Dcn (decorin) - Rat Genome Database

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Gene: Dcn (decorin) Rattus norvegicus
Analyze
Symbol: Dcn
Name: decorin
RGD ID: 61895
Description: Enables collagen binding activity and protein N-terminus binding activity. Involved in several processes, including animal organ development; response to lipopolysaccharide; and wound healing. Located in extracellular matrix. Part of collagen type VI trimer. Biomarker of asthma; myocardial infarction; and obesity. Human ortholog(s) of this gene implicated in breast carcinoma; congenital stromal corneal dystrophy; and high grade glioma. Orthologous to human DCN (decorin); PARTICIPATES IN transforming growth factor-beta Smad dependent signaling pathway; transforming growth factor-beta superfamily mediated signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,2-dimethylhydrazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: bone proteoglycan II; dermatan sulfate proteoglycan-II (decorin); DSPG; MGC94682; PG-S2; PG40
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2732,281,252 - 32,321,291 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl732,281,252 - 32,321,270 (+)Ensembl
Rnor_6.0738,742,250 - 38,782,282 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,742,051 - 38,782,323 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0738,783,714 - 38,823,746 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4735,004,234 - 35,045,191 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1735,029,274 - 35,065,458 (+)NCBI
Celera729,318,664 - 29,358,499 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,5-hexanedione  (EXP)
2-butoxyethanol  (ISO)
2-methylcholine  (ISO)
2-nitrofluorene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
anthracen-2-amine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
benzylpenicillin  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bucladesine  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
calcium dichloride  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
chlordecone  (ISO)
chlorohydrocarbon  (EXP)
chloroprene  (EXP)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
entinostat  (ISO)
ethanol  (ISO)
folic acid  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
genistein  (EXP)
graphite  (EXP)
hydrogen peroxide  (ISO)
indinavir  (ISO)
indometacin  (ISO)
isoflavones  (EXP)
isoprenaline  (ISO)
L-methionine  (ISO)
lamivudine  (ISO)
levonorgestrel  (ISO)
losartan  (EXP)
medroxyprogesterone acetate  (ISO)
melphalan  (ISO)
mercury dichloride  (EXP)
methotrexate  (ISO)
methylmercury chloride  (EXP)
mifepristone  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenformin  (EXP)
phenobarbital  (ISO)
PhIP  (EXP)
potassium dichromate  (ISO)
retinyl acetate  (ISO)
Salinomycin  (ISO)
saquinavir  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
sulforaphane  (ISO)
sulindac  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (EXP,ISO)
testosterone undecanoate  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
Thiotepa  (ISO)
thyroxine  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trichloroethene  (EXP)
triclosan  (ISO)
troglitazone  (ISO)
Tungsten carbide  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vitamin E  (ISO)
zidovudine  (ISO)

References

References - curated
1. Asundi VK and Dreher KL, Eur J Cell Biol 1992 Dec;59(2):314-21.
2. Batbayal T, etal., Connect Tissue Res. 2006;47(4):235-41.
3. Biglari A, etal., Cancer Gene Ther. 2004 Nov;11(11):721-32.
4. Bolton K, etal., Int J Obes (Lond). 2008 Jul;32(7):1113-21. Epub 2008 Apr 15.
5. Chen CP, etal., Placenta. 2007 Feb-Mar;28(2-3):97-106. Epub 2006 Apr 21.
6. De Cosmo S, etal., Nephron. 2002 Sep;92(1):72-6.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Goldoni S, etal., Am J Pathol. 2008 Sep;173(3):844-55. Epub 2008 Aug 7.
10. Jeansson M, etal., Diabetologia. 2006 Sep;49(9):2200-9. Epub 2006 Jul 26.
11. Jones MR and Ravid K, J Biol Chem. 2004 Feb 13;279(7):5306-13. Epub 2003 Nov 22.
12. Knoll KE, etal., Physiol Genomics. 2005 Apr 14;21(2):222-9. Epub 2005 Feb 15.
13. MGD data from the GO Consortium
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. Nishimura T, etal., Biochem Biophys Res Commun. 2007 Oct 5;361(4):896-902. Epub 2007 Jul 30.
16. Ohno T, etal., Otolaryngol Head Neck Surg. 2009 May;140(5):757-61. Epub 2009 Feb 26.
17. OMIM Disease Annotation Pipeline
18. Pini L, etal., Am J Physiol Lung Cell Mol Physiol. 2006 Jun;290(6):L1052-8. Epub 2005 Dec 30.
19. Pipeline to import KEGG annotations from KEGG into RGD
20. RGD automated data pipeline
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Roberts HC, etal., Eur J Oral Sci. 2008 Jun;116(3):207-16.
24. Schaefer L, etal., FASEB J. 2001 Mar;15(3):559-61. Epub 2001 Jan 19.
25. Shi Y and Massague J, Cell. 2003 Jun 13;113(6):685-700.
26. Simkhovich BZ, etal., Arch Biochem Biophys. 2003 Dec 15;420(2):268-78.
27. Steer DL, etal., Dev Biol. 2004 Aug 15;272(2):310-27.
28. Suzuki K, etal., Exp Mol Pathol. 2005 Aug;79(1):68-73. Epub 2005 Mar 29.
29. Tang M and Mao JJ, Cell Tissue Res. 2006 Jun;324(3):467-74. Epub 2006 Mar 7.
30. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
31. Toeda K, etal., Mol Cell Biochem. 2005 Dec;280(1-2):47-56.
32. Wiberg C, etal., J Biol Chem 2003 Sep 26;278(39):37698-704.
33. Williams KJ, etal., Am J Pathol. 2007 Nov;171(5):1441-50. Epub 2007 Sep 20.
34. Zhang J, etal., Am J Physiol Endocrinol Metab. 2007 Jan 23;.
Additional References at PubMed
PMID:1390895   PMID:2764879   PMID:12477932   PMID:15489334   PMID:15811857   PMID:17933714   PMID:18346460   PMID:18518935   PMID:18757743   PMID:19753304   PMID:20551380   PMID:20665669  
PMID:22279542   PMID:22658674   PMID:22880013   PMID:23106098   PMID:23798385   PMID:23978385   PMID:24006456   PMID:25931508   PMID:26316108   PMID:27068509   PMID:27559042   PMID:28290552  
PMID:32731559  


