Muc1 (mucin 1, cell surface associated) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Muc1 (mucin 1, cell surface associated) Rattus norvegicus
Analyze
Symbol: Muc1
Name: mucin 1, cell surface associated
RGD ID: 3122
Description: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; p53 binding activity; and transcription coregulator activity. Involved in several processes, including cellular response to retinoic acid; female pregnancy; and response to hypoxia. Located in apical plasma membrane and cytoplasm. Used to study allergic rhinitis. Biomarker of allergic rhinitis; cholangiocarcinoma; chronic obstructive pulmonary disease; cystic fibrosis; and otitis media. Human ortholog(s) of this gene implicated in several diseases, including biliary tract benign neoplasm; dry eye syndrome; familial juvenile hyperuricemic nephropathy; mucinous adenocarcinoma; and pancreatic cancer (multiple). Orthologous to human MUC1 (mucin 1, cell surface associated); PARTICIPATES IN p53 signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2-acetamidofluorene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: MGC188069; mucin 1; mucin 1, transmembrane; mucin-1; Mucin1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Muc1em1Mcwi   Muc1em1Cgen  
Genetic Models: SD-Muc1em1Cgen FHH-Muc1em1Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22174,635,559 - 174,640,738 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2174,635,995 - 174,640,733 (+)Ensembl
Rnor_6.02188,543,137 - 188,547,874 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2188,543,137 - 188,547,874 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02207,957,206 - 207,962,396 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42181,399,482 - 181,403,640 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12181,352,002 - 181,353,687 (+)NCBI
Celera2168,578,421 - 168,583,038 (+)NCBICelera
RH 3.4 Map21155.0RGD
Cytogenetic Map2q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
adult respiratory distress syndrome  (ISO)
allergic conjunctivitis  (ISO)
allergic rhinitis  (IEP,IMP,ISO)
asthma  (ISO)
Autosomal Dominant Tubulointerstitial Kidney Disease 2  (ISO)
bacterial conjunctivitis  (ISO)
biliary tract benign neoplasm  (ISO)
bird fancier's lung  (ISO)
blepharitis  (ISO)
breast adenocarcinoma  (ISO)
breast cancer  (ISO)
bronchiolitis obliterans  (ISO)
Bronchopulmonary Dysplasia  (ISO)
cholangiocarcinoma  (IEP,ISO)
chronic obstructive pulmonary disease  (ISO)
common bile duct neoplasm  (ISO)
cystic fibrosis  (ISO)
Diabetes Complications  (IEP)
dry eye syndrome  (ISO)
Fetal Growth Retardation  (IEP)
Gallbladder Neoplasms  (ISO)
gastrointestinal stromal tumor  (ISO)
heart disease  (ISO)
Hematologic Neoplasms  (ISO)
idiopathic pulmonary fibrosis  (ISO)
interstitial lung disease  (ISO)
Kidney Reperfusion Injury  (IDA)
Liver Reperfusion Injury  (IEP)
lung adenocarcinoma  (ISO)
lung disease  (ISO)
Lymphatic Metastasis  (ISO)
malignant mesothelioma  (ISO)
Mammary Neoplasms, Experimental  (ISO)
measles  (ISO)
Mesothelioma  (ISO)
mucinous adenocarcinoma  (ISO)
multiple myeloma  (ISO)
Neoplasm Metastasis  (ISO)
Neoplastic Cell Transformation  (ISO)
obstructive sleep apnea  (ISO)
otitis media  (IEP)
pancreatic cancer  (ISO)
pancreatic ductal carcinoma  (ISO)
parathyroid carcinoma  (ISO)
Peritoneal Neoplasms  (ISO)
pneumocystosis  (ISO)
pneumonia  (ISO)
pre-malignant neoplasm  (ISO)
prostate cancer  (ISO)
pulmonary sarcoidosis  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IEP)
Stomach Neoplasms  (ISO)
systemic scleroderma  (ISO)
Tubulointerstitial Nephritis and Uveitis  (ISO)
urinary bladder cancer  (ISO)
Viral Bronchiolitis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-acetamidofluorene  (EXP)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,4-dichloroaniline  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-tert-Octylphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (EXP)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
boric acids  (ISO)
bortezomib  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
ceric oxide  (ISO)
chitin  (ISO)
chloroquine  (ISO)
chlorothalonil  (ISO)
choline  (ISO)
cisplatin  (ISO)
cyclosporin A  (EXP,ISO)
deguelin  (ISO)
dexamethasone  (ISO)
dibenzo[a,l]pyrene  (ISO)
diethylstilbestrol  (EXP,ISO)
dioxygen  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
enilconazole  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
hydralazine  (ISO)
indole-3-methanol  (EXP,ISO)
isoniazide  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
mancozeb  (ISO)
medroxyprogesterone acetate  (ISO)
mifepristone  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (EXP)
naphthalene  (EXP)
nickel sulfate  (ISO)
nitrofen  (EXP)
ochratoxin A  (ISO)
p-tert-Amylphenol  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
potassium bromate  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
prostaglandin E2  (ISO)
pyrimidifen  (ISO)
quercetin  (EXP)
raloxifene  (EXP,ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sulforaphane  (ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
titanium dioxide  (EXP,ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vandetanib  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Al-Salmi QA, etal., Chest. 2005 Jan;127(1):403-7.
