Gc (GC, vitamin D binding protein) - Rat Genome Database

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Gene: Gc (GC, vitamin D binding protein) Rattus norvegicus
Analyze
Symbol: Gc
Name: GC, vitamin D binding protein
RGD ID: 2667
Description: Enables vitamin D binding activity. Involved in several processes, including female pregnancy; lactation; and response to estradiol. Located in several cellular components, including axon; extracellular space; and perinuclear region of cytoplasm. Biomarker of brain ischemia and hepatocellular carcinoma. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); chronic obstructive pulmonary disease; hepatocellular carcinoma; human immunodeficiency virus infectious disease; and rheumatic fever. Orthologous to human GC (GC vitamin D binding protein); INTERACTS WITH 1-naphthyl isothiocyanate; 2,6-dinitrotoluene; 2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: DBP; DBP02; gc-globulin; group specific component; group-specific component; Group-specific component (vitamin D-binding protein); RATDBP02; VDB; Vdbp; vitamin D-binding protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   Scl11  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21418,632,146 - 18,667,563 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1418,632,135 - 18,667,567 (+)Ensembl
Rnor_6.01420,267,023 - 20,302,577 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1420,266,891 - 20,302,581 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01420,173,467 - 20,209,021 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41420,166,243 - 20,197,060 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11420,166,180 - 20,201,613 (+)NCBI
Celera1417,992,337 - 18,027,605 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bexarotene  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
calcitriol  (EXP,ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbon atom  (ISO)
carbon nanotube  (ISO)
chromium trinitrate  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (EXP,ISO)
diclofenac  (EXP)
doxorubicin  (EXP,ISO)
elemental carbon  (ISO)
ethanol  (ISO)
folic acid  (ISO)
furan  (EXP)
genistein  (EXP)
lead diacetate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
methylmercury(1+)  (EXP)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
nitrofen  (EXP)
O-methyleugenol  (ISO)
ochratoxin A  (EXP)
olanzapine  (ISO)
ouabain  (ISO)
p-toluidine  (EXP)
paracetamol  (EXP,ISO)
parathion  (ISO)
perfluorododecanoic acid  (EXP)
phenethyl caffeate  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
sarin  (EXP)
silicon dioxide  (EXP)
sodium arsenite  (ISO)
tacrolimus hydrate  (EXP,ISO)
terbufos  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
verapamil  (EXP)
vitamin D  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. Albrethsen J, etal., Biochim Biophys Acta. 2011 Oct;1814(10):1367-76. Epub 2011 Jun 6.
2. Albuquerque LM, etal., J Proteome Res. 2009 Dec;8(12):5431-41.
3. Bahr GM, etal., Immunology. 1989 May;67(1):126-8.
4. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
5. Borkowski J, etal., Postepy Hig Med Dosw (Online). 2008 Mar 3;62:103-9.
6. Bouillon R, etal., Endocrinology. 1978 Jun;102(6):1710-5.
7. Cooke NE J Biol Chem 1986 Mar 5;261(7):3441-50.
8. Daiger SP, etal., Proc Natl Acad Sci U S A. 1975 Jun;72(6):2076-80.
9. Di Bacco M, etal., Coll Antropol. 2002 Jun;26(1):77-84.
10. Doherty NS, etal., Electrophoresis. 1998 Feb;19(2):355-63.
11. Eales LJ, etal., Lancet. 1987 May 2;1(8540):999-1002.
12. Eloranta JJ, etal., Pharmacogenet Genomics. 2011 Sep;21(9):559-64.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. GOA data from the GO Consortium
15. Gressner OA, etal., Clin Chim Acta. 2009 Feb;400(1-2):86-90. Epub 2008 Oct 30.
16. Huang NF, etal., Am J Transl Res. 2011 Feb;3(2):139-48. Epub 2010 Nov 21.
17. Izmerov NF, etal., Cent Eur J Public Health. 2002 Jun;10(1-2):35-41.
18. Jimenez CR, etal., Mol Cell Proteomics. 2005 Feb;4(2):120-32. Epub 2004 Oct 25.
19. Jirikowski GF, etal., Histochem Cell Biol. 2009 Mar;131(3):365-70. Epub 2008 Nov 26.
20. Jung KH, etal., J Rheumatol. 2011 Oct;38(10):2224-9. Epub 2011 Aug 15.
21. Kurylowicz A, etal., Exp Clin Endocrinol Diabetes. 2006 Jun;114(6):329-35.
22. Laing CJ and Fraser DR, Br J Nutr. 2002 Aug;88(2):133-9.
23. Lee SH, etal., Am J Respir Crit Care Med. 2011 Sep 1;184(5):528-36.
24. Levy J, etal., J Endocrinol. 1984 Mar;100(3):265-9.
25. Lu YT, etal., Proteomics Clin Appl. 2008 Sep;2(9):1208-22. doi: 10.1002/prca.200800069. Epub 2008 Aug 7.
26. McLeod JF and Cooke NE, J Biol Chem 1989 Dec 25;264(36):21760-9.
27. MGD data from the GO Consortium
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Niino M, etal., J Neuroimmunol. 2002 Jun;127(1-2):177-9.
30. Nyomba BL, etal., Endocrinology. 1985 Jun;116(6):2483-8.
31. OMIM Disease Annotation Pipeline
32. Ongagna JC, etal., Clin Biochem. 2001 Feb;34(1):59-63.
33. Ottervald J, etal., J Proteomics. 2010 Apr 18;73(6):1117-32. Epub 2010 Jan 20.
34. Ouchi M, etal., Exp Eye Res. 2005 Aug;81(2):176-82.
35. Pani MA, etal., J Clin Endocrinol Metab. 2002 Jun;87(6):2564-7.
36. Peng Q, etal., PLoS One. 2014 Dec 26;9(12):e116026. doi: 10.1371/journal.pone.0116026. eCollection 2014.
37. Qin Z, etal., Cell Mol Neurobiol. 2009 Mar;29(2):203-10. Epub 2008 Sep 19.
38. Ray K, etal., J Biol Chem 1991 Apr 5;266(10):6221-9.
39. RGD automated data pipeline
40. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
41. RGD automated import pipeline for gene-chemical interactions
42. Rithidech KN, etal., Mult Scler. 2009 Apr;15(4):455-64.
43. Rozek W, etal., J Proteome Res. 2007 Nov;6(11):4189-99. Epub 2007 Oct 12.
44. Schellenberg D, etal., Am J Respir Crit Care Med. 1998 Mar;157(3 Pt 1):957-61.
45. Schiodt FV, etal., Scand J Gastroenterol. 2001 Sep;36(9):998-1003.
46. Sironi L, etal., Stroke. 2001 Mar;32(3):753-60.
47. Song YH, etal., J Biol Chem 1998 Oct 23;273(43):28408-18.
48. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
49. Tang WX, etal., Anal Biochem. 1996 Jun 1;237(2):245-51.
50. Verhaeghe J, etal., Endocrinology. 1986 Mar;118(3):1019-25.
51. Wang HY, etal., Nephrol Dial Transplant. 2010 Jun;25(6):1955-63. Epub 2010 Jan 6.
52. Yang MY, etal., Plast Reconstr Surg. 2014 Jan;133(1):59-68. doi: 10.1097/01.prs.0000439050.08733.cf.
Additional References at PubMed
PMID:3713442   PMID:11799400   PMID:12119014   PMID:15225763   PMID:16502470   PMID:22516433   PMID:23339019   PMID:23376485   PMID:23533145   PMID:31792309  


Genomics

Comparative Map Data
Gc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21418,632,146 - 18,667,563 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1418,632,135 - 18,667,567 (+)Ensembl
Rnor_6.01420,267,023 - 20,302,577 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1420,266,891 - 20,302,581 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01420,173,467 - 20,209,021 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41420,166,243 - 20,197,060 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11420,166,180 - 20,201,613 (+)NCBI
Celera1417,992,337 - 18,027,605 (+)NCBICelera
Cytogenetic Map14p22NCBI
GC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl471,741,696 - 71,804,041 (-)EnsemblGRCh38hg38GRCh38
GRCh38471,741,693 - 71,805,520 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37472,607,410 - 72,671,237 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36472,826,274 - 72,868,752 (-)NCBINCBI36hg18NCBI36
Build 34472,972,446 - 73,014,923NCBI
Celera469,964,129 - 70,006,624 (-)NCBI
Cytogenetic Map4q13.3NCBI
HuRef468,412,706 - 68,476,557 (-)NCBIHuRef
CHM1_1472,643,398 - 72,707,216 (-)NCBICHM1_1
Gc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39589,565,370 - 89,605,757 (-)NCBIGRCm39mm39
GRCm39 Ensembl589,565,381 - 89,605,757 (-)Ensembl
GRCm38589,417,511 - 89,457,898 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl589,417,522 - 89,457,898 (-)EnsemblGRCm38mm10GRCm38
MGSCv37589,846,547 - 89,886,790 (-)NCBIGRCm37mm9NCBIm37
MGSCv36590,492,721 - 90,532,964 (-)NCBImm8
Celera587,554,559 - 87,593,435 (-)NCBICelera
Cytogenetic Map5E1NCBI
cM Map544.32NCBI
Gc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554471,361,566 - 1,402,491 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554471,361,698 - 1,400,633 (+)NCBIChiLan1.0ChiLan1.0
GC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1458,749,384 - 58,792,073 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl458,729,236 - 58,792,073 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0452,431,196 - 52,473,762 (+)NCBIMhudiblu_PPA_v0panPan3
GC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11360,795,305 - 60,828,038 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1360,795,305 - 60,827,929 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1360,528,533 - 60,561,906 (-)NCBI
ROS_Cfam_1.01361,603,086 - 61,636,545 (-)NCBI
UMICH_Zoey_3.11361,215,897 - 61,249,598 (-)NCBI
UNSW_CanFamBas_1.01360,708,804 - 60,742,244 (-)NCBI
UU_Cfam_GSD_1.01361,856,182 - 61,889,922 (-)NCBI
Gc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528514,767,874 - 14,809,615 (+)NCBI
SpeTri2.0NW_0049365983,220,029 - 3,256,091 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl868,326,301 - 68,360,262 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1868,326,293 - 68,360,262 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2872,227,896 - 72,261,806 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1720,254,604 - 20,298,384 (-)NCBI
ChlSab1.1 Ensembl720,253,879 - 20,298,265 (-)Ensembl
Vero_WHO_p1.0NW_0236660842,553,410 - 2,596,840 (+)NCBI
Gc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248903,274,239 - 3,318,281 (-)NCBI

Position Markers
D14Mgh3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21418,631,345 - 18,631,470 (+)MAPPERmRatBN7.2
Rnor_6.01420,266,223 - 20,266,347NCBIRnor6.0
Rnor_5.01420,172,667 - 20,172,791UniSTSRnor5.0
RGSC_v3.41420,165,393 - 20,165,518RGDRGSC3.4
RGSC_v3.41420,165,394 - 20,165,518UniSTSRGSC3.4
RGSC_v3.11420,165,393 - 20,165,518RGD
Celera1417,991,537 - 17,991,661UniSTS
RH 3.4 Map14265.8UniSTS
RH 3.4 Map14265.8RGD
RH 2.0 Map14260.2RGD
Cytogenetic Map14p22UniSTS
D14Wox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21418,644,043 - 18,644,232 (+)MAPPERmRatBN7.2
Rnor_6.01420,278,921 - 20,279,109NCBIRnor6.0
Rnor_5.01420,185,365 - 20,185,553UniSTSRnor5.0
RGSC_v3.41420,178,091 - 20,178,280RGDRGSC3.4
RGSC_v3.41420,178,092 - 20,178,280UniSTSRGSC3.4
RGSC_v3.11420,178,091 - 20,178,280RGD
Celera1418,004,268 - 18,004,454UniSTS
RH 3.4 Map14264.4UniSTS
RH 3.4 Map14264.4RGD
RH 2.0 Map14263.7RGD
Cytogenetic Map14p22UniSTS
D14Arb17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21418,644,012 - 18,644,233 (+)MAPPERmRatBN7.2
Rnor_6.01420,278,890 - 20,279,110NCBIRnor6.0
Rnor_5.01420,185,334 - 20,185,554UniSTSRnor5.0
RGSC_v3.41420,178,060 - 20,178,281RGDRGSC3.4
RGSC_v3.41420,178,061 - 20,178,281UniSTSRGSC3.4
RGSC_v3.11420,178,060 - 20,178,281RGD
Celera1418,004,237 - 18,004,455UniSTS
SHRSP x BN Map146.9UniSTS
SHRSP x BN Map146.9RGD
Cytogenetic Map14p22UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141757341219726296Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:17
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000004174
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 33 33 27
Medium 1 17 14 14 2 2 1 9 2 3 2
Low 7 13 18 6 7 14 22 27 5 6
Below cutoff 3 4 1 10 4 9 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH002167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474060 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210683 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211064 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218396 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219081 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219314 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J05148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M12450 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004174   ⟹   ENSRNOP00000004174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1418,632,135 - 18,667,567 (+)Ensembl
Rnor_6.0 Ensembl1420,266,891 - 20,302,581 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098849   ⟹   ENSRNOP00000083512
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1418,642,699 - 18,658,586 (+)Ensembl
RefSeq Acc Id: NM_012564   ⟹   NP_036696
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21418,632,146 - 18,667,563 (+)NCBI
Rnor_6.01420,267,023 - 20,302,577 (+)NCBI
Rnor_5.01420,173,467 - 20,209,021 (+)NCBI
RGSC_v3.41420,166,243 - 20,197,060 (+)RGD
Celera1417,992,337 - 18,027,605 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036696   ⟸   NM_012564
- Peptide Label: precursor
- UniProtKB: Q68FY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004174   ⟸   ENSRNOT00000004174
RefSeq Acc Id: ENSRNOP00000083512   ⟸   ENSRNOT00000098849
Protein Domains
Albumin

Transcriptome

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

Promoters
RGD ID:13699237
Promoter ID:EPDNEW_R9761
Type:initiation region
Name:Gc_1
Description:GC, vitamin D binding protein
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_6.01420,267,014 - 20,267,074EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/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)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/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
ACI/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
BBDP/Wor (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
BN-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/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
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/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
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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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)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2667 AgrOrtholog
Ensembl Genes ENSRNOG00000003119 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004174 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004174 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7130137 IMAGE-MGC_LOAD
InterPro ALB/AFP/VDB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Serum_albumin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VitD-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VitD-bind_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24384 UniProtKB/TrEMBL
MGC_CLONE MGC:93612 IMAGE-MGC_LOAD
NCBI Gene 24384 ENTREZGENE
PANTHER PTHR11385 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11385:SF11 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Serum_albumin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VitD-bind_III UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gc PhenoGen
PRINTS SERUMALBUMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VITAMNDBNDNG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ALBUMIN_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ALBUMIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ALBUMIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48552 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P04276 ENTREZGENE
  Q68FY4 ENTREZGENE, UniProtKB/TrEMBL
  VTDB_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-03-07 Gc  GC, vitamin D binding protein  Gc  group specific component  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Gc  Group-specific component (vitamin D-binding protein)      Symbol and Name status set to approved 70586 APPROVED