Genomics

Comparative Map Data
Dcn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2732,281,252 - 32,321,291 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl732,281,252 - 32,321,270 (+)Ensembl
Rnor_6.0738,742,250 - 38,782,282 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,742,051 - 38,782,323 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0738,783,714 - 38,823,746 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4735,004,234 - 35,045,191 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1735,029,274 - 35,065,458 (+)NCBI
Celera729,318,664 - 29,358,499 (+)NCBICelera
Cytogenetic Map7q13NCBI
DCN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1291,140,484 - 91,183,217 (-)EnsemblGRCh38hg38GRCh38
GRCh381291,140,484 - 91,182,817 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371291,534,261 - 91,576,594 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361290,063,166 - 90,100,937 (-)NCBINCBI36hg18NCBI36
Build 341290,041,503 - 90,074,797NCBI
Celera1291,210,186 - 91,247,962 (-)NCBI
Cytogenetic Map12q21.33NCBI
HuRef1288,606,804 - 88,644,468 (-)NCBIHuRef
CHM1_11291,504,053 - 91,541,824 (-)NCBICHM1_1
Dcn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391097,315,362 - 97,354,025 (+)NCBIGRCm39mm39
GRCm39 Ensembl1097,315,471 - 97,354,005 (+)Ensembl
GRCm381097,479,500 - 97,518,163 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1097,479,609 - 97,518,143 (+)EnsemblGRCm38mm10GRCm38
MGSCv371096,942,134 - 96,980,796 (+)NCBIGRCm37mm9NCBIm37
MGSCv361096,912,055 - 96,947,839 (+)NCBImm8
Celera1099,450,242 - 99,488,904 (+)NCBICelera
Cytogenetic Map10C3NCBI
cM Map1050.27NCBI
Dcn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540528,332,545 - 28,372,323 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540528,335,493 - 28,371,912 (-)NCBIChiLan1.0ChiLan1.0
DCN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11291,994,129 - 92,031,258 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1291,994,129 - 92,031,413 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01288,678,791 - 88,715,677 (-)NCBIMhudiblu_PPA_v0panPan3
DCN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11531,833,492 - 31,887,699 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1531,833,746 - 31,877,417 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1532,288,559 - 32,331,901 (-)NCBI
ROS_Cfam_1.01532,489,958 - 32,545,511 (-)NCBI
UMICH_Zoey_3.11531,782,615 - 31,825,998 (-)NCBI
UNSW_CanFamBas_1.01531,846,288 - 31,889,835 (-)NCBI
UU_Cfam_GSD_1.01532,139,738 - 32,182,940 (-)NCBI
Dcn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494528,312,653 - 28,348,182 (+)NCBI
SpeTri2.0NW_0049365077,887,259 - 7,923,055 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DCN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl591,678,608 - 91,714,235 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1591,678,601 - 91,713,925 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2596,109,666 - 96,144,030 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DCN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11186,552,392 - 86,590,229 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1186,551,072 - 86,586,891 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037158,594,516 - 158,631,419 (+)NCBIVero_WHO_p1.0
Dcn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475015,466,938 - 15,517,475 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128134  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2732,320,889 - 32,321,071 (+)MAPPERmRatBN7.2
Rnor_6.0738,781,881 - 38,782,062NCBIRnor6.0
Rnor_5.0738,823,345 - 38,823,526UniSTSRnor5.0
RGSC_v3.4735,044,794 - 35,044,975UniSTSRGSC3.4
Celera729,358,102 - 29,358,283UniSTS
Cytogenetic Map7q13UniSTS
AU047216  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2732,304,350 - 32,304,586 (+)MAPPERmRatBN7.2
Rnor_6.0738,765,346 - 38,765,579NCBIRnor6.0
Rnor_5.0738,806,810 - 38,807,043UniSTSRnor5.0
RGSC_v3.4735,028,259 - 35,028,492UniSTSRGSC3.4
Celera729,341,758 - 29,341,991UniSTS
Cytogenetic Map7q13UniSTS
AA799757  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2732,320,714 - 32,320,911 (+)MAPPERmRatBN7.2
Rnor_6.0738,781,706 - 38,781,902NCBIRnor6.0
Rnor_5.0738,823,170 - 38,823,366UniSTSRnor5.0
RGSC_v3.4735,044,619 - 35,044,815UniSTSRGSC3.4
Celera729,357,927 - 29,358,123UniSTS
RH 3.4 Map7250.8UniSTS
Cytogenetic Map7q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:216
Count of miRNA genes:142
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000006070
Prediction methods:Microtar, 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 10
Medium 3 39 40 24 16 24 8 11 62 35 24 11 8