2. Aubert S, etal., Cancer Res. 2009 Jul 15;69(14):5707-15. Epub 2009 Jun 23.
3. Beckerman R and Prives C, Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000935. doi: 10.1101/cshperspect.a000935. Epub 2010 Apr 28.
4. Briassoulis G, etal., Pediatr Pulmonol. 2006 Aug;41(8):790-5.
5. Chang HJ, etal., Pathol Int. 2004 Aug;54(8):576-84.
6. Chhieng DC, etal., Cancer. 2003 Dec 25;99(6):365-71.
7. Cozzi PJ, etal., Clin Exp Metastasis. 2005;22(7):565-73. Epub 2006 Feb 11.
8. de Paiva Haddad LB, etal., J Gastrointest Surg. 2010 Apr;14(4):719-28. Epub 2010 Jan 27.
9. DeSouza MM, etal., Biol Reprod 1998 Jun;58(6):1503-7.
10. Dogru M, etal., Clin Exp Allergy. 2006 Dec;36(12):1556-65.
11. Dorai T, etal., J Urol. 2011 Dec;186(6):2448-54. doi: 10.1016/j.juro.2011.08.010. Epub 2011 Oct 21.
12. Fanca-Berthon P, etal., Pediatr Res. 2009 Jul;66(1):47-52. doi: 10.1203/PDR.0b013e3181a2047e.
13. Farina A, etal., J Proteome Res. 2009 Jan;8(1):159-69.
14. Fujita K, etal., Br J Cancer. 1999 Apr;80(1-2):301-8.
15. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. Ghosh SK, etal., Int J Cancer. 2013 Apr 15;132(8):1860-7. doi: 10.1002/ijc.27872. Epub 2012 Oct 25.
