Runx1 (RUNX family transcription factor 1) - Rat Genome Database

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Gene: Runx1 (RUNX family transcription factor 1) Rattus norvegicus
Analyze
Symbol: Runx1
Name: RUNX family transcription factor 1
RGD ID: 2283
Description: Enables promoter-specific chromatin binding activity and sequence-specific double-stranded DNA binding activity. Involved in several processes, including ovulation; positive regulation of progesterone secretion; and response to denervation involved in regulation of muscle adaptation. Located in chromatin and nucleus. Used to study middle cerebral artery infarction. Biomarker of endometriosis. Human ortholog(s) of this gene implicated in acute myeloid leukemia and esophagus squamous cell carcinoma. Orthologous to human RUNX1 (RUNX family transcription factor 1); PARTICIPATES IN transforming growth factor-beta Smad dependent signaling pathway; acute myeloid leukemia pathway; chronic myeloid leukemia pathway; INTERACTS WITH (+)-schisandrin B; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: acute myeloid leukemia 1; Aml1; B; CBF-alpha-2; Cbfa2; core-binding factor runt domain alpha subunit 2 (acute myeloid leukemia 1 oncogene); core-binding factor subunit alpha-2; oncogene AML-1; PEA2-alpha; PEA2-alpha B; PEBP2-alpha; PEBP2-alpha B; polyomavirus enhancer-binding protein 2 alpha B subunit; runt related transcription factor 1; runt-related transcription factor 1
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21131,839,880 - 32,074,427 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1131,843,764 - 32,074,542 (-)Ensembl
Rnor_6.01132,765,147 - 33,003,061 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1132,769,165 - 33,003,021 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01136,367,315 - 36,601,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41132,623,461 - 32,725,404 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11132,679,703 - 32,781,647 (-)NCBI
Celera1131,494,069 - 31,582,728 (-)NCBICelera
RH 3.4 Map11214.7RGD
Cytogenetic Map11q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute lymphoblastic leukemia  (ISO)
acute megakaryocytic leukemia  (ISO)
acute myeloid leukemia  (ISO)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
anaplastic ependymoma  (ISO)
asthma  (ISO)
autoimmune disease  (ISO)
B-lymphoblastic leukemia/lymphoma  (ISO)
blood platelet disease  (ISO)
Bone Fractures  (IEP)
cardiomyopathy  (ISO)
colon signet ring adenocarcinoma  (ISO)
colorectal adenocarcinoma  (ISO)
colorectal cancer  (ISO)
endometrial cancer  (ISO)
endometriosis  (IEP)
esophagus squamous cell carcinoma  (ISO)
Experimental Leukemia  (ISO)
Familial Platelet Disorder with Associated Myeloid Malignancy  (ISO)
glioblastoma  (ISO)
hemorrhagic disease  (ISO)
hepatocellular carcinoma  (ISO)
Intestinal Neoplasms  (ISO)
intrahepatic cholangiocarcinoma  (ISO)
juvenile myelomonocytic leukemia  (ISO)
long QT syndrome 6  (ISO)
lung adenocarcinoma  (ISO)
lung non-small cell carcinoma  (ISO)
Lymphatic Metastasis  (ISO)
lymphoid leukemia  (ISO)
Mammary Neoplasms, Experimental  (IEP)
middle cerebral artery infarction  (IAGP)
multicentric Castleman disease  (ISO)
multiple myeloma  (ISO)
myelodysplastic syndrome  (ISO)
myeloid neoplasm  (ISO)
pancytopenia  (ISO)
Parkinson's disease 20  (ISO)
platelet storage pool deficiency  (ISO)
Prostatic Neoplasms  (ISO)
rheumatoid arthritis  (ISO)
sciatic neuropathy  (ISO)
Spina Bifida Cystica  (IDA)
stomach cancer  (ISO)
T-cell acute lymphoblastic leukemia  (ISO)
T-Cell Lymphoma  (ISO)
Therapy-related Acute Myeloid Leukemia  (ISO)
thrombocytopenia  (ISO)
transient myeloproliferative syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-cotinine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
asbestos  (ISO)
atrazine  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beryllium sulfate  (ISO)
bifenthrin  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butanal  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroacetaldehyde  (ISO)
chlorpromazine  (EXP)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (EXP,ISO)
clodronic acid  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (EXP)
colforsin daropate hydrochloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (EXP)
DDE  (ISO)
dexamethasone  (EXP)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
etoposide  (ISO)
folic acid  (ISO)
hydroxyurea  (ISO)
indometacin  (ISO)
irinotecan  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead nitrate  (ISO)
leflunomide  (ISO)
malathion  (ISO)
medroxyprogesterone acetate  (ISO)
metformin  (EXP)
methapyrilene  (ISO)
N,N-diethyl-m-toluamide  (EXP)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
permethrin  (EXP,ISO)
quercetin  (EXP)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
tamibarotene  (ISO)
tamoxifen  (ISO)
Tesaglitazar  (EXP)
testosterone  (EXP,ISO)
tetrachloromethane  (EXP)
topotecan  (EXP)
trichloroethene  (ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
tungsten  (ISO)
Tungsten carbide  (ISO)
undecane  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
warfarin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
behavioral response to pain  (ISO)
cellular response to transforming growth factor beta stimulus  (ISO)
central nervous system development  (ISO)
chondrocyte differentiation  (IBA)
definitive hemopoiesis  (ISO)
embryonic hemopoiesis  (ISO)
hair follicle morphogenesis  (ISO)
hemopoiesis  (IBA,ISO)
in utero embryonic development  (ISO)
liver development  (ISO)
myeloid cell differentiation  (ISO)
myeloid leukocyte differentiation  (ISO)
myeloid progenitor cell differentiation  (ISO)
negative regulation of CD4-positive, alpha-beta T cell differentiation  (ISO,ISS)
negative regulation of cell population proliferation  (ISO)
negative regulation of granulocyte differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO,ISS)
negative regulation of transcription, DNA-templated  (ISO)
neuron development  (ISO)
neuron differentiation  (IBA,ISO)
neuron fate commitment  (ISO)
ossification  (IBA)
ovulation  (IEP)
positive regulation of angiogenesis  (ISO,ISS)
positive regulation of CD8-positive, alpha-beta T cell differentiation  (ISO,ISS)
positive regulation of cell maturation  (ISO)
positive regulation of granulocyte differentiation  (ISO,ISS)
positive regulation of interferon-gamma production  (ISO)
positive regulation of interleukin-2 production  (ISO)
positive regulation of progesterone secretion  (IMP)
positive regulation of transcription by RNA polymerase II  (IMP,ISO)
positive regulation of transcription, DNA-templated  (IEA,IMP,ISO,ISS)
regulation of cell differentiation  (IBA)
regulation of hair follicle cell proliferation  (ISO)
regulation of signal transduction  (ISO)
regulation of T cell anergy  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (ISO)
response to denervation involved in regulation of muscle adaptation  (IEP)
response to retinoic acid  (ISO)
skeletal system development  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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4. Chen CY, etal., Br J Haematol. 2007 Nov;139(3):405-14.
5. Cho EK, etal., Korean J Intern Med. 2003 Mar;18(1):13-20.
6. Choi SJ, etal., Blood. 2003 May 15;101(10):3778-83. Epub 2003 Jan 30.
7. Daino K, etal., Int J Cancer. 2018 Jul 15;143(2):343-354. doi: 10.1002/ijc.31309. Epub 2018 Feb 23.
8. Edfeldt K, etal., Endocr Relat Cancer. 2011 Jul 11;18(4):479-89. doi: 10.1530/ERC-10-0256. Print 2011 Aug.
9. Fijneman RJ, etal., Cancer Sci. 2012 Mar;103(3):593-9. doi: 10.1111/j.1349-7006.2011.02189.x. Epub 2012 Jan 19.
10. Ford AM, etal., Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4584-8.
11. Gattenlohner S, etal., Am J Pathol 2003 Sep;163(3):1081-90.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. GOA data from the GO Consortium
14. Gonzalez de Aguilar JL, etal., Physiol Genomics. 2008 Jan 17;32(2):207-18. Epub 2007 Nov 13.
15. Grossmann V, etal., Haematologica. 2011 Dec;96(12):1874-7. doi: 10.3324/haematol.2011.043919. Epub 2011 Aug 9.
16. Growney JD, etal., Blood. 2005 Jul 15;106(2):494-504. Epub 2005 Mar 22.
17. Haley KJ, etal., Am J Physiol Lung Cell Mol Physiol. 2011 Nov;301(5):L693-701. Epub 2011 Jul 29.
18. Ishikawa R, etal., Jpn J Clin Oncol. 2016 Feb;46(2):185-9. doi: 10.1093/jjco/hyv187. Epub 2015 Dec 18.
19. Jo M and Curry TE Jr, Mol Endocrinol. 2006 Sep;20(9):2156-72. Epub 2006 May 4.
20. Jung J, etal., BMC Proc. 2009 Dec 15;3 Suppl 7:S76.
21. Kara M, etal., Gene. 2015 Aug 1;567(1):81-6. doi: 10.1016/j.gene.2015.04.065. Epub 2015 Apr 27.
22. Komlosi K, etal., Clin Exp Rheumatol. 2008 Jan-Feb;26(1):61-6.
23. Konno R, etal., Am J Reprod Immunol. 2007 Oct;58(4):330-43.
24. Kundu M, etal., Blood. 2005 Nov 15;106(10):3621-4. Epub 2005 Jul 28.
25. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
26. Liang M, etal., Cancer Manag Res. 2020 Dec 30;12:13451-13459. doi: 10.2147/CMAR.S272165. eCollection 2020.
27. Liang Z, etal., Biosci Rep. 2019 May 21;39(5). pii: BSR20181573. doi: 10.1042/BSR20181573. Print 2019 May 31.
28. Liu J, etal., Endocrinology. 2009 Jul;150(7):3291-300. doi: 10.1210/en.2008-1527. Epub 2009 Apr 2.
29. Ma W, etal., Birth Defects Res A Clin Mol Teratol. 2015 Sep;103(9):772-9. doi: 10.1002/bdra.23401. Epub 2015 Jul 14.
30. Massagué J, etal., Genes Dev. 2005 Dec 1;19(23):2783-810.
31. MGD data from the GO Consortium
32. Miyagawa K, etal., Anticancer Res. 2006 Sep-Oct;26(5B):3633-43.
33. Nam JY, etal., Transl Oncol. 2018 Aug;11(4):836-844. doi: 10.1016/j.tranon.2018.04.007. Epub 2018 May 7.
34. Nariman-Saleh-Fam Z, etal., Pathol Oncol Res. 2020 Apr;26(2):681-692. doi: 10.1007/s12253-019-00579-3. Epub 2019 Jan 21.
35. NCBI rat LocusLink and RefSeq merged data July 26, 2002
36. OMIM Disease Annotation Pipeline
37. Orozco G, etal., J Rheumatol. 2006 Jul;33(7):1235-9.
38. Patel A, etal., Neurosci Lett. 2011 Jan 7;487(2):144-8. Epub 2010 Oct 12.
39. Pipeline to import KEGG annotations from KEGG into RGD
40. Preudhomme C, etal., Blood. 2000 Oct 15;96(8):2862-9.
41. Ramsey J, etal., J Cell Physiol. 2018 Apr;233(4):3487-3497. doi: 10.1002/jcp.26201. Epub 2017 Nov 1.
42. Reichard KK, etal., Mod Pathol. 2011 Dec;24(12):1606-11. doi: 10.1038/modpathol.2011.118. Epub 2011 Aug 5.
43. RGD automated data pipeline
44. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
45. RGD automated import pipeline for gene-chemical interactions
46. RGD comprehensive gene curation
47. Ross S and Hill CS, Int J Biochem Cell Biol. 2008;40(3):383-408. Epub 2007 Oct 7.
48. Roulston D, etal., Blood. 1998 Oct 15;92(8):2879-85.
49. Sakakura C, etal., Int J Cancer. 2005 Jan 10;113(2):221-8. doi: 10.1002/ijc.20551.
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51. Shintaku Y, etal., Cells Tissues Organs. 2011;194(1):38-48. doi: 10.1159/000322557. Epub 2011 Jan 22.
52. Takata Y, etal., J Hum Genet. 2008;53(2):163-73. Epub 2007 Dec 18.
53. Tang JL, etal., Blood. 2009 Dec 17;114(26):5352-61. doi: 10.1182/blood-2009-05-223784. Epub 2009 Oct 6.
54. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
55. Ugarte GD, etal., J Cell Physiol. 2012 Apr;227(4):1645-52. doi: 10.1002/jcp.22882.
56. Wang T, etal., PLoS One. 2011;6(12):e28908. Epub 2011 Dec 21.
57. Wong WF, etal., J Immunol. 2012 May 2.
58. Wotton S, etal., Cancer Res. 2002 Dec 15;62(24):7181-5.
59. Yanagida M, etal., Oncogene. 2005 Jun 30;24(28):4477-85.
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Additional References at PubMed
PMID:7774816   PMID:7862156   PMID:8413232   PMID:9199349   PMID:10207087   PMID:10207104   PMID:10856244   PMID:10943840   PMID:11742995   PMID:12217689   PMID:12551949   PMID:12807883  
PMID:14970218   PMID:15240886   PMID:15389629   PMID:16174759   PMID:16446141   PMID:17011173   PMID:17377532   PMID:18439490   PMID:19090621   PMID:19182774   PMID:20972335   PMID:21151104  
PMID:21464233   PMID:21873977   PMID:22082260   PMID:23018770   PMID:23861879   PMID:24582971   PMID:25834056  


Genomics

Comparative Map Data
Runx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21131,839,880 - 32,074,427 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1131,843,764 - 32,074,542 (-)Ensembl
Rnor_6.01132,765,147 - 33,003,061 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1132,769,165 - 33,003,021 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01136,367,315 - 36,601,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41132,623,461 - 32,725,404 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11132,679,703 - 32,781,647 (-)NCBI
Celera1131,494,069 - 31,582,728 (-)NCBICelera
RH 3.4 Map11214.7RGD
Cytogenetic Map11q11NCBI
RUNX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2134,787,801 - 36,004,667 (-)EnsemblGRCh38hg38GRCh38
GRCh382134,787,801 - 35,049,334 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372136,160,098 - 36,421,599 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map21q22.12NCBI
HuRef2121,639,088 - 21,900,490 (-)NCBIHuRef
CHM1_12135,722,384 - 35,983,819 (-)NCBICHM1_1
Runx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391692,398,354 - 92,622,962 (-)NCBIGRCm39mm39
GRCm39 Ensembl1692,398,354 - 92,623,037 (-)Ensembl
GRCm381692,601,466 - 92,826,074 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1692,601,466 - 92,826,149 (-)EnsemblGRCm38mm10GRCm38
MGSCv371692,601,711 - 92,826,311 (-)NCBIGRCm37mm9NCBIm37
MGSCv361692,492,963 - 92,586,187 (-)NCBImm8
Celera1693,683,427 - 93,779,296 (-)NCBICelera
Cytogenetic Map16C4NCBI
cM Map1653.7NCBI
RUNX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13130,170,859 - 30,420,344 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3130,170,605 - 30,420,839 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3129,270,454 - 29,519,721 (-)NCBI
ROS_Cfam_1.03129,472,070 - 29,721,306 (-)NCBI
UMICH_Zoey_3.13129,337,954 - 29,586,748 (-)NCBI
UNSW_CanFamBas_1.03129,353,308 - 29,602,472 (-)NCBI
UU_Cfam_GSD_1.03129,843,623 - 30,092,833 (-)NCBI
RUNX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13198,371,835 - 198,638,189 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113198,371,835 - 198,635,648 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213208,205,560 - 208,304,379 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
D26532  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21131,843,898 - 31,844,078 (+)MAPPERmRatBN7.2
Rnor_6.01132,769,170 - 32,769,349NCBIRnor6.0
Rnor_5.01136,371,338 - 36,371,517UniSTSRnor5.0
RGSC_v3.41132,623,466 - 32,623,645UniSTSRGSC3.4
Celera1131,494,204 - 31,494,383UniSTS
Cytogenetic Map11q11UniSTS
RH94454  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21131,843,894 - 31,844,083 (+)MAPPERmRatBN7.2
Rnor_6.01132,769,166 - 32,769,354NCBIRnor6.0
Rnor_5.01136,371,334 - 36,371,522UniSTSRnor5.0
RGSC_v3.41132,623,462 - 32,623,650UniSTSRGSC3.4
Celera1131,494,200 - 31,494,388UniSTS
RH 3.4 Map11214.7UniSTS
Cytogenetic Map11q11UniSTS
AI462102  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21131,935,941 - 31,936,039 (+)MAPPERmRatBN7.2
Rnor_6.01132,859,334 - 32,859,431NCBIRnor6.0
Rnor_5.01136,461,473 - 36,461,570UniSTSRnor5.0
RGSC_v3.41132,725,914 - 32,726,011UniSTSRGSC3.4
Celera1131,583,238 - 31,583,335UniSTS
Cytogenetic Map11q11UniSTS
AW532993  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21131,899,854 - 31,900,033 (+)MAPPERmRatBN7.2
Rnor_6.01132,823,272 - 32,823,450NCBIRnor6.0
Rnor_5.01136,425,577 - 36,425,755UniSTSRnor5.0
RGSC_v3.41132,688,701 - 32,688,879UniSTSRGSC3.4
Celera1131,547,295 - 31,547,473UniSTS
RH 3.4 Map11205.5UniSTS
Cytogenetic Map11q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111647204744285911Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:30
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000002313
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 8 14 5 6
Low 3 31 37 29 5 29 8 11 39 35 27 5 8
Below cutoff 12 12 12 12 35 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002313   ⟹   ENSRNOP00000002313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1131,843,764 - 31,935,431 (-)Ensembl
Rnor_6.0 Ensembl1132,769,165 - 32,858,830 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084134   ⟹   ENSRNOP00000070750
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1131,843,764 - 32,074,542 (-)Ensembl
Rnor_6.0 Ensembl1132,769,219 - 33,003,021 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096598   ⟹   ENSRNOP00000080156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1131,843,764 - 31,935,431 (-)Ensembl
RefSeq Acc Id: NM_017325   ⟹   NP_059021
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21131,843,764 - 31,935,431 (-)NCBI
Rnor_6.01132,769,035 - 32,858,825 (-)NCBI
Rnor_5.01136,367,315 - 36,601,674 (-)NCBI
RGSC_v3.41132,623,461 - 32,725,404 (-)RGD
Celera1131,494,069 - 31,582,728 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768598   ⟹   XP_008766820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21131,839,880 - 32,074,427 (-)NCBI
Rnor_6.01132,765,147 - 33,003,061 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768599   ⟹   XP_008766821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21131,839,880 - 32,074,427 (-)NCBI
Rnor_6.01132,765,147 - 33,003,061 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017598053   ⟹   XP_017453542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21131,839,880 - 32,074,427 (-)NCBI
Rnor_6.01132,765,147 - 33,003,061 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088599   ⟹   XP_038944527
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21131,839,880 - 32,074,360 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_059021   ⟸   NM_017325
- UniProtKB: Q63046 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008766821   ⟸   XM_008768599
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008766820   ⟸   XM_008768598
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017453542   ⟸   XM_017598053
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JYQ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002313   ⟸   ENSRNOT00000002313
RefSeq Acc Id: ENSRNOP00000070750   ⟸   ENSRNOT00000084134
RefSeq Acc Id: XP_038944527   ⟸   XM_039088599
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000080156   ⟸   ENSRNOT00000096598
Protein Domains
Runt

Transcriptome

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

Promoters
RGD ID:13698070
Promoter ID:EPDNEW_R8594
Type:single initiation site
Name:Runx1_2
Description:runt-related transcription factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8595  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01132,858,782 - 32,858,842EPDNEW
RGD ID:13698075
Promoter ID:EPDNEW_R8595
Type:multiple initiation site
Name:Runx1_1
Description:runt-related transcription factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R8594  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01133,003,012 - 33,003,072EPDNEW

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)
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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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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)
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:2283 AgrOrtholog
Ensembl Genes ENSRNOG00000001704 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002313 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000070750 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002313 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000084134 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.720 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  4.10.770.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro AML1_Runt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  p53-like_TF_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  p53/RUNT-type_TF_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Runt_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Runx_central_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RunxI_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_Runt-rel_RUNX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:50662 UniProtKB/Swiss-Prot
NCBI Gene 50662 ENTREZGENE
PANTHER PTHR11950 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Runt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RunxI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB RUNX1 RGD
PhenoGen Runx1 PhenoGen
PIRSF TF_Runt-rel_RUNX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS ONCOGENEAML1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE RUNT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49417 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC220056
UniProt A0A0G2JYQ4 ENTREZGENE, UniProtKB/TrEMBL
  Q63046 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Runx1  RUNX family transcription factor 1  Runx1  runt-related transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-17 Runx1  runt-related transcription factor 1  Runx1  runt related transcription factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2001-06-26 Runx1  Runt related transcription factor 1      Symbol and Name updated to reflect Human and Mouse nomenclature 67952 APPROVED
2001-06-26 Cbfa2  Core-binding factor, runt domain, alpha subunit 2 (acute myeloid leukemia 1 oncogene)      Symbol and Name withdrawn 67952 WITHDRAWN

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog is responsible for a form of acute myeloid leukemia 634721
gene_function human homolog is a DNA binding protein 634721
gene_process involved in skeletal muscle gene regulation 634721