Odc1 (ornithine decarboxylase 1) - Rat Genome Database

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Gene: Odc1 (ornithine decarboxylase 1) Rattus norvegicus
Analyze
Symbol: Odc1
Name: ornithine decarboxylase 1
RGD ID: 3227
Description: Exhibits ornithine decarboxylase activity. Involved in putrescine biosynthetic process. Localizes to perinuclear region of cytoplasm. Orthologous to human ODC1 (ornithine decarboxylase 1); PARTICIPATES IN polyamine metabolic pathway; putrescine metabolic pathway; spermidine metabolic pathway; INTERACTS WITH (+)-pilocarpine; (R)-noradrenaline; (S)-colchicine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Odc; ornithine decarboxylase; Ornitine decarboxylase; RNODC
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2640,329,831 - 40,336,444 (+)NCBI
Rnor_6.0 Ensembl642,852,683 - 42,859,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0642,852,529 - 42,859,142 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0652,565,188 - 52,571,773 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4641,309,211 - 41,315,796 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1641,312,265 - 41,318,665 (+)NCBI
Celera639,628,825 - 39,635,308 (+)NCBICelera
Cytogenetic Map6q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-pilocarpine  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-noradrenaline  (EXP)
(S)-(-)-perillyl alcohol  (ISO)
(S)-colchicine  (EXP,ISO)
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (EXP)
1,2-dibromoethane  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (EXP)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4,6-trinitrotoluene  (EXP)
2,4-dinitrobenzenesulfonic acid  (ISO)
2,4-dinitrotoluene  (EXP)
2,5-dihydroxybenzoic acid  (ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
2-nitrofluorene  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloroperbenzoic acid  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP,ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroperoxycyclophosphamide  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-methylthio-2-oxobutanoic acid  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acetaldehyde  (ISO)
acetylsalicylic acid  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (EXP)
alprenolol  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
aniline  (ISO)
apomorphine  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
Asimicin  (ISO)
bathocuproine disulfonic acid  (ISO)
belinostat  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzoates  (ISO)
Benzoyl peroxide  (ISO)
berberine  (EXP)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bucladesine  (ISO)
butanal  (ISO)
butyric acid  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloroform  (EXP)
chloropicrin  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
clenbuterol  (ISO)
clobetasol  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
clotrimazole  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (EXP)
cumene hydroperoxide  (ISO)
curcumin  (ISO)
cycloartenol  (ISO)
cycloheximide  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
Deguelin  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP)
Diallyl sulfide  (ISO)
diarsenic trioxide  (EXP,ISO)
diazepam  (EXP)
dibenz[a,h]anthracene  (ISO)
dibenzoylmethane  (ISO)
dibutyl phthalate  (ISO)
dichlorine  (EXP)
diethyl malate  (ISO)
diethylstilbestrol  (EXP)
dimethyl sulfoxide  (ISO)
dimethylarsinous acid  (ISO)
dioxygen  (EXP,ISO)
disodium selenite  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
ethanol  (EXP,ISO)
fenarimol  (EXP)
fenazaquin  (ISO)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
formic acid  (ISO)
fulvestrant  (EXP)
furan  (EXP,ISO)
gallic acid  (ISO)
gamma-hexachlorocyclohexane  (EXP)
geraniol  (ISO)
glafenine  (EXP)
glutathione  (ISO)
hexane  (EXP)
hydrogen peroxide  (ISO)
hydroxyl  (EXP)
Iopodic acid  (EXP)
iron atom  (ISO)
iron dextran  (ISO)
iron(0)  (ISO)
iron(III) nitrilotriacetate  (EXP)
isoprenaline  (ISO)
isotretinoin  (ISO)