Low 4 17 17 3 17 12 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_024129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006241285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC083750 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210569 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219808 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223184 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ223539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229041 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ229786 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X59859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000006070   ⟹   ENSRNOP00000006070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl732,281,252 - 32,321,270 (+)Ensembl
Rnor_6.0 Ensembl738,742,051 - 38,782,323 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100641   ⟹   ENSRNOP00000088475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl732,284,655 - 32,321,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116661   ⟹   ENSRNOP00000086944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl732,284,389 - 32,321,270 (+)Ensembl
RefSeq Acc Id: NM_024129   ⟹   NP_077043
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2732,281,252 - 32,321,287 (+)NCBI
Rnor_6.0738,742,250 - 38,782,278 (+)NCBI
Rnor_5.0738,783,714 - 38,823,746 (+)NCBI
RGSC_v3.4735,004,234 - 35,045,191 (+)RGD
Celera729,318,664 - 29,358,499 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241285   ⟹   XP_006241347
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2732,283,998 - 32,321,291 (+)NCBI
Rnor_6.0738,744,993 - 38,782,282 (+)NCBI
Rnor_5.0738,783,714 - 38,823,746 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_077043   ⟸   NM_024129
- Peptide Label: precursor
- UniProtKB: Q01129 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241347   ⟸   XM_006241285
- Peptide Label: isoform X1
- UniProtKB: Q01129 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006070   ⟸   ENSRNOT00000006070
RefSeq Acc Id: ENSRNOP00000086944   ⟸   ENSRNOT00000116661
RefSeq Acc Id: ENSRNOP00000088475   ⟸   ENSRNOT00000100641

Transcriptome

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

Promoters
RGD ID:13695161
Promoter ID:EPDNEW_R5686
Type:initiation region
Name:Dcn_1
Description:decorin
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_6.0738,742,099 - 38,742,159EPDNEW

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)
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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/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)
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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
LEXF2B/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
LEXF3/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
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)
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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
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)
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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
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)
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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
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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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)
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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:61895 AgrOrtholog
Ensembl Genes ENSRNOG00000004554 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000006070 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006070 UniProtKB/Swiss-Prot
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7192499 IMAGE-MGC_LOAD
InterPro Decorin UniProtKB/Swiss-Prot
  Leu-rich_rpt UniProtKB/Swiss-Prot
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot
  LRR_dom_sf UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
  SLRP_I_decor/aspor/byglycan UniProtKB/Swiss-Prot
KEGG Report rno:29139 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94682 IMAGE-MGC_LOAD
NCBI Gene 29139 ENTREZGENE
PANTHER PTHR45712:SF14 UniProtKB/Swiss-Prot
Pfam LRR_8 UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
PhenoGen Dcn PhenoGen
PIRSF SLRP_I UniProtKB/Swiss-Prot
PROSITE LRR UniProtKB/Swiss-Prot
SMART LRR_TYP UniProtKB/Swiss-Prot
  LRRNT UniProtKB/Swiss-Prot
TIGR TC204131
UniProt PGS2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Dcn  decorin      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction may act in complex with matrilin-1 to link collagen VI microfibrils and aggrecan or collagen II 728372