Ddc (dopa decarboxylase) - Rat Genome Database

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Gene: Ddc (dopa decarboxylase) Rattus norvegicus
Analyze
Symbol: Ddc
Name: dopa decarboxylase
RGD ID: 2494
Description: Enables several functions, including amino acid binding activity; aromatic-L-amino-acid decarboxylase activity; and pyridoxal phosphate binding activity. Involved in several processes, including aminergic neurotransmitter loading into synaptic vesicle; phenol-containing compound biosynthetic process; and response to pyrethroid. Located in axon; neuronal cell body; and synaptic vesicle. Used to study Parkinson's disease. Biomarker of Parkinson's disease; end stage renal disease; nephrotic syndrome; and portal hypertension. Human ortholog(s) of this gene implicated in Parkinson's disease; aromatic L-amino acid decarboxylase deficiency; bipolar disorder; and inherited metabolic disorder. Orthologous to human DDC (dopa decarboxylase); PARTICIPATES IN alkaptonuria pathway; aromatic L-amino acid decarboxylase deficiency pathway; catecholamine biosynthetic pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AADC; aromatic L-amino acid decarboxylase; aromatic-L-amino-acid decarboxylase; dopa decarboxylase (aromatic L-amino acid decarboxylase); L-Dopa decarboxylase; MGC93628
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
mRatBN7.21486,378,685 - 86,469,189 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1486,378,685 - 86,469,208 (-)Ensembl
Rnor_6.01491,905,919 - 91,996,816 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1491,905,919 - 91,996,774 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01491,689,894 - 91,793,700 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41492,698,636 - 92,788,635 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11492,714,598 - 92,790,197 (-)NCBI
Celera1485,380,254 - 85,470,515 (-)NCBICelera
RH 3.4 Map14636.18RGD
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(2,4,5-trichlorophenoxy)acetic acid  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-Amino-3-methyl-9H-pyrido[2,3-b]indole  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-Amino-1-methyl-5H-pyrido[4,3-b]indole  (EXP,ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-hydroxytryptophan  (EXP)
aflatoxin B1  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
andrographolide  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
azathioprine  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
buspirone  (EXP)
Butylbenzyl phthalate  (EXP)
cadmium dichloride  (EXP)
cadmium sulfate  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
cefaloridine  (EXP)
chlorpyrifos  (EXP)
chrysene  (ISO)
clozapine  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
flutamide  (EXP)
folic acid  (ISO)
furan  (EXP)
genistein  (ISO)
glafenine  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
homocysteine  (ISO)
indole-3-methanol  (EXP)
isotretinoin  (ISO)
ketanserin  (ISO)
lead diacetate  (EXP)
leflunomide  (EXP)
levofloxacin  (EXP)
menadione  (ISO)
metergoline  (ISO)
N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (ISO)
N-Nitrosopyrrolidine  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
nitric oxide  (EXP)
O-methyleugenol  (ISO)
oxidopamine  (EXP)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (EXP)
permethrin  (EXP)
phenobarbital  (EXP,ISO)
PhIP  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (EXP)
pregnenolone 16alpha-carbonitrile  (ISO)
propanal  (ISO)
quercetin  (ISO)
reserpine  (EXP)
