Orm1 (orosomucoid 1) - Rat Genome Database

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Gene: Orm1 (orosomucoid 1) Rattus norvegicus
Analyze
Symbol: Orm1
Name: orosomucoid 1
RGD ID: 67390
Description: Enables small molecule binding activity. Involved in several processes, including cellular response to hormone stimulus; cellular response to retinoic acid; and inflammatory response to antigenic stimulus. Located in extracellular space. Orthologous to several human genes including ORM1 (orosomucoid 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: AAG; AGP; Agpa1; alpha-1-acid glycoprotein; OMD; Orm; orosomucoid
RGD Orthologs
Human
Mouse
Chinchilla
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2576,766,637 - 76,776,149 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl576,772,941 - 76,776,154 (+)Ensembl
Rnor_6.0579,179,668 - 79,182,820 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl579,179,417 - 79,182,820 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0583,293,902 - 83,297,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4580,325,042 - 80,328,194 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1580,330,154 - 80,333,307 (+)NCBI
Celera575,706,909 - 75,710,061 (+)NCBICelera
RH 3.4 Map5578.8RGD
Cytogenetic Map5q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(2E,4E)-hexa-2,4-dienoic acid  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,7-dihydropurine-6-thione  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-nitro-1,2-phenylenediamine  (ISO)
7,12-dimethyltetraphene  (ISO)
8-anilinonaphthalene-1-sulfonic acid  (ISO)
acetamide  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
atrazine  (ISO)
azathioprine  (EXP)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
biphenyl-2-ol  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calcitriol  (ISO)
carbon nanotube  (EXP,ISO)
carmustine  (EXP)
chlorpromazine  (ISO)
cholic acid  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
cycloheximide  (EXP)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
DDE  (ISO)
dehydroepiandrosterone  (EXP)
dexamethasone  (EXP,ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
diclofenac  (EXP,ISO)
dimethyl sulfoxide  (EXP)
dipyridamole  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP)
elemental selenium  (EXP)
endosulfan  (EXP)
erythrosin B  (ISO)
flavonoids  (EXP)
furan  (EXP)
glafenine  (EXP)
graphite  (EXP)
hexachlorobenzene  (EXP)
indometacin  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
lidocaine  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (ISO)
mercaptopurine  (EXP)
methotrexate  (EXP)
methoxychlor  (EXP)
Mezerein  (ISO)
naphthalene  (ISO)
nimesulide  (EXP)
nitrofen  (EXP)
nitrofurantoin  (EXP)
O-methyleugenol  (ISO)
okadaic acid  (ISO)
oleanolic acid  (EXP)
oxycodone  (EXP)
ozone  (ISO)
palytoxin  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraoxon  (EXP)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP,ISO)
phenylmercury acetate  (ISO)
PhIP  (ISO)
phorone  (EXP)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propionic acid  (ISO)
propranolol  (EXP)
prostaglandin E2  (EXP)
purine-6-thiol  (EXP)
quartz  (EXP)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP,ISO)
rosuvastatin calcium  (ISO)
rotenone  (EXP)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
saccharin  (ISO)
SB 431542  (ISO)
selenium atom  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
streptozocin  (EXP)
styrene oxide  (ISO)
sulforaphane  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tin(II) chloride (anhydrous)  (ISO)
tioguanine  (EXP)
titanium dioxide  (EXP,ISO)
tremolite asbestos  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (EXP)
vitamin K  (EXP)
warfarin  (ISO)
zinc dichloride  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
extracellular space  (IBA,IDA,IEA,ISO)

