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: Enables ornithine decarboxylase activity. Involved in putrescine biosynthetic process. Located in 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
Previously 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: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8646,058,439 - 46,065,148 (+)NCBIGRCr8
mRatBN7.2640,329,831 - 40,336,444 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl640,329,964 - 40,336,440 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx640,657,182 - 40,663,666 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0640,971,864 - 40,978,348 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0640,405,122 - 40,411,607 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0642,852,529 - 42,859,142 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl642,852,683 - 42,859,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0652,565,188 - 52,571,773 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4641,309,211 - 41,315,796 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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-hydroxy-TEMPO  (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)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (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 atom  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chlordecone  (ISO)
chloroform  (EXP)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
Cinobufagin  (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)
diquat  (ISO)
disodium selenite  (ISO)
diuron  (EXP,ISO)
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)
gentamycin  (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)
ketoconazole  (EXP)
L-methionine  (ISO)
leflunomide  (EXP)
lipopolysaccharide  (EXP,ISO)
mancozeb  (ISO)
masoprocol  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
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,ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,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 arsenite  (ISO)
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  (EXP,ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (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
# Reference Title Reference Citation
1. Regulation of ornithine decarboxylase and polyamine import by hypoxia in pulmonary artery endothelial cells. Babal P, etal., Am J Physiol Lung Cell Mol Physiol 2002 Apr;282(4):L840-6.
2. Increased expression of ornithine decarboxylase in distal tubules of early diabetic rat kidneys: are polyamines paracrine hypertrophic factors? Deng A, etal., Diabetes. 2003 May;52(5):1235-9.
3. Aminooxy analogues of spermidine as inhibitors of spermine synthase and substrates of hepatic polyamine acetylating activity. Eloranta TO, etal., J Biochem. 1990 Oct;108(4):593-8.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. The role of polyamines in growth factor induced DNA synthesis in cultured rat hepatocytes. Higaki I, etal., Hepatogastroenterology. 1999 May-Jun;46(27):1874-9.
7. Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide. Hillary RA and Pegg AE, Biochim Biophys Acta. 2003 Apr 11;1647(1-2):161-6.
8. KEGG: Kyoto Encyclopedia of Genes and Genomes KEGG
9. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
12. The ornithine decarboxylase gene is essential for cell survival during early murine development. Pendeville H, etal., Mol Cell Biol. 2001 Oct;21(19):6549-58.
13. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
14. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
15. GOA pipeline RGD automated data pipeline
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Immunocytochemical detection of ornithine decarboxylase. Schipper RG, etal., J Histochem Cytochem. 1999 Nov;47(11):1395-404.
18. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
19. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
20. Messenger RNA profiles in liver injury and stress: a comparison of lethal and nonlethal rat models. Tygstrup N, etal., Biochem Biophys Res Commun 2002 Jan 11;290(1):518-25.
21. Cloning and nucleotide sequence of rat ornithine decarboxylase cDNA. van Kranen HJ, etal., Gene 1987;60(2-3):145-55.
22. Nucleotide sequence of the rat ornithine decarboxylase gene. van Steeg H, etal., Nucleic Acids Res 1988 Aug 25;16(16):8173-4.
23. A perspective of polyamine metabolism. Wallace HM, etal., Biochem J. 2003 Nov 15;376(Pt 1):1-14.
24. Effect of putrescine on S-adenosylmethionine decarboxylase in a small intestinal crypt cell line. Wang JY, etal., Am J Physiol. 1992 Oct;263(4 Pt 1):G494-501.
25. Rat ornithine decarboxylase gene. Nucleotide sequence, potential regulatory elements, and comparison to the mouse gene. 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
GRCr8646,058,439 - 46,065,148 (+)NCBIGRCr8
mRatBN7.2640,329,831 - 40,336,444 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl640,329,964 - 40,336,440 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx640,657,182 - 40,663,666 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0640,971,864 - 40,978,348 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0640,405,122 - 40,411,607 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0642,852,529 - 42,859,142 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl642,852,683 - 42,859,927 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0652,565,188 - 52,571,773 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4641,309,211 - 41,315,796 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh38210,439,968 - 10,448,327 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl210,439,968 - 10,448,327 (-)EnsemblGRCh38hg38GRCh38
GRCh37210,580,094 - 10,588,453 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36210,497,959 - 10,505,904 (-)NCBINCBI36Build 36hg18NCBI36
Build 34210,531,105 - 10,539,051NCBI
Celera210,496,293 - 10,504,232 (-)NCBICelera
Cytogenetic Map2p25.1NCBI
HuRef210,432,740 - 10,440,685 (-)NCBIHuRef
CHM1_1210,509,903 - 10,517,848 (-)NCBICHM1_1
T2T-CHM13v2.0210,469,577 - 10,477,937 (-)NCBIT2T-CHM13v2.0
Odc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391217,594,906 - 17,601,503 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1217,594,795 - 17,601,506 (+)EnsemblGRCm39 Ensembl
GRCm381217,544,808 - 17,551,502 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1217,544,794 - 17,551,505 (+)EnsemblGRCm38mm10GRCm38
MGSCv371217,551,679 - 17,558,308 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361217,570,570 - 17,576,557 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v212116,062,594 - 116,072,320 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A116,066,565 - 116,076,289 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A10,443,308 - 10,451,412 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A10,598,125 - 10,607,152 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A10,598,125 - 10,607,152 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0177,467,169 - 7,474,927 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl177,457,350 - 7,472,111 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1177,357,671 - 7,365,425 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0177,360,253 - 7,368,002 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0177,374,368 - 7,382,137 (-)NCBIUU_Cfam_GSD_1.0
Odc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629251,826,681 - 51,831,970 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365326,581,717 - 6,587,116 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ODC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3126,087,242 - 126,096,051 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13126,087,013 - 126,095,644 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ODC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11497,173,338 - 97,182,253 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604515,117,435 - 15,125,604 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Odc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248654,851,878 - 4,860,558 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248654,851,565 - 4,858,868 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Odc1
35 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
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)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63569161857730540Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat

Markers in Region
D6Arb8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2640,335,037 - 40,335,394 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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 (+)MAPPERmRatBN7.2
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


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

Nucleotide Sequences
RefSeq Transcripts NM_001302083 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239907 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239908 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017594030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063261544 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA860013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB613128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DV728774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ151473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04791 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  J04792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000006 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M16982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X07944 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSRNOT00000007259   ⟹   ENSRNOP00000007259
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl640,329,964 - 40,336,440 (+)Ensembl
Rnor_6.0 Ensembl642,854,888 - 42,858,759 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000079185   ⟹   ENSRNOP00000073349
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
GRCr8646,058,665 - 46,065,148 (+)NCBI
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
GRCr8646,058,665 - 46,065,148 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8646,058,545 - 46,064,766 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8646,058,545 - 46,064,766 (+)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8646,058,439 - 46,064,766 (+)NCBI
mRatBN7.2640,329,831 - 40,336,444 (+)NCBI
Rnor_6.0642,852,529 - 42,859,142 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063261544   ⟹   XP_063117614
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8646,058,545 - 46,064,766 (+)NCBI
RefSeq Acc Id: NP_036747   ⟸   NM_012615
- UniProtKB: P09057 (UniProtKB/Swiss-Prot),   A6HAU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239969   ⟸   XM_006239907
- Peptide Label: isoform X1
- UniProtKB: P09057 (UniProtKB/Swiss-Prot),   A6HAU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006239970   ⟸   XM_006239908
- Peptide Label: isoform X1
- UniProtKB: P09057 (UniProtKB/Swiss-Prot),   A6HAU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001289012   ⟸   NM_001302083
- UniProtKB: P09057 (UniProtKB/Swiss-Prot),   A6HAU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449519   ⟸   XM_017594030
- Peptide Label: isoform X1
- UniProtKB: P09057 (UniProtKB/Swiss-Prot),   A6HAU9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073349   ⟸   ENSRNOT00000079185
RefSeq Acc Id: ENSRNOP00000007259   ⟸   ENSRNOT00000007259
RefSeq Acc Id: XP_063117614   ⟸   XM_063261544
- Peptide Label: isoform X1
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P09057-F1-model_v2 AlphaFold P09057 1-461 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3227 AgrOrtholog
BioCyc Gene G2FUF-38053 BioCyc
BioCyc Pathway PWY-46 [putrescine biosynthesis III] BioCyc
BioCyc Pathway Image PWY-46 BioCyc
Ensembl Genes ENSRNOG00000005424 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055005635 UniProtKB/Swiss-Prot
  ENSRNOG00060003971 UniProtKB/Swiss-Prot
  ENSRNOG00065005649 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000007259 ENTREZGENE
  ENSRNOT00000007259.5 UniProtKB/Swiss-Prot
  ENSRNOT00055009060 UniProtKB/Swiss-Prot
  ENSRNOT00060006624 UniProtKB/Swiss-Prot
  ENSRNOT00065008423 UniProtKB/Swiss-Prot
Gene3D-CATH 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, UniProtKB/TrEMBL
MGC_CLONE MGC:93569 IMAGE-MGC_LOAD
NCBI Gene 24609 ENTREZGENE
PANTHER ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE UniProtKB/TrEMBL
  ORNITHINE DECARBOXYLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11482 UniProtKB/Swiss-Prot
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
RatGTEx ENSRNOG00000005424 RatGTEx
  ENSRNOG00055005635 RatGTEx
  ENSRNOG00060003971 RatGTEx
  ENSRNOG00065005649 RatGTEx
Superfamily-SCOP Alanine racemase C-terminal domain-like UniProtKB/TrEMBL
  PLP-binding barrel UniProtKB/TrEMBL
  SSF50621 UniProtKB/Swiss-Prot
  SSF51419 UniProtKB/Swiss-Prot
TIGR TC204042
UniProt A6HAU9 ENTREZGENE, 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