17. Gipson IK, etal., Cornea. 2011 Dec;30(12):1346-52. doi: 10.1097/ICO.0b013e31820d852a.
18. Guzman K, etal., Am J Physiol 1996 May;270(5 Pt 1):L846-53.
19. Hamada H, etal., Intern Med. 1998 Mar;37(3):307-10.
20. Hant FN, etal., J Rheumatol. 2009 Apr;36(4):773-80. Epub 2009 Mar 13.
21. Ho SB, etal., Cancer Res. 1993 Feb 1;53(3):641-51.
22. Imai T, etal., Pediatr Pulmonol. 2002 Feb;33(2):135-41.
23. Imbert Y, etal., Exp Eye Res. 2009 Mar;88(3):334-8. doi: 10.1016/j.exer.2008.05.019. Epub 2008 Jun 20.
24. Isaacs J and Murphy CR, Acta Histochem. 2003;105(3):239-43.
25. Ishikawa N, etal., Respiration. 2011 Apr 7.
26. Jan YY, etal., Ann Surg. 2004 Jul;240(1):89-94.
27. Janssen R, etal., Chest. 2003 Dec;124(6):2119-25.
28. Janssen R, etal., Sarcoidosis Vasc Diffuse Lung Dis. 2005 Mar;22(1):51-7.
29. Kardon R, etal., Invest Ophthalmol Vis Sci. 1999 Jun;40(7):1328-35.
30. Kase S, etal., Am J Kidney Dis. 2006 Dec;48(6):935-41.
31. Kashiwagi H, etal., Oncol Rep. 2001 May-Jun;8(3):485-9.
32. Kaufman HL, etal., J Transl Med. 2007 Nov 26;5:60.
33. Kawamoto T, etal., Clin Exp Metastasis. 2004;21(4):353-62.
34. Kawaoka T, etal., Oncol Rep. 2008 Jul;20(1):155-63.
35. Kawasaki Y, etal., J Med Virol. 2009 Dec;81(12):2104-8.
36. Kim DH, etal., Neonatology. 2008;93(4):223-9. Epub 2007 Nov 16.
37. Kinoshita F, etal., Respir Med. 2004 Nov;98(11):1131-7.
38. Kirby A, etal., Nat Genet. 2013 Mar;45(3):299-303. doi: 10.1038/ng.2543. Epub 2013 Feb 10.
39. Kitamura H, etal., Jpn J Cancer Res. 1996 Jun;87(6):631-40.
40. Kohlgraf KG, etal., Cancer Res. 2003 Aug 15;63(16):5011-20.
41. Kondo H, etal., Anticancer Res. 2008 Jan-Feb;28(1B):379-87.
42. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
43. Lacunza E, etal., Eur J Histochem. 2010 Nov 26;54(4):e49.
44. Laes JF, etal., Cytogenet Cell Genet 2001;92(1-2):130-3.
45. Lederer DJ, etal., Eur Respir J. 2009 Apr;33(4):793-6.
46. Lepisto AJ, etal., Cancer Ther. 2008;6(B):955-964.
47. MGD data from the GO Consortium
48. Mukherjee P, etal., J Immunol. 2009 Jan 1;182(1):216-24.
49. NCBI rat LocusLink and RefSeq merged data July 26, 2002
50. Nguyen GK, etal., PLoS One. 2013 Aug 14;8(8):e71628. doi: 10.1371/journal.pone.0071628.
51. Ogihara T, etal., J Pediatr. 2000 Aug;137(2):280-2.
52. Ohshimo S, etal., Sarcoidosis Vasc Diffuse Lung Dis. 2009 Jul;26(1):47-53.
53. OMIM Disease Annotation Pipeline
54. Park SY, etal., Oncol Rep. 2009 Sep;22(3):649-57.
55. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
56. RGD automated import pipeline for gene-chemical interactions
57. RGD comprehensive gene curation
58. Samukawa T, etal., BMC Pulm Med. 2012 Sep 11;12:55. doi: 10.1186/1471-2466-12-55.
59. Seregni E, etal., Anticancer Res. 1996 Jul-Aug;16(4B):2209-13.
60. Shimamoto T, etal., Pancreas. 2010 Mar 30.
61. Simms MS, etal., BJU Int. 1999 Aug;84(3):350-2.
62. Sirica AE, etal., Hepatology. 2008 Apr;47(4):1178-90.
63. Tanaka M, etal., Hematology. 2002 Apr;7(2):105-8.
64. Tang W, etal., World J Gastroenterol. 2005 Sep 21;11(35):5450-4.
65. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
66. Tian F, etal., Transplantation. 2011 Sep 15;92(5):529-35. doi: 10.1097/TP.0b013e318229f785.
67. Tinder TL, etal., J Immunol. 2008 Sep 1;181(5):3116-25.
68. Tsuboi Y, etal., Int J Pediatr Otorhinolaryngol. 2001 Oct 19;61(1):23-30.
69. Tsutsumida H, etal., Clin Cancer Res. 2006 May 15;12(10):2976-87.
70. Vesely R, etal., J Rheumatol. 2004 Apr;31(4):795-800.
71. von Mensdorff-Pouilly S, etal., Eur J Cancer. 1996 Jul;32A(8):1325-31.
72. Walter JN, etal., Transplantation. 2006 Sep 15;82(5):709-11.
73. Xu H, etal., Hepatogastroenterology. 2008 Nov-Dec;55(88):2000-4.
74. Yamasaki H, etal., Int J Oncol. 2004 Jan;24(1):107-13.
75. Yamato T, etal., J Pathol. 1999 May;188(1):30-7.
76. Ye Q, etal., Lab Invest. 2011 May;91(5):778-87. doi: 10.1038/labinvest.2011.12. Epub 2011 Feb 21.
77. Zhou LB, etal., J Allergy Clin Immunol. 2019 Dec;144(6):1716-1719.e5. doi: 10.1016/j.jaci.2019.07.042. Epub 2019 Aug 16.