L-methionine  (ISO)
leflunomide  (EXP)
lipopolysaccharide  (EXP)
mancozeb  (ISO)
masoprocol  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methiocarb  (EXP)
methoctramine tetrahydrochloride  (ISO)
methotrexate  (ISO)
methoxychlor  (EXP)
methyl methanesulfonate  (ISO)
metoprolol  (ISO)
metsulfuron methyl  (EXP)
Mezerein  (ISO)
miconazole  (ISO)
mirex  (EXP)
myriocin  (ISO)
N-acetyl-beta-D-glucosamine  (ISO)
N-acetyl-D-glucosamine  (ISO)
N-acetylsphingosine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nefazodone  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nimesulide  (EXP)
ochratoxin A  (ISO)
organophosphorus compound  (ISO)
ozone  (EXP)
paracetamol  (EXP,ISO)
paraquat  (ISO)
patulin  (ISO)
Pentagastrin  (EXP)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
perillyl alcohol  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (EXP,ISO)
phorbol 13-acetate 12-myristate  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
podophyllotoxin  (ISO)
potassium iodide  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
proanthocyanidin  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (EXP,ISO)
propiconazole  (ISO)
propranolol  (ISO)
prostaglandins E  (ISO)
putrescine  (EXP,ISO)
pyridaben  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
quinpirole  (ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
reserpine  (EXP,ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
rottlerin  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (EXP)
silicon dioxide  (ISO)
simazine  (EXP)
sodium fluoride  (ISO)
Soman  (EXP)
spermidine  (EXP,ISO)
spermine  (EXP,ISO)
succimer  (ISO)
sulfasalazine  (ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
teniposide  (ISO)
terbutaline  (EXP)
tert-butyl hydroperoxide  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
Testosterone propionate  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
thioacetamide  (EXP)
thyroxine  (EXP)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
Trenbolone  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (EXP)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vincaleukoblastine  (ISO)
vinclozolin  (EXP)
vitamin E  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Babal P, etal., Am J Physiol Lung Cell Mol Physiol 2002 Apr;282(4):L840-6.
2. Deng A, etal., Diabetes. 2003 May;52(5):1235-9.
3. Eloranta TO, etal., J Biochem. 1990 Oct;108(4):593-8.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Higaki I, etal., Hepatogastroenterology. 1999 May-Jun;46(27):1874-9.
7. Hillary RA and Pegg AE, Biochim Biophys Acta. 2003 Apr 11;1647(1-2):161-6.
8. KEGG
9. MGD data from the GO Consortium
10. NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. OMIM Disease Annotation Pipeline
12. Pendeville H, etal., Mol Cell Biol. 2001 Oct;21(19):6549-58.
13. Pipeline to import KEGG annotations from KEGG into RGD
14. Pipeline to import SMPDB annotations from SMPDB into RGD
15. RGD automated data pipeline
16. RGD automated import pipeline for gene-chemical interactions
17. Schipper RG, etal., J Histochem Cytochem. 1999 Nov;47(11):1395-404.
18. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
19. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
20. Tygstrup N, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):518-25.
21. van Kranen HJ, etal., Gene 1987;60(2-3):145-55.
22. van Steeg H, etal., Nucleic Acids Res 1988 Aug 25;16(16):8173-4.
23. Wallace HM, etal., Biochem J. 2003 Nov 15;376(Pt 1):1-14.
24. Wang JY, etal., Am J Physiol. 1992 Oct;263(4 Pt 1):G494-501.
25. Wen L, etal., J Biol Chem 1989 May 25;264(15):9016-21.
Additional References at PubMed
PMID:2006916   PMID:2365701   PMID:8328969   PMID:8889548   PMID:12452334   PMID:15489334   PMID:15616584   PMID:15989779   PMID:16138831   PMID:16548883   PMID:16916800   PMID:17673438  
PMID:17900240   PMID:17914980   PMID:18008394   PMID:18562630   PMID:19331812   PMID:19449338   PMID:20013009   PMID:20848911   PMID:22230191   PMID:24464033   PMID:24967154   PMID:28986097  


