Asph (aspartate-beta-hydroxylase) - Rat Genome Database

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Gene: Asph (aspartate-beta-hydroxylase) Rattus norvegicus
Analyze
Symbol: Asph
Name: aspartate-beta-hydroxylase
RGD ID: 1312000
Description: Predicted to enable calcium ion binding activity. Involved in regulation of