resveratrol  (ISO)
rotenone  (EXP)
S-adenosyl-L-methioninate  (ISO)
S-adenosyl-L-methionine  (ISO)
sarin  (ISO)
scopolamine  (EXP)
Securinine  (ISO)
serotonin  (EXP)
silicon dioxide  (EXP,ISO)
simazine  (EXP,ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
thifluzamide  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triphenyl phosphate  (EXP)
tunicamycin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
vigabatrin  (EXP)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. J. Inherit. Metab. Dis. 21: 4 only, 1998.
2. Borglum AD, etal., Am J Med Genet B Neuropsychiatr Genet 2003 Feb;117(1):18-22.
3. Brown ST, etal., J Neurochem. 2009 Jul;110(2):622-30. Epub 2009 May 8.
4. Brun L, etal., Neurology. 2010 Jul 6;75(1):64-71. Epub 2010 May 26.
5. Cartier EA, etal., J Biol Chem. 2010 Jan 15;285(3):1957-66. Epub 2009 Nov 10.
6. Chiou SH, etal., Anal Biochem. 2007 Apr 1;363(1):46-57. Epub 2007 Jan 17.
7. Coll M, etal., J Hepatol. 2008 Jul;49(1):43-51. Epub 2008 Apr 18.
8. Cruz-Muros I, etal., Exp Neurol. 2007 Mar;204(1):147-61. Epub 2006 Nov 16.
9. DasBanerjee T, etal., Am J Med Genet B Neuropsychiatr Genet. 2008 Dec 5;147B(8):1554-63.
10. de Lonlay P, etal., J Clin Endocrinol Metab. 2006 Mar;91(3):933-40. Epub 2006 Jan 10.
11. Ershov PV, etal., J Chem Neuroanat. 2005 Jul;30(1):27-33.
12. Fan DS, etal., Hum Gene Ther. 1998 Nov 20;9(17):2527-35.
13. Foster SB, etal., Chem Res Toxicol. 2003 Oct;16(10):1372-84.
14. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. Gil S, etal., Cell Mol Neurobiol. 2010 Aug;30(6):817-25. Epub 2010 Mar 16.
16. GOA data from the GO Consortium
17. Harrill JA, etal., BMC Genomics. 2008 Nov 18;9:546.
18. Hayashi H, etal., Biochemistry. 1993 Jan 26;32(3):812-8.
19. Hayashi H, etal., Biochemistry. 1999 Nov 23;38(47):15615-22.
20. Ishida Y, etal., Genes Cells 2002 May;7(5):447-59.
21. Jin CM, etal., Eur J Pharmacol. 2008 Sep 4;591(1-3):88-95. Epub 2008 Jun 19.
22. Jin CM, etal., J Asian Nat Prod Res. 2008 Jul-Aug;10(7-8):747-55.
23. KEGG
24. Kitahama K, etal., J Chem Neuroanat. 2009 Oct;38(2):130-40. Epub 2009 Jul 7.
25. Kvetnansky R, etal., Physiol Rev. 2009 Apr;89(2):535-606.
26. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
27. Lee JJ, etal., Molecules. 2008 Feb 27;13(2):475-87.
28. Moreira-Rodrigues M, etal., Life Sci. 2009 Mar 27;84(13-14):409-14. Epub 2009 Jan 8.
29. NCBI rat LocusLink and RefSeq merged data July 26, 2002
30. OMIM Disease Annotation Pipeline
31. Pipeline to import KEGG annotations from KEGG into RGD
32. Pipeline to import SMPDB annotations from SMPDB into RGD
33. RGD automated data pipeline
34. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
35. RGD automated import pipeline for gene-chemical interactions
36. Rorsman F, etal., Proc Natl Acad Sci U S A 1995 Sep 12;92(19):8626-9.
37. Sampaio-Maia B, etal., Nephrol Dial Transplant. 2006 Feb;21(2):314-23. Epub 2005 Oct 4.
38. Shen H, etal., Tohoku J Exp Med. 2003 Mar;199(3):149-59.
39. Tanaka T, etal., Proc Natl Acad Sci U S A 1989 Oct;86(20):8142-6.
40. Tehranian R, etal., J Neurochem. 2006 Nov;99(4):1188-96. Epub 2006 Sep 18.
41. Vieira-Coelho MA, etal., Life Sci. 1999;64(1):69-81.
42. Yamazaki N and Sudo J, Jpn J Pharmacol. 1988 Feb;46(2):193-6.
43. Yang YJ, etal., J Neurosci Res. 2009 Jun;87(8):1929-37.
Additional References at PubMed
PMID:1465439   PMID:7904615   PMID:8889823   PMID:12477932   PMID:15489334   PMID:16338639   PMID:19056867   PMID:19703902   PMID:22829864   PMID:23010799   PMID:23376485   PMID:23863468  