Additional References at PubMed
PMID:1569123   PMID:7698991   PMID:12477932   PMID:14999001   PMID:15326289   PMID:15710329   PMID:16240224   PMID:16472605   PMID:16502470   PMID:17187413   PMID:17545040   PMID:19056867  
PMID:19190083   PMID:19199708   PMID:23376485   PMID:23533145   PMID:24298937   PMID:29847197  


Genomics

Comparative Map Data
Muc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22174,635,559 - 174,640,738 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2174,635,995 - 174,640,733 (+)Ensembl
Rnor_6.02188,543,137 - 188,547,874 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2188,543,137 - 188,547,874 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02207,957,206 - 207,962,396 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42181,399,482 - 181,403,640 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12181,352,002 - 181,353,687 (+)NCBI
Celera2168,578,421 - 168,583,038 (+)NCBICelera
RH 3.4 Map21155.0RGD
Cytogenetic Map2q34NCBI
MUC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1155,185,824 - 155,192,916 (-)EnsemblGRCh38hg38GRCh38
GRCh381155,185,824 - 155,192,915 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371155,158,300 - 155,162,706 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361153,424,924 - 153,429,324 (-)NCBINCBI36hg18NCBI36
Build 341151,971,671 - 151,975,732NCBI
Celera1128,229,565 - 128,235,983 (-)NCBI
Cytogenetic Map1q22NCBI
HuRef1126,521,570 - 126,525,810 (-)NCBIHuRef
CHM1_11156,554,155 - 156,558,213 (-)NCBICHM1_1
Muc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39389,136,363 - 89,140,688 (+)NCBIGRCm39mm39
GRCm39 Ensembl389,136,364 - 89,140,688 (+)Ensembl
GRCm38389,229,056 - 89,233,381 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl389,229,057 - 89,233,381 (+)EnsemblGRCm38mm10GRCm38
MGSCv37389,032,974 - 89,037,291 (+)NCBIGRCm37mm9NCBIm37
MGSCv36389,314,979 - 89,319,296 (+)NCBImm8
Celera389,262,943 - 89,267,242 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map339.02NCBI
Muc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555451,657,728 - 1,662,112 (-)NCBIChiLan1.0ChiLan1.0
MUC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11134,141,969 - 134,146,791 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1134,141,969 - 134,145,850 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01130,533,508 - 130,537,866 (-)NCBIMhudiblu_PPA_v0panPan3
MUC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1742,338,939 - 42,344,690 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl742,340,375 - 42,344,690 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha741,831,252 - 41,835,267 (+)NCBI
ROS_Cfam_1.0742,208,174 - 42,213,894 (+)NCBI
UMICH_Zoey_3.1741,989,397 - 41,993,712 (+)NCBI
UNSW_CanFamBas_1.0742,043,322 - 42,047,575 (+)NCBI
UU_Cfam_GSD_1.0742,326,882 - 42,331,197 (+)NCBI
Muc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505825,661,448 - 25,667,022 (-)NCBI
SpeTri2.0NW_0049365804,691,870 - 4,694,092 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MUC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1494,626,317 - 94,631,194 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24103,409,143 - 103,413,841 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MUC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1208,641,701 - 8,646,739 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl208,642,842 - 8,646,962 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660387,970,061 - 7,974,280 (+)NCBIVero_WHO_p1.0
Muc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248852,339,281 - 2,343,351 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94427  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map21155.0UniSTS
Cytogenetic Map2q34UniSTS
AU047994  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22174,639,799 - 174,639,956 (+)MAPPERmRatBN7.2
Rnor_6.02188,546,942 - 188,547,096NCBIRnor6.0
Rnor_5.02207,961,460 - 207,961,614UniSTSRnor5.0
RGSC_v3.42181,402,708 - 181,402,862UniSTSRGSC3.4
Celera2168,582,106 - 168,582,260UniSTS
Cytogenetic Map2q34UniSTS
Muc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22174,637,758 - 174,638,821 (+)MAPPERmRatBN7.2
mRatBN7.22174,637,932 - 174,638,821 (+)MAPPERmRatBN7.2
Rnor_6.02188,545,075 - 188,545,963NCBIRnor6.0
Rnor_6.02188,544,901 - 188,545,963NCBIRnor6.0
Rnor_5.02207,959,419 - 207,960,481UniSTSRnor5.0
Rnor_5.02207,959,593 - 207,960,481UniSTSRnor5.0
RGSC_v3.42181,400,365 - 181,401,729UniSTSRGSC3.4
Celera2168,580,239 - 168,581,127UniSTS
Celera2168,580,065 - 168,581,127UniSTS
Cytogenetic Map2q34UniSTS
Muc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22174,639,085 - 174,640,651 (+)MAPPERmRatBN7.2
Rnor_6.02188,546,228 - 188,547,791NCBIRnor6.0
Rnor_5.02207,960,746 - 207,962,309UniSTSRnor5.0
RGSC_v3.42181,401,994 - 181,403,557UniSTSRGSC3.4
Celera2168,581,392 - 168,582,955UniSTS
Cytogenetic Map2q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
61457Niddm8Non-insulin dependent diabetes mellitus QTL 84.10.01blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2174543008175950118Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61469Bp16Blood pressure QTL 165.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
61473Bp19Blood pressure QTL 196.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2172710921175950118Rat
70162Bp63Blood pressure QTL 635.64arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)2169745596214745596Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168358098223265385Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2168594495213594495Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