Genomics

Comparative Map Data
Odc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2640,329,831 - 40,336,444 (+)NCBI
Rnor_6.0 Ensembl642,852,683 - 42,859,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0642,852,529 - 42,859,142 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0652,565,188 - 52,571,773 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4641,309,211 - 41,315,796 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1641,312,265 - 41,318,665 (+)NCBI
Celera639,628,825 - 39,635,308 (+)NCBICelera
Cytogenetic Map6q16NCBI
ODC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl210,439,968 - 10,448,327 (-)EnsemblGRCh38hg38GRCh38
GRCh38210,439,968 - 10,448,327 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37210,580,094 - 10,588,453 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36210,497,959 - 10,505,904 (-)NCBINCBI36hg18NCBI36
Build 34210,531,105 - 10,539,051NCBI
Celera210,496,293 - 10,504,232 (-)NCBI
Cytogenetic Map2p25.1NCBI
HuRef210,432,740 - 10,440,685 (-)NCBIHuRef
CHM1_1210,509,892 - 10,518,046 (-)NCBICHM1_1
Odc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391217,594,809 - 17,601,503 (+)NCBIGRCm39mm39
GRCm39 Ensembl1217,594,795 - 17,601,506 (+)Ensembl
GRCm381217,544,808 - 17,551,502 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1217,544,794 - 17,551,505 (+)EnsemblGRCm38mm10GRCm38
MGSCv371217,551,679 - 17,558,308 (+)NCBIGRCm37mm9NCBIm37
MGSCv361217,570,570 - 17,576,557 (+)NCBImm8
Celera1217,867,446 - 17,874,062 (+)NCBICelera
Cytogenetic Map12A1.1- A1.2NCBI
cM Map128.11NCBI
Odc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554875,603,722 - 5,608,386 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554875,603,722 - 5,608,386 (-)NCBIChiLan1.0ChiLan1.0
ODC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A10,598,125 - 10,607,152 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A10,598,125 - 10,607,152 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A10,443,308 - 10,451,412 (-)NCBIMhudiblu_PPA_v0panPan3
ODC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1177,368,699 - 7,376,970 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl177,369,232 - 7,376,975 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha177,294,922 - 7,302,658 (-)NCBI
ROS_Cfam_1.0177,467,169 - 7,474,927 (-)NCBI
UMICH_Zoey_3.1177,357,671 - 7,365,425 (-)NCBI
UNSW_CanFamBas_1.0177,360,253 - 7,368,002 (-)NCBI
UU_Cfam_GSD_1.0177,374,368 - 7,382,137 (-)NCBI
Odc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629251,826,681 - 51,831,970 (-)NCBI
SpeTri2.0NW_0049365326,581,717 - 6,587,116 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ODC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3126,078,418 - 126,132,577 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13126,087,013 - 126,095,644 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ODC1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11497,173,338 - 97,182,253 (+)NCBI
Odc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248654,851,565 - 4,858,868 (+)NCBI