Genomics

Comparative Map Data
Ddc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21486,378,685 - 86,469,189 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1486,378,685 - 86,469,208 (-)Ensembl
Rnor_6.01491,905,919 - 91,996,816 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1491,905,919 - 91,996,774 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01491,689,894 - 91,793,700 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41492,698,636 - 92,788,635 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11492,714,598 - 92,790,197 (-)NCBI
Celera1485,380,254 - 85,470,515 (-)NCBICelera
RH 3.4 Map14636.18RGD
Cytogenetic Map14q21NCBI
DDC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl750,458,436 - 50,565,405 (-)EnsemblGRCh38hg38GRCh38
GRCh38750,458,436 - 50,565,460 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37750,526,140 - 50,633,102 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36750,493,628 - 50,600,648 (-)NCBINCBI36hg18NCBI36
Build 34750,300,344 - 50,402,960NCBI
Celera750,591,055 - 50,698,048 (-)NCBI
Cytogenetic Map7p12.2-p12.1NCBI
HuRef750,376,100 - 50,483,099 (-)NCBIHuRef
CHM1_1750,528,427 - 50,635,428 (-)NCBICHM1_1
CRA_TCAGchr7v2750,532,205 - 50,639,203 (-)NCBI
Ddc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391111,764,101 - 11,848,144 (-)NCBIGRCm39mm39
GRCm39 Ensembl1111,764,101 - 11,848,144 (-)Ensembl
GRCm381111,814,101 - 11,898,144 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1111,814,101 - 11,898,144 (-)EnsemblGRCm38mm10GRCm38
MGSCv371111,714,104 - 11,798,147 (-)NCBIGRCm37mm9NCBIm37
MGSCv361111,714,445 - 11,780,657 (-)NCBImm8
Celera1112,273,377 - 12,350,184 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map117.09NCBI
Ddc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554563,513,042 - 3,582,911 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554563,513,779 - 3,582,851 (+)NCBIChiLan1.0ChiLan1.0
DDC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1751,345,228 - 51,449,710 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl751,345,228 - 51,449,710 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0751,101,169 - 51,206,031 (-)NCBIMhudiblu_PPA_v0panPan3
DDC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1181,802,239 - 1,876,714 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl181,803,273 - 1,867,616 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha181,793,310 - 1,867,692 (-)NCBI
ROS_Cfam_1.0181,860,735 - 1,935,186 (-)NCBI
UMICH_Zoey_3.1181,833,628 - 1,907,793 (-)NCBI
UNSW_CanFamBas_1.0181,830,057 - 1,904,284 (-)NCBI
UU_Cfam_GSD_1.0181,966,951 - 2,041,333 (-)NCBI
Ddc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118105,117,869 - 105,222,691 (-)NCBI
SpeTri2.0NW_0049366861,322,153 - 1,405,434 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9136,495,891 - 136,571,197 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19136,496,364 - 136,571,220 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29150,076,907 - 150,157,225 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DDC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1218,235,396 - 8,343,086 (+)NCBI
ChlSab1.1 Ensembl218,235,343 - 8,343,361 (+)Ensembl
Vero_WHO_p1.0NW_02366606213,938,028 - 14,045,297 (-)NCBI
Ddc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247403,674,727 - 3,732,058 (+)NCBI