Molecular Function

References

References - curated
1. Chauvelot-Moachon L, etal., J Pharmacol Exp Ther. 1988 Mar;244(3):1103-8.
2. Fischer A, etal., Biochem Biophys Res Commun. 2001 Jul 13;285(2):470-5.
3. Fournier T, etal., J Immunol. 1999 Sep 1;163(5):2883-90.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Hung DY, etal., Am J Physiol Gastrointest Liver Physiol. 2006 Feb;290(2):G343-51. Epub 2005 Sep 15.
6. Jensen SA J Gastroenterol Hepatol. 2001 May;16(5):525-30.
7. Kondraganti SR, etal., Chem Res Toxicol. 2005 Nov;18(11):1634-41.
8. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
9. Mejdoubi N, etal., Biochem Biophys Res Commun. 1999 Jan 8;254(1):93-9.
10. Mejdoubi N, etal., Hepatology. 1999 Jan;29(1):186-94.
11. Mouthiers A, etal., Biochim Biophys Acta. 2004 May 25;1678(2-3):135-44.
12. Projean D, etal., Pharm Res. 2005 Jan;22(1):62-70.
13. Remmers EF, etal., Transplant Proc 1999 May;31(3):1549-54.
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Ricca GA and Taylor JM, J Biol Chem 1981 Nov 10;256(21):11199-202.
18. Ricca GA, etal., Ann N Y Acad Sci 1982;389:88-105.
19. Ricca GA, etal., J Biol Chem 1981 Oct 25;256(20):10362-8.
20. Shimoishi K, etal., Eur J Pharmacol. 2001 May 25;420(2-3):91-5.
21. Tygstrup N, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):518-25.
Additional References at PubMed
PMID:2943986   PMID:3838547   PMID:8774350   PMID:15502707   PMID:16502470   PMID:17234708   PMID:21669904   PMID:22516433   PMID:22916107   PMID:23376485   PMID:23533145   PMID:23973664  
PMID:26740279   PMID:27068509   PMID:27559042   PMID:30707086   PMID:33134382  


Genomics

Comparative Map Data
Orm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2576,766,637 - 76,776,149 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl576,772,941 - 76,776,154 (+)Ensembl
Rnor_6.0579,179,668 - 79,182,820 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl579,179,417 - 79,182,820 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0583,293,902 - 83,297,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4580,325,042 - 80,328,194 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1580,330,154 - 80,333,307 (+)NCBI
Celera575,706,909 - 75,710,061 (+)NCBICelera
RH 3.4 Map5578.8RGD
Cytogenetic Map5q24NCBI
ORM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9114,323,098 - 114,326,479 (+)EnsemblGRCh38hg38GRCh38
GRCh389114,323,098 - 114,326,479 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379117,085,378 - 117,088,759 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369116,125,157 - 116,128,578 (+)NCBINCBI36hg18NCBI36
Build 349114,164,889 - 114,168,311NCBI
Celera987,732,978 - 87,736,434 (+)NCBI
Cytogenetic Map9q32NCBI
HuRef986,691,053 - 86,694,374 (+)NCBIHuRef
CHM1_19117,232,023 - 117,235,479 (+)NCBICHM1_1
Orm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39463,262,793 - 63,266,400 (+)NCBIGRCm39mm39
GRCm39 Ensembl463,262,797 - 63,266,400 (+)Ensembl
GRCm38463,344,556 - 63,348,163 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl463,344,560 - 63,348,163 (+)EnsemblGRCm38mm10GRCm38
MGSCv37463,005,600 - 63,009,196 (+)NCBIGRCm37mm9NCBIm37
MGSCv36462,830,927 - 62,834,523 (+)NCBImm8
Celera462,001,528 - 62,005,125 (+)NCBICelera
Cytogenetic Map4B3NCBI
cM Map433.96NCBI
Orm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541913,262,119 - 13,264,986 (-)NCBIChiLan1.0ChiLan1.0
ORM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11254,939,154 - 254,943,065 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21286,190,518 - 286,194,344 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap1q210-q212NCBI
LOC103218970
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11225,257,002 - 25,261,255 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1225,256,969 - 25,260,446 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603517,564,284 - 17,568,317 (+)NCBIVero_WHO_p1.0