631522Bp74Blood pressure QTL 740.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2172710921184114403Rat
1302793Bw16Body weight QTL 1650.0001body mass (VT:0001259)body weight (CMO:0000012)2157142209202446871Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1598838Bp290Blood pressure QTL 2901.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2166539266211539266Rat
2301415Cm67Cardiac mass QTL 670.003heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2152413072175950118Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2161699179222436696Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1549833Bp257Blood pressure QTL 2570.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2168354880185122374Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2164073756227146641Rat
1358900Bw48Body weight QTL 484.88body mass (VT:0001259)body weight (CMO:0000012)2157142078211086598Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1359032Hrtrt18Heart rate QTL 18heart pumping trait (VT:2000009)heart rate (CMO:0000002)2157142078192625452Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2143657569184114274Rat
7488904Bp363Blood pressure QTL 3630.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2172982062175950118Rat
7488925Bp364Blood pressure QTL 3640.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2160564068205564068Rat
7488927Bp365Blood pressure QTL 3650.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2162765032207765032Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2157142078226277316Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
12879846Cm90Cardiac mass QTL 900.011heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)2152413072175950118Rat
12879836Kidm61Kidney mass QTL 610.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2152413072185122374Rat
12879839Cm85Cardiac mass QTL 850.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)2152413072185122374Rat
11565181Bw176Body weight QTL 1760.002body mass (VT:0001259)body weight (CMO:0000012)2152413072175950118Rat
12879838Cm86Cardiac mass QTL 860.002heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2152413072185122374Rat
12879840Bw179Body weight QTL 1790.005body mass (VT:0001259)body weight (CMO:0000012)2152413072185122374Rat
12879845Cm89Cardiac mass QTL 890.008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)2152413072175950118Rat
11565180Kidm56Kidney mass QTL 560.003kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2152413072175950118Rat
12879837Am2Aortic mass QTL 20.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2152413072185122374Rat
12879847Am4Aortic mass QTL 40.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)2152413072175950118Rat


Genetic Models
This gene Muc1 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:48
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000027850
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 25 9 11
Low 3 20 33 33 8 33 66 10 30
Below cutoff 15 19 8 11 8 7 8 8 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027850   ⟹   ENSRNOP00000027850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2174,635,995 - 174,640,733 (+)Ensembl
Rnor_6.0 Ensembl2188,543,137 - 188,547,874 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103512   ⟹   ENSRNOP00000096371
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2174,636,309 - 174,640,733 (+)Ensembl
RefSeq Acc Id: XM_039103761   ⟹   XP_038959689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22174,635,559 - 174,640,738 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038959689 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB62948 (Get FASTA)   NCBI Sequence Viewer  
  AAI66505 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000027850   ⟸   ENSRNOT00000027850
RefSeq Acc Id: XP_038959689   ⟸   XM_039103761
RefSeq Acc Id: ENSRNOP00000096371   ⟸   ENSRNOT00000103512
Protein Domains
SEA

Transcriptome

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

Promoters
RGD ID:13691464
Promoter ID:EPDNEW_R1989
Type:single initiation site
Name:Muc1_1
Description:mucin 1, cell surface associated
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_6.02188,543,130 - 188,543,190EPDNEW

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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3122 AgrOrtholog
Ensembl Genes ENSRNOG00000020539 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027850 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027850 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.600 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7122817 IMAGE-MGC_LOAD
InterPro SEA UniProtKB/TrEMBL
  SEA_dom_sf UniProtKB/TrEMBL
MGC_CLONE MGC:188069 IMAGE-MGC_LOAD
NCBI Gene 24571 ENTREZGENE
Pfam SEA UniProtKB/TrEMBL
PhenoGen Muc1 PhenoGen
PROSITE SEA UniProtKB/TrEMBL
SMART SEA UniProtKB/TrEMBL
Superfamily-SCOP SSF82671 UniProtKB/TrEMBL
TIGR TC219475
UniProt B2GV31_RAT UniProtKB/TrEMBL
  O35770_RAT UniProtKB/TrEMBL
UniProt Secondary F1LMZ5 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-08-29 Muc1  mucin 1, cell surface associated  Muc1  mucin 1, transmembrane  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Muc1  mucin 1, transmembrane    mucin 1  Name updated 1299863 APPROVED
2002-06-10 Muc1  Mucin1      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expression is decreased at Day 5 of pregnancy in the uterine epithelium 633409