Position Markers
RH130833  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21486,381,993 - 86,382,203 (+)MAPPERmRatBN7.2
Rnor_6.01491,909,228 - 91,909,437NCBIRnor6.0
Rnor_5.01491,693,203 - 91,693,412UniSTSRnor5.0
RGSC_v3.41492,698,762 - 92,698,971UniSTSRGSC3.4
Celera1485,383,563 - 85,383,772UniSTS
RH 3.4 Map14635.59UniSTS
Cytogenetic Map14q21UniSTS
RH143134  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21486,378,764 - 86,378,934 (+)MAPPERmRatBN7.2
Rnor_6.01491,905,999 - 91,906,168NCBIRnor6.0
Rnor_5.01491,689,974 - 91,690,143UniSTSRnor5.0
RGSC_v3.41492,695,533 - 92,695,702UniSTSRGSC3.4
Celera1485,380,334 - 85,380,503UniSTS
RH 3.4 Map14636.59UniSTS
Cytogenetic Map14q21UniSTS
RH94401  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21486,381,868 - 86,382,056 (+)MAPPERmRatBN7.2
Rnor_6.01491,909,103 - 91,909,290NCBIRnor6.0
Rnor_5.01491,693,078 - 91,693,265UniSTSRnor5.0
RGSC_v3.41492,698,637 - 92,698,824UniSTSRGSC3.4
Celera1485,383,438 - 85,383,625UniSTS
RH 3.4 Map14636.18UniSTS
Cytogenetic Map14q21UniSTS
BF408245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21486,379,946 - 86,380,092 (+)MAPPERmRatBN7.2
Rnor_6.01491,907,181 - 91,907,326NCBIRnor6.0
Rnor_5.01491,691,156 - 91,691,301UniSTSRnor5.0
RGSC_v3.41492,696,715 - 92,696,860UniSTSRGSC3.4
Celera1485,381,516 - 85,381,661UniSTS
RH 3.4 Map14635.99UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat
4889951Bss92Bone structure and strength QTL 923.9tibia area (VT:1000281)tibia-fibula cortical bone total cross-sectional area (CMO:0001721)148205747195876975Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1020
Count of miRNA genes:336
Interacting mature miRNAs:460
Transcripts:ENSRNOT00000005851, ENSRNOT00000057051, ENSRNOT00000073892
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 2 37 25 21 21 13 19 9 1
Low 1 6 25 20 2 20 8 11 61 16 29 10 8
Below cutoff 7 17 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270852 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270853 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_012545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251474 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251475 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039091617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC115644 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH003559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC087032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JF273828 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M27716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U31884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000005851   ⟹   ENSRNOP00000005851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1486,378,685 - 86,469,208 (-)Ensembl
Rnor_6.0 Ensembl1491,905,919 - 91,996,774 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000057051   ⟹   ENSRNOP00000053885
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1486,378,685 - 86,462,016 (-)Ensembl
Rnor_6.0 Ensembl1491,905,919 - 91,989,307 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000073892   ⟹   ENSRNOP00000064520
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1486,378,685 - 86,469,175 (-)Ensembl
Rnor_6.0 Ensembl1491,905,919 - 91,979,500 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093904   ⟹   ENSRNOP00000085523
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1486,378,685 - 86,469,208 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103628   ⟹   ENSRNOP00000082788
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1486,378,685 - 86,452,371 (-)Ensembl
RefSeq Acc Id: NM_001270852   ⟹   NP_001257781
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21486,378,685 - 86,452,210 (-)NCBI
Rnor_6.01491,905,919 - 91,979,500 (-)NCBI
Rnor_5.01491,689,894 - 91,793,700 (-)NCBI
Celera1485,380,254 - 85,453,633 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001270853   ⟹   NP_001257782
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21486,378,685 - 86,462,016 (-)NCBI
Rnor_6.01491,905,919 - 91,989,307 (-)NCBI
Rnor_5.01491,689,894 - 91,793,700 (-)NCBI
Celera1485,380,254 - 85,463,439 (-)NCBI
Sequence:
RefSeq Acc Id: NM_012545   ⟹   NP_036677
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21486,378,685 - 86,469,175 (-)NCBI
Rnor_6.01491,905,919 - 91,996,774 (-)NCBI
Rnor_5.01491,689,894 - 91,793,700 (-)NCBI
RGSC_v3.41492,698,636 - 92,788,635 (-)RGD
Celera1485,380,254 - 85,470,515 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770253   ⟹   XP_008768475
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21486,381,866 - 86,469,183 (-)NCBI
Rnor_6.01491,909,100 - 91,996,816 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770254   ⟹   XP_008768476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21486,392,275 - 86,469,183 (-)NCBI
Rnor_6.01491,917,320 - 91,996,816 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091617   ⟹   XP_038947545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21486,390,147 - 86,469,189 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_036677   ⟸   NM_012545
- Peptide Label: isoform a
- UniProtKB: P14173 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001257782   ⟸   NM_001270853
- Peptide Label: isoform b
- UniProtKB: P14173 (UniProtKB/Swiss-Prot),   D3ZMA5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257781   ⟸   NM_001270852
- Peptide Label: isoform a
- UniProtKB: P14173 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008768475   ⟸   XM_008770253
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768476   ⟸   XM_008770254
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000053885   ⟸   ENSRNOT00000057051
RefSeq Acc Id: ENSRNOP00000064520   ⟸   ENSRNOT00000073892
RefSeq Acc Id: ENSRNOP00000005851   ⟸   ENSRNOT00000005851
RefSeq Acc Id: XP_038947545   ⟸   XM_039091617
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000082788   ⟸   ENSRNOT00000103628
RefSeq Acc Id: ENSRNOP00000085523   ⟸   ENSRNOT00000093904

Transcriptome

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

Promoters
RGD ID:13699496
Promoter ID:EPDNEW_R10018
Type:multiple initiation site
Name:Ddc_1
Description:dopa decarboxylase
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_6.01491,996,774 - 91,996,834EPDNEW

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)
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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
LL/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
LN/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
LN/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
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)
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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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2494 AgrOrtholog
Ensembl Genes ENSRNOG00000004327 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005851 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000053885 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000064520 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000005851 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000057051 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000073892 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.640.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.1150.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7098083 IMAGE-MGC_LOAD
InterPro Aromatic_deC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_de-COase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_dom1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PyrdxlP-dep_Trfase_major UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pyridoxal-P_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24311 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93628 IMAGE-MGC_LOAD
NCBI Gene 24311 ENTREZGENE
Pfam Pyridoxal_deC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB DDC RGD
PhenoGen Ddc PhenoGen
PRINTS YHDCRBOXLASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DDC_GAD_HDC_YDC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53383 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D3ZMA5 ENTREZGENE, UniProtKB/TrEMBL
  DDC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary F8TLS6 UniProtKB/TrEMBL
  Q6LEG4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-09 Ddc  dopa decarboxylase  Ddc  dopa decarboxylase (aromatic L-amino acid decarboxylase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Ddc  dopa decarboxylase (aromatic L-amino acid decarboxylase)  Ddc  dopa decarboxylase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Ddc  dopa decarboxylase    Dopa decarboxylase (aromatic L-amino acid decarboxylase)  Name updated 625702 APPROVED
2002-06-10 Ddc  Dopa decarboxylase (aromatic L-amino acid decarboxylase)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease an autoantigen in autoimmune polyendocrine syndrome type I 727686
gene_other pyrodoxal phosphate is a cofactor for enzyme activity 727686