Position Markers
D6Arb8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,335,037 - 40,335,394 (+)MAPPER
Rnor_6.0642,857,736 - 42,858,092NCBIRnor6.0
Rnor_5.0652,570,367 - 52,570,723UniSTSRnor5.0
RGSC_v3.4641,314,390 - 41,314,746UniSTSRGSC3.4
Celera639,633,902 - 39,634,258UniSTS
Cytogenetic Map6q16UniSTS
D6Wox24  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,335,165 - 40,335,238 (+)MAPPER
Rnor_6.0642,857,864 - 42,857,936NCBIRnor6.0
Rnor_5.0652,570,495 - 52,570,567UniSTSRnor5.0
RGSC_v3.4641,314,518 - 41,314,590UniSTSRGSC3.4
Celera639,634,030 - 39,634,102UniSTS
Cytogenetic Map6q16UniSTS
RH128139  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,336,112 - 40,336,298 (+)MAPPER
Rnor_6.0642,858,811 - 42,858,996NCBIRnor6.0
Rnor_5.0652,571,442 - 52,571,627UniSTSRnor5.0
RGSC_v3.4641,315,465 - 41,315,650UniSTSRGSC3.4
Celera639,634,977 - 39,635,162UniSTS
RH 3.4 Map6197.2UniSTS
Cytogenetic Map6q16UniSTS
RH94600  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,332,133 - 40,332,291 (+)MAPPER
Rnor_6.0642,854,832 - 42,854,989NCBIRnor6.0
Rnor_5.0652,567,463 - 52,567,620UniSTSRnor5.0
RGSC_v3.4641,311,486 - 41,311,643UniSTSRGSC3.4
Celera639,630,998 - 39,631,155UniSTS
Cytogenetic Map6q16UniSTS
ODC1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,332,839 - 40,333,224 (+)MAPPER
Rnor_6.0642,855,538 - 42,855,922NCBIRnor6.0
Rnor_5.0652,568,169 - 52,568,553UniSTSRnor5.0
RGSC_v3.4641,312,192 - 41,312,576UniSTSRGSC3.4
Celera639,631,704 - 39,632,088UniSTS
Cytogenetic Map6q16UniSTS
PMC99801P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,332,327 - 40,332,582 (+)MAPPER
Rnor_6.0642,855,026 - 42,855,280NCBIRnor6.0
Rnor_5.0652,567,657 - 52,567,911UniSTSRnor5.0
RGSC_v3.4641,311,680 - 41,311,934UniSTSRGSC3.4
Celera639,631,192 - 39,631,446UniSTS
Cytogenetic Map6q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)61941788764417887Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62151530265784818Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63425776653855198Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63626028860606186Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63819641260606431Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:254
Count of miRNA genes:167
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000007259
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
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007259   ⟹   ENSRNOP00000007259
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl642,854,888 - 42,858,759 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079185   ⟹   ENSRNOP00000073349
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl642,852,683 - 42,859,927 (+)Ensembl
RefSeq Acc Id: NM_001302083   ⟹   NP_001289012
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2640,329,961 - 40,336,444 (+)NCBI
Rnor_6.0642,852,659 - 42,859,142 (+)NCBI
Celera639,628,825 - 39,635,308 (+)NCBI
Sequence:
RefSeq Acc Id: NM_012615   ⟹   NP_036747
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2640,329,961 - 40,336,444 (+)NCBI
Rnor_6.0642,852,659 - 42,859,142 (+)NCBI
Rnor_5.0652,565,188 - 52,571,773 (+)NCBI
RGSC_v3.4641,309,211 - 41,315,796 (+)RGD
Celera639,628,825 - 39,635,308 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239907   ⟹   XP_006239969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2640,329,849 - 40,336,067 (+)NCBI
Rnor_6.0642,852,573 - 42,859,142 (+)NCBI
Rnor_5.0652,565,188 - 52,571,773 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006239908   ⟹   XP_006239970
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2640,329,849 - 40,336,067 (+)NCBI
Rnor_6.0642,852,573 - 42,859,142 (+)NCBI
Rnor_5.0652,565,188 - 52,571,773 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017594030   ⟹   XP_017449519
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2640,329,831 - 40,336,444 (+)NCBI
Rnor_6.0642,852,529 - 42,859,142 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036747   ⟸   NM_012615
- UniProtKB: P09057 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239969   ⟸   XM_006239907
- Peptide Label: isoform X1
- UniProtKB: P09057 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239970   ⟸   XM_006239908
- Peptide Label: isoform X1
- UniProtKB: P09057 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001289012   ⟸   NM_001302083
- UniProtKB: P09057 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449519   ⟸   XM_017594030
- Peptide Label: isoform X1
- UniProtKB: P09057 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073349   ⟸   ENSRNOT00000079185
RefSeq Acc Id: ENSRNOP00000007259   ⟸   ENSRNOT00000007259
Protein Domains
Orn_Arg_deC_N   Orn_DAP_Arg_deC

Transcriptome

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

Promoters
RGD ID:13694511
Promoter ID:EPDNEW_R5034
Type:multiple initiation site
Name:Odc1_1
Description:ornithine decarboxylase 1
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_6.0642,852,660 - 42,852,720EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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 (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: 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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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
SHRSP/Gcrc (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
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (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
WAG/Rij (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/Gcrc (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/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
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)
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
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 42856142 42856143 A T snv WKY/N (MCW)
6 42858395 42858396 C T snv SR/JrHsd (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 41312328 41312329 C T snv FHL/EurMcwi (MCW)
6 41312796 41312797 A T snv WKY/N (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3227 AgrOrtholog
Ensembl Genes ENSRNOG00000005424 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007259 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000073349 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007259 UniProtKB/Swiss-Prot
  ENSRNOT00000079185 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.40.37.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.20.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115603 IMAGE-MGC_LOAD
InterPro Ala_racemase/Decarboxylase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  De-COase2_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  De-COase2_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  De-COase2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  De-COase2_pyr-phos_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Orn/DAP/Arg_de-COase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Orn_de-COase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PLP-binding_barrel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24609 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93569 IMAGE-MGC_LOAD
NCBI Gene 24609 ENTREZGENE
PANTHER PTHR11482 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Orn_Arg_deC_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Orn_DAP_Arg_deC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Odc1 PhenoGen
PRINTS ODADCRBXLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ORNDCRBXLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ODR_DC_2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ODR_DC_2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50621 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF51419 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC204042
UniProt A0A0G2K5A1_RAT UniProtKB/TrEMBL
  DCOR_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-11-06 Odc1  ornithine decarboxylase 1    Ornitine decarboxylase  Name updated 625702 APPROVED
2002-06-10 Odc1  Ornitine decarboxylase      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression induced expression during hepatocyte regeneration after certain types of liver damage 70249