Position Markers
D5Arb8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2576,775,487 - 76,775,749 (+)MAPPERmRatBN7.2
Rnor_6.0579,182,160 - 79,182,421NCBIRnor6.0
Rnor_5.0583,296,394 - 83,296,655UniSTSRnor5.0
RGSC_v3.4580,327,533 - 80,327,795RGDRGSC3.4
RGSC_v3.4580,327,534 - 80,327,795UniSTSRGSC3.4
RGSC_v3.1580,332,646 - 80,332,908RGD
Celera575,709,401 - 75,709,662UniSTS
Cytogenetic Map5q24UniSTS
RH94673  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2576,776,202 - 76,776,374 (+)MAPPERmRatBN7.2
Rnor_6.0579,182,875 - 79,183,046NCBIRnor6.0
Rnor_5.0583,297,109 - 83,297,280UniSTSRnor5.0
RGSC_v3.4580,328,249 - 80,328,420UniSTSRGSC3.4
Celera575,710,116 - 75,710,287UniSTS
RH 3.4 Map5578.8UniSTS
Cytogenetic Map5q24UniSTS
RH94674  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2576,772,592 - 76,772,772 (+)MAPPERmRatBN7.2
Rnor_6.0579,179,265 - 79,179,444NCBIRnor6.0
Rnor_5.0583,293,499 - 83,293,678UniSTSRnor5.0
RGSC_v3.4580,324,639 - 80,324,818UniSTSRGSC3.4
Celera575,706,506 - 75,706,685UniSTS
Cytogenetic Map5q24UniSTS
RH138430  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2576,774,739 - 76,776,114 (+)MAPPERmRatBN7.2
Rnor_6.0579,181,412 - 79,182,786NCBIRnor6.0
Rnor_5.0583,295,646 - 83,297,020UniSTSRnor5.0
RGSC_v3.4580,326,786 - 80,328,160UniSTSRGSC3.4
Celera575,708,653 - 75,710,027UniSTS
RH 3.4 Map11655.2UniSTS
Cytogenetic Map5q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1598845Mcs14Mammary carcinoma susceptibility QTL 140.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)57636977680813390Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:78
Count of miRNA genes:71
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000010454
Prediction methods:Microtar, 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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 8 3 3
Medium 19 18 18 2 5
Low 11 31 16 18 16 2 2 15 4 17 9 2
Below cutoff 20 4 4 1 4 6 6 12 22 17 2 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473978 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219945 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220896 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221848 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228353 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228466 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228667 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228800 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230009 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J00696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000161 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M10614 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M11329 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000010454   ⟹   ENSRNOP00000010454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl576,772,941 - 76,776,154 (+)Ensembl
Rnor_6.0 Ensembl579,179,417 - 79,182,820 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107594   ⟹   ENSRNOP00000081272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl576,772,989 - 76,776,154 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112746   ⟹   ENSRNOP00000081825
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl576,772,941 - 76,775,549 (+)Ensembl
RefSeq Acc Id: NM_053288   ⟹   NP_445740
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,772,996 - 76,776,148 (+)NCBI
Rnor_6.0579,179,668 - 79,182,820 (+)NCBI
Rnor_5.0583,293,902 - 83,297,054 (+)NCBI
RGSC_v3.4580,325,042 - 80,328,194 (+)RGD
Celera575,706,909 - 75,710,061 (+)RGD
Sequence:
RefSeq Acc Id: XM_039109268   ⟹   XP_038965196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,766,637 - 76,776,149 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445740   ⟸   NM_053288
- Peptide Label: precursor
- UniProtKB: P02764 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010454   ⟸   ENSRNOT00000010454
RefSeq Acc Id: XP_038965196   ⟸   XM_039109268
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000081825   ⟸   ENSRNOT00000112746
RefSeq Acc Id: ENSRNOP00000081272   ⟸   ENSRNOT00000107594
Protein Domains
Lipocln_cytosolic_FA-bd_dom

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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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)
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)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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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)
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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
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)
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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/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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:67390 AgrOrtholog
Ensembl Genes ENSRNOG00000007886 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000010454 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010454 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro A1A_glycop UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calycin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24614 UniProtKB/Swiss-Prot
NCBI Gene 24614 ENTREZGENE
Pfam Lipocalin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB ORM1 RGD
PhenoGen Orm1 PhenoGen
PIRSF AGP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS A1AGLPROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHF8_RAT UniProtKB/TrEMBL
  A1AG_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-28 Orm1  orosomucoid 1  Orm  Orosomucoid 1  Data Merged 628472 APPROVED
2003-04-09 Orm1  orosomucoid 1      Symbol and Name updated 629477 APPROVED
2003-03-06 Orm1  orosomucoid 1  Agpa1  alpha-1-acid glycoprotein  Data Merged 628472 PROVISIONAL
2002-06-10 Orm1        Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Orm  Orosomucoid 1      Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Agpa1  alpha-1-acid glycoprotein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression maybe induced during regeneration of hepatocytes after liver damage 61515
gene_expression maybe induced during regeneration of hepatocytes after liver damage 70249
gene_regulation induction regulated by glucocorticoids 729158