
Additional References at PubMed
PMID:8167409   PMID:9054360   PMID:9160667   PMID:9787155   PMID:10021340   PMID:10557084   PMID:10893270   PMID:11092808   PMID:12086864   PMID:12142021   PMID:12839624   PMID:12841867  
PMID:12952940   PMID:15037319   PMID:15040835   PMID:15073149   PMID:15143170   PMID:15309358   PMID:15748172   PMID:16115200   PMID:16246260   PMID:16601243   PMID:16602827   PMID:16723543  
PMID:17035633   PMID:17244647   PMID:17433286   PMID:17486081   PMID:17804636   PMID:17848411   PMID:17898001   PMID:17976063   PMID:17986005   PMID:17986384   PMID:18070933   PMID:18096705  
PMID:18174455   PMID:18287027   PMID:18351662   PMID:18413325   PMID:18703641   PMID:18804104   PMID:18929644   PMID:18953410   PMID:18986540   PMID:18991062   PMID:19048125   PMID:19056682  
PMID:19099253   PMID:19100252   PMID:19100728   PMID:19177143   PMID:19251946   PMID:19277043   PMID:19300477   PMID:19332546   PMID:19399181   PMID:19520808   PMID:19795512   PMID:19847889  
PMID:19878652   PMID:19910923   PMID:19918918   PMID:20032469   PMID:20034610   PMID:20093360   PMID:20106871   PMID:20573888   PMID:21106844   PMID:21177867   PMID:21212964   PMID:21483795  
PMID:21501682   PMID:21539518   PMID:21857966   PMID:21870110   PMID:22521824   PMID:22553398   PMID:22569553   PMID:22609204   PMID:23109420   PMID:23324743   PMID:23337931   PMID:23396967  
PMID:23517308   PMID:23569434   PMID:23598468   PMID:23625269   PMID:23677472   PMID:23709620   PMID:24088568   PMID:24091014   PMID:24305805   PMID:24440698   PMID:24681597   PMID:24879894  
PMID:24891513   PMID:24966909   PMID:25120137   PMID:25331176   PMID:25336659   PMID:25593127   PMID:25744836   PMID:25749876   PMID:25813538   PMID:25825749   PMID:26218875   PMID:26311509  
PMID:26547443   PMID:26566235   PMID:27402827   PMID:27878554   PMID:28851071   PMID:28870803   PMID:29152652   PMID:29164146   PMID:29339085   PMID:29510185   PMID:30543046   PMID:30562750  
PMID:30593464   PMID:31341413   PMID:33116025  


Genomics

Comparative Map Data
Wnt5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2163,695,667 - 3,718,234 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl163,697,032 - 3,718,234 (+)Ensembl
Rnor_6.0164,469,451 - 4,490,271 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl164,469,468 - 4,489,860 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0164,414,512 - 4,433,990 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4163,782,025 - 3,799,625 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1163,782,022 - 3,799,623 (+)NCBI
Celera163,644,605 - 3,665,720 (+)NCBICelera
Cytogenetic Map16p16NCBI
WNT5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl355,465,715 - 55,490,539 (-)EnsemblGRCh38hg38GRCh38
GRCh38355,465,715 - 55,505,261 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37355,499,743 - 55,521,334 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36355,474,783 - 55,496,371 (-)NCBINCBI36hg18NCBI36
Build 34355,474,783 - 55,496,371NCBI
Celera355,465,957 - 55,488,272 (-)NCBI
Cytogenetic Map3p14.3NCBI
HuRef355,548,623 - 55,570,480 (-)NCBIHuRef
CHM1_1355,451,089 - 55,473,010 (-)NCBICHM1_1
Wnt5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391428,224,962 - 28,249,405 (+)NCBIGRCm39mm39
GRCm39 Ensembl1428,226,707 - 28,249,405 (+)Ensembl
GRCm381428,504,543 - 28,527,448 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1428,504,750 - 28,527,448 (+)EnsemblGRCm38mm10GRCm38
MGSCv371429,318,659 - 29,338,620 (+)NCBIGRCm37mm9NCBIm37
MGSCv361427,332,339 - 27,352,300 (+)NCBImm8
Celera1424,754,276 - 24,774,180 (+)NCBICelera
Cytogenetic Map14A3NCBI
cM Map1416.8NCBI
Wnt5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554305,304,745 - 5,325,684 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554305,304,817 - 5,325,684 (-)NCBIChiLan1.0ChiLan1.0
WNT5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1356,617,006 - 56,639,367 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl356,621,380 - 56,638,051 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0355,396,279 - 55,418,579 (-)NCBIMhudiblu_PPA_v0panPan3
WNT5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12034,756,430 - 34,790,937 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2034,769,930 - 34,786,673 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2034,700,143 - 34,711,111 (+)NCBI
ROS_Cfam_1.02035,028,713 - 35,063,140 (+)NCBI
UMICH_Zoey_3.12034,490,948 - 34,501,920 (+)NCBI
UNSW_CanFamBas_1.02034,851,115 - 34,862,094 (+)NCBI
UU_Cfam_GSD_1.02035,066,932 - 35,077,922 (+)NCBI
Wnt5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118172,893,045 - 172,913,645 (-)NCBI
SpeTri2.0NW_0049364736,031,627 - 6,052,211 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
WNT5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1337,344,699 - 37,367,207 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11337,344,684 - 37,367,215 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21340,872,351 - 40,892,735 (-)NCBISscrofa10.2Sscrofa10.2susScr3
WNT5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12216,809,454 - 16,836,815 (-)NCBI
ChlSab1.1 Ensembl2216,809,451 - 16,825,048 (-)Ensembl
Vero_WHO_p1.0NW_023666041150,043,734 - 150,071,018 (+)NCBI
Wnt5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248221,824,378 - 1,843,599 (+)NCBI

Position Markers
BF396653  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2163,695,750 - 3,695,964 (+)MAPPERmRatBN7.2
Rnor_6.0164,468,170 - 4,468,383NCBIRnor6.0
Rnor_5.0164,413,231 - 4,413,444UniSTSRnor5.0
RGSC_v3.4163,780,744 - 3,780,957UniSTSRGSC3.4
Celera163,643,324 - 3,643,537UniSTS
RH 3.4 Map163.0UniSTS
Cytogenetic Map16p16UniSTS
Wnt5a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2163,713,568 - 3,713,757 (+)MAPPERmRatBN7.2
Rnor_6.0164,485,992 - 4,486,180NCBIRnor6.0
Rnor_5.0164,431,275 - 4,431,463UniSTSRnor5.0
RGSC_v3.4163,798,787 - 3,798,975UniSTSRGSC3.4
Celera163,661,066 - 3,661,254UniSTS
Cytogenetic Map16p16UniSTS
Wnt5a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2163,713,568 - 3,713,789 (+)MAPPERmRatBN7.2
Rnor_6.0164,485,992 - 4,486,212NCBIRnor6.0
Rnor_5.0164,431,275 - 4,431,495UniSTSRnor5.0
RGSC_v3.4163,798,787 - 3,799,007UniSTSRGSC3.4
Celera163,661,066 - 3,661,286UniSTS
Cytogenetic Map16p16UniSTS
Wnt5a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2163,703,022 - 3,704,443 (+)MAPPERmRatBN7.2
Rnor_6.0164,475,447 - 4,476,866NCBIRnor6.0
Rnor_5.0164,420,730 - 4,422,149UniSTSRnor5.0
RGSC_v3.4163,788,242 - 3,789,661UniSTSRGSC3.4
Celera163,650,569 - 3,651,988UniSTS
Cytogenetic Map16p16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
12903955Kidm69Kidney mass QTL 690.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)168323804227609Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:54
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000021164
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 20 6 43 29 36 8
Low 3 23 32 22 19 22 8 11 31 6 5 3 8
Below cutoff 19 19 19

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021164   ⟹   ENSRNOP00000021164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl163,697,032 - 3,718,234 (+)Ensembl
Rnor_6.0 Ensembl164,469,468 - 4,489,860 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096855   ⟹   ENSRNOP00000078870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl163,703,354 - 3,718,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114996   ⟹   ENSRNOP00000076426
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl163,702,524 - 3,718,234 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117958   ⟹   ENSRNOP00000090132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl163,702,728 - 3,718,234 (+)Ensembl
RefSeq Acc Id: NM_022631   ⟹   NP_072153
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2163,697,032 - 3,718,234 (+)NCBI
Rnor_6.0164,469,451 - 4,490,271 (+)NCBI
Rnor_5.0164,414,512 - 4,433,990 (+)NCBI
RGSC_v3.4163,782,025 - 3,799,625 (+)RGD
Celera163,644,605 - 3,665,720 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252664   ⟹   XP_006252726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2163,702,118 - 3,718,230 (+)NCBI
Rnor_6.0164,474,926 - 4,488,707 (+)NCBI
Rnor_5.0164,414,512 - 4,433,990 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094812   ⟹   XP_038950740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2163,695,667 - 3,718,230 (+)NCBI
RefSeq Acc Id: XM_039094813   ⟹   XP_038950741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2163,701,703 - 3,718,230 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_072153   ⟸   NM_022631
- Peptide Label: precursor
- UniProtKB: F2Z3U1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252726   ⟸   XM_006252664
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000021164   ⟸   ENSRNOT00000021164
RefSeq Acc Id: XP_038950740   ⟸   XM_039094812
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038950741   ⟸   XM_039094813
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000076426   ⟸   ENSRNOT00000114996
RefSeq Acc Id: ENSRNOP00000090132   ⟸   ENSRNOT00000117958
RefSeq Acc Id: ENSRNOP00000078870   ⟸   ENSRNOT00000096855

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/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)
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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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69250 AgrOrtholog
Ensembl Genes ENSRNOG00000015618 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021164 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021164 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.2460.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Wnt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Wnt5a UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Wnt_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Wnt_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64566 UniProtKB/TrEMBL
NCBI Gene 64566 ENTREZGENE
PANTHER PTHR12027 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12027:SF33 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam wnt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Wnt5a PhenoGen
PRINTS WNTPROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE WNT1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART WNT1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F2Z3U1 ENTREZGENE, UniProtKB/TrEMBL
  Q14UC9_RAT UniProtKB/TrEMBL
  Q9QXQ7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5PY99 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-29 Wnt5a  Wnt family member 5A  Wnt5a  wingless-type MMTV integration site family, member 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-11-14 Wnt5a  wingless-type MMTV integration site family, member 5A  Wnt5a  wingless-related MMTV integration site 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Wnt5a  wingless-related MMTV integration site 5A  Wnt5a  wingless-type MMTV integration site 5A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Wnt5a  wingless-type MMTV integration site 5A      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference