B2m (beta-2 microglobulin) - Rat Genome Database

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Gene: B2m (beta-2 microglobulin) Rattus norvegicus
Analyze
Symbol: B2m
Name: beta-2 microglobulin
RGD ID: 2189
Description: Predicted to have protein homodimerization activity. Involved in response to cadmium ion and response to drug. Localizes to extracellular space. Biomarker of acute kidney failure; pyelonephritis; and ureteral obstruction. Human ortholog(s) of this gene implicated in arthritis; familial visceral amyloidosis; immunodeficiency 43; and inflammatory bowel disease. Orthologous to human B2M (beta-2-microglobulin); PARTICIPATES IN interleukin-12 signaling pathway; antigen processing and presentation pathway; INTERACTS WITH 1,3-dinitrobenzene; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Beta-2-microglobulin; beta-2-microglobulin C-terminal fragment (55 AA)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23109,095,740 - 109,101,764 (+)NCBI
Rnor_6.0 Ensembl3114,087,287 - 114,093,309 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03114,087,287 - 114,093,311 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03120,627,499 - 120,633,523 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43108,927,919 - 108,932,718 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13108,833,491 - 108,838,291 (+)NCBI
Celera3107,993,988 - 108,000,012 (+)NCBICelera
RH 3.4 Map3954.3RGD
Cytogenetic Map3q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (IEP,ISO)
AGAT deficiency  (ISO)
Albuminuria  (ISO)
arteriosclerosis  (ISO)
arthritis  (ISO)
autoimmune disease  (ISO)
Bloom syndrome  (ISO)
carotid artery disease  (ISO)
cataract  (ISO)
colon cancer  (ISO)
Colorectal Neoplasms  (ISO)
diffuse large B-cell lymphoma  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
encephalomyelitis  (ISO)
esophagus squamous cell carcinoma  (ISO)
Experimental Autoimmune Encephalomyelitis  (ISO)
Experimental Liver Cirrhosis  (IEP)
familial visceral amyloidosis  (ISO)
gastric adenocarcinoma  (ISO)
head and neck squamous cell carcinoma  (ISO)
heart disease  (ISO)
hemochromatosis  (ISS)
hereditary spastic paraplegia 11  (ISO)
Hypergammaglobulinemia  (ISO)
hypertension  (ISO)
Hypoproteinemia  (ISO)
immunodeficiency 43  (ISO)
inflammatory bowel disease  (ISO)
kidney disease  (ISO)
Knee Osteoarthritis  (ISO)
lung adenocarcinoma  (ISO)
lung oat cell carcinoma  (ISO)
lung small cell carcinoma  (ISO)
lung squamous cell carcinoma  (ISO)
lymphoproliferative syndrome  (ISO)
measles  (ISO)
melanoma  (ISO)
multiple myeloma  (ISO)
non-Hodgkin lymphoma  (ISO)
obesity  (ISO)
ovarian serous cystadenocarcinoma  (ISO)
Paraproteinemias  (ISO)
Parkinson's disease  (ISO)
peripheral artery disease  (ISO)
peripheral T-cell lymphoma  (ISO)
plasma cell neoplasm  (ISO)
plasmacytoma  (ISO)
Prostatic Neoplasms  (ISO)
proteinuria  (ISO)
pyelonephritis  (IEP)
skin melanoma  (ISO)
Spondylarthritis  (ISO)
Systemic Inflammatory Response Syndrome  (ISO)
type 1 diabetes mellitus  (ISO)
type 2 diabetes mellitus  (ISO)
ureteral obstruction  (IEP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,3-dinitrobenzene  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
3-phenylprop-2-enal  (ISO)
4-hydroxynon-2-enal  (ISO)
4-tert-Octylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
adefovir  (EXP)
aldehydo-D-ribose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
anthocyanin  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
asbestos  (ISO)
atenolol  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A5  (ISO)
bortezomib  (ISO)
butyric acid  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
cerium trichloride  (ISO)
chloropicrin  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (ISO)
cytarabine  (ISO)
D-ribofuranose  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
entinostat  (ISO)
ethanol  (ISO)
eugenol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (EXP)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP,ISO)
glafenine  (EXP)
Hexachloro-1,3-butadiene  (EXP)
hydrogen peroxide  (ISO)
ifosfamide  (ISO)
irinotecan  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
L-ascorbic acid  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
mercury dichloride  (ISO)
metformin  (EXP)
methylmercury chloride  (ISO)
methylparaben  (ISO)
muramyl dipeptide  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
nitric oxide  (ISO)
nitroglycerin  (ISO)
ozone  (ISO)
p-tert-Amylphenol  (EXP)
p-toluidine  (EXP)
pamidronate  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
phlorizin  (ISO)
phosphoramide mustard  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
sarin  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sodium chromate  (EXP)
sodium dichromate  (ISO)
sodium fluoride  (EXP)
streptozocin  (EXP)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
tobramycin  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
trovafloxacin  (ISO)
uranium atom  (ISO)
urea  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
amyloid fibril formation  (ISO)
antibacterial humoral response  (ISO)
antigen processing and presentation of endogenous peptide antigen via MHC class I  (ISO)
antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent  (ISO)
antimicrobial humoral immune response mediated by antimicrobial peptide  (ISO)
cellular response to iron ion  (ISO)
cellular response to iron(III) ion  (ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to nicotine  (ISO)
defense response to Gram-negative bacterium  (ISO)
defense response to Gram-positive bacterium  (ISO)
immune response  (IEA)
innate immune response  (ISO)
iron ion homeostasis  (ISO)
iron ion transport  (ISO)
learning or memory  (ISO)
modulation of age-related behavioral decline  (ISO)
multicellular organism development  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of forebrain neuron differentiation  (ISO)
negative regulation of neurogenesis  (ISO)
negative regulation of neuron projection development  (ISO)
negative regulation of receptor binding  (ISO)
positive regulation of cellular senescence  (ISO)
positive regulation of ferrous iron binding  (ISO)
positive regulation of protein binding  (ISO)
positive regulation of receptor binding  (ISO)
positive regulation of receptor-mediated endocytosis  (ISO)
positive regulation of T cell cytokine production  (ISO)
positive regulation of T cell mediated cytotoxicity  (ISO)
positive regulation of transferrin receptor binding  (ISO)
protein homotetramerization  (ISO)
protein refolding  (ISO)
regulation of erythrocyte differentiation  (ISO)
regulation of iron ion transport  (ISO)
regulation of membrane depolarization  (ISO)
response to cadmium ion  (IEP)
response to drug  (IEP)
response to molecule of bacterial origin  (ISO)
retina homeostasis  (ISO)
T cell differentiation in thymus  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aksun SA, etal., Exp Clin Endocrinol Diabetes. 2004 Apr;112(4):195-200.
2. Amighi J, etal., Stroke. 2011 Jul;42(7):1826-33. Epub 2011 May 5.
3. Baekken M, etal., Nephrol Dial Transplant. 2008 Oct;23(10):3130-7. Epub 2008 May 9.
4. Csernus K, etal., Eur J Pediatr. 2005 Jan;164(1):44-9. Epub 2004 Oct 28.
5. Denic A, etal., Brain Pathol. 2012 Feb 15. doi: 10.1111/j.1750-3639.2012.00576.x.
6. Dihazi H, etal., Clin Chem. 2007 Sep;53(9):1636-45. Epub 2007 Jul 18.
7. Duek A, etal., Isr Med Assoc J. 2006 Dec;8(12):828-31.
8. Griffin DE, etal., J Infect Dis. 1992 Nov;166(5):1170-3.
9. Hamerski MG, etal., Clin Exp Obstet Gynecol. 2006;33(4):233-7.
10. Hamilton-Williams EE, etal., Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11533-8.
11. Kals J, etal., Scand J Clin Lab Invest. 2011 Jul;71(4):257-63. Epub 2011 Feb 14.
12. Koller BH, etal., Science 1990 Jun 8;248(4960):1227-30.
13. Koltun M, etal., Am J Physiol Heart Circ Physiol 2004 Nov 11;.
14. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
15. Linker RA, etal., Neurobiol Dis. 2005 Jun-Jul;19(1-2):218-28.
16. Matsumoto K, etal., Biochem Genet. 1986 Feb;24(1-2):93-102.
17. Mauxion F and Kress M, Nucleic Acids Res 1987 Sep 25;15(18):7638.
18. Melikoglu MA, etal., Ir J Med Sci. 2009 Jun;178(2):151-4. Epub 2008 Sep 16.
19. MGD data from the GO Consortium
20. Milia AF, etal., J Cell Mol Med. 2011 Feb;15(2):270-9. doi: 10.1111/j.1582-4934.2009.00984.x.
21. Mogi M, etal., J Neural Transm Park Dis Dement Sect. 1995;9(1):87-92.
22. NCBI rat LocusLink and RefSeq merged data July 26, 2002
23. Nishimaki S, etal., J Obstet Gynaecol Res. 2009 Jun;35(3):472-6.
24. Ohba K, etal., J Toxicol Sci. 2007 Feb;32(1):103-5.
25. OMIM Disease Annotation Pipeline
26. Ozer BA, etal., Ren Fail. 2005;27(3):247-53.
27. Pipeline to import KEGG annotations from KEGG into RGD
28. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
29. RGD automated data pipeline
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. RGD comprehensive gene curation
33. Sasaki TM, etal., Clin Transplant. 1997 Feb;11(1):29-33.
34. Smyth R, etal., Cell Biol Toxicol. 2009 Oct;25(5):499-512. Epub 2008 Sep 7.
35. Surquin M, etal., J Immunol 2002 Jul 1;169(1):500-6.
36. Tancheva S, etal., Folia Med (Plovdiv). 2011 Apr-Jun;53(2):63-8.
37. Tarakanova VL, etal., J Virol. 2005 Dec;79(23):14668-79.
38. Tran TM, etal., Arthritis Rheum. 2006 Apr;54(4):1317-27.
39. Tsuda H, etal., Clin Exp Nephrol. 2009 Dec;13(6):567-70. Epub 2009 Jun 18.
40. Wani MA, etal., Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5084-9. Epub 2006 Mar 20.
41. Xia X, etal., Yan Ke Xue Bao. 2001 Sep;17(3):180-2.
42. Young HY, etal., Transplantation. 2004 Aug 27;78(4):509-15.
43. Zumrutdal A, etal., Nephrology (Carlton). 2005 Oct;10(5):453-8.
Additional References at PubMed
PMID:1538753   PMID:2689174   PMID:2911353   PMID:7969498   PMID:9465039   PMID:9493268   PMID:9531620   PMID:9990067   PMID:10912502   PMID:11113132   PMID:11163232   PMID:12847084  
PMID:15505791   PMID:16299293   PMID:16502470   PMID:16920948   PMID:17108084   PMID:17929129   PMID:18353247   PMID:18579777   PMID:18776904   PMID:19056867   PMID:19172750   PMID:19199708  
PMID:19564620   PMID:19565478   PMID:19946888   PMID:20018625   PMID:20826442   PMID:21131979   PMID:21220305   PMID:21263072   PMID:21423176   PMID:21569201   PMID:22289140   PMID:22575645  
PMID:22664934   PMID:23144825   PMID:23376485   PMID:23533145   PMID:23580065   PMID:24006456   PMID:24643698   PMID:25187167   PMID:25766467   PMID:25865156   PMID:26147761   PMID:28213472  
PMID:28468825   PMID:28864206  


Genomics

Comparative Map Data
B2m
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23109,095,740 - 109,101,764 (+)NCBI
Rnor_6.0 Ensembl3114,087,287 - 114,093,309 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03114,087,287 - 114,093,311 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03120,627,499 - 120,633,523 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43108,927,919 - 108,932,718 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13108,833,491 - 108,838,291 (+)NCBI
Celera3107,993,988 - 108,000,012 (+)NCBICelera
RH 3.4 Map3954.3RGD
Cytogenetic Map3q35NCBI
B2M
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1544,711,487 - 44,718,851 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1544,711,487 - 44,718,877 (+)EnsemblGRCh38hg38GRCh38
GRCh381544,711,492 - 44,718,145 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371545,003,715 - 45,010,343 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361542,790,977 - 42,797,649 (+)NCBINCBI36hg18NCBI36
Build 341542,790,976 - 42,797,649NCBI
Celera1521,893,442 - 21,900,114 (+)NCBI
Cytogenetic Map15q21.1NCBI
HuRef1521,827,296 - 21,833,968 (+)NCBIHuRef
CHM1_11545,121,781 - 45,128,453 (+)NCBICHM1_1
B2m
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392121,978,168 - 121,983,563 (+)NCBIGRCm39mm39
GRCm39 Ensembl2121,978,167 - 121,983,564 (+)Ensembl
GRCm382122,147,687 - 122,153,082 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2122,147,686 - 122,153,083 (+)EnsemblGRCm38mm10GRCm38
MGSCv372121,973,423 - 121,978,818 (+)NCBIGRCm37mm9NCBIm37
MGSCv362121,839,128 - 121,844,523 (+)NCBImm8
Celera2123,294,935 - 123,300,323 (+)NCBICelera
Cytogenetic Map2E5NCBI
cM Map260.55NCBI
B2m
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541611,204,849 - 11,215,568 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541611,205,503 - 11,211,325 (+)NCBIChiLan1.0ChiLan1.0
B2M
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11541,836,321 - 41,842,991 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1541,836,345 - 41,842,991 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01523,668,108 - 23,674,791 (+)NCBIMhudiblu_PPA_v0panPan3
B2M
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13011,331,574 - 11,337,991 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3011,331,569 - 11,337,997 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3011,388,144 - 11,392,829 (+)NCBI
ROS_Cfam_1.03011,468,141 - 11,474,563 (+)NCBI
UMICH_Zoey_3.13011,375,114 - 11,379,792 (+)NCBI
UNSW_CanFamBas_1.03011,497,731 - 11,502,419 (+)NCBI
UU_Cfam_GSD_1.03011,616,856 - 11,621,737 (+)NCBI
B2m
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864089,798,404 - 89,807,593 (+)NCBI
SpeTri2.0NW_0049364717,646,504 - 7,655,656 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
B2M
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1126,835,143 - 126,981,582 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11126,837,721 - 126,844,043 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
B2M
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12638,331,818 - 38,338,785 (-)NCBI
ChlSab1.1 Ensembl2638,331,442 - 38,338,809 (-)Ensembl
B2m
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480411,514,728 - 11,521,625 (-)NCBI

Position Markers
RH127442  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23109,098,610 - 109,098,799 (+)MAPPER
Rnor_6.03114,090,158 - 114,090,346NCBIRnor6.0
Rnor_5.03120,630,370 - 120,630,558UniSTSRnor5.0
RGSC_v3.43108,930,777 - 108,930,965UniSTSRGSC3.4
Celera3107,996,859 - 107,997,047UniSTS
Cytogenetic Map3q35UniSTS
RH94575  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23109,100,346 - 109,100,532 (+)MAPPER
Rnor_6.03114,091,894 - 114,092,079NCBIRnor6.0
Rnor_5.03120,632,106 - 120,632,291UniSTSRnor5.0
RGSC_v3.43108,932,513 - 108,932,698UniSTSRGSC3.4
Celera3107,998,595 - 107,998,780UniSTS
RH 3.4 Map3954.3UniSTS
Cytogenetic Map3q35UniSTS
PMC18810P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01206,487,422 - 206,487,559NCBIRnor5.0
RGSC_v3.41187,303,086 - 187,303,222UniSTSRGSC3.4
Celera1180,278,983 - 180,279,119UniSTS
Cytogenetic Map18p11UniSTS
Cytogenetic Map3q35UniSTS
Cytogenetic Map1q22UniSTS
Cytogenetic Map8q24UniSTS
PMC350564P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01206,487,427 - 206,487,551NCBIRnor5.0
RGSC_v3.41187,303,091 - 187,303,214UniSTSRGSC3.4
Celera1180,278,988 - 180,279,111UniSTS
Cytogenetic Map18p11UniSTS
Cytogenetic Map3q35UniSTS
Cytogenetic Map1q22UniSTS
Cytogenetic Map8q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)310639528127023997Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)330114912123700444Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)345406058127023997Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)348562146115249962Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)351821836124513579Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)351822008120917851Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)354630948119830094Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)354630948119830094Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)362922868127023997Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)366711607119830094Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)366711607119830094Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)372672290127023997Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)372973445127023997Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)378700444123700444Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)383817637119509260Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)388910015133910015Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3100730984119830094Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3106900427119830094Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:172
Count of miRNA genes:126
Interacting mature miRNAs:144
Transcripts:ENSRNOT00000023017
Prediction methods:Microtar, Miranda, 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 4 1 14 9 13 9 5 9
Medium 1 42 44 32 6 32 8 11 74 35 36 2 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012512 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC112350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB714511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM032790 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM042487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM080788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210804 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211419 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212410 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225647 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225686 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226642 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227656 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230402 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231135 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231182 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231856 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ231894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232233 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232819 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232937 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232943 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ233849 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234349 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234581 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ234885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X16956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y00441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y08531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000023017   ⟹   ENSRNOP00000023017
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3114,087,287 - 114,093,309 (+)Ensembl
RefSeq Acc Id: NM_012512   ⟹   NP_036644
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23109,095,740 - 109,101,764 (+)NCBI
Rnor_6.03114,087,287 - 114,093,311 (+)NCBI
Rnor_5.03120,627,499 - 120,633,523 (+)NCBI
RGSC_v3.43108,927,919 - 108,932,718 (+)RGD
Celera3107,993,988 - 108,000,012 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_036644 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA34830 (Get FASTA)   NCBI Sequence Viewer  
  CAA68498 (Get FASTA)   NCBI Sequence Viewer  
  CAA69847 (Get FASTA)   NCBI Sequence Viewer  
  EDL80017 (Get FASTA)   NCBI Sequence Viewer  
  P07151 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036644   ⟸   NM_012512
- Peptide Label: precursor
- UniProtKB: P07151 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000023017   ⟸   ENSRNOT00000023017
Protein Domains
Ig-like C1-type

Transcriptome

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

Promoters
RGD ID:13692364
Promoter ID:EPDNEW_R2889
Type:multiple initiation site
Name:B2m_1
Description:beta-2 microglobulin
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_6.03114,087,275 - 114,087,335EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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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)
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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/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 (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2189 AgrOrtholog
Ensembl Genes ENSRNOG00000017123 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000023017 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023017 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
InterPro B2Microglobulin UniProtKB/Swiss-Prot
  Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig/MHC_CS UniProtKB/Swiss-Prot
  Ig_C1-set UniProtKB/Swiss-Prot
KEGG Report rno:24223 UniProtKB/Swiss-Prot
NCBI Gene 24223 ENTREZGENE
PANTHER PTHR19944:SF62 UniProtKB/Swiss-Prot
Pfam C1-set UniProtKB/Swiss-Prot
PharmGKB B2M RGD
PhenoGen B2m PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
  IG_MHC UniProtKB/Swiss-Prot
SMART IGc1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt B2MG_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 B2m  Beta-2-microglobulin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process mouse homolog is required for the normal expression of T cells 631787
gene_process mouse homolog is required for the assembly and surface expression of MHC class I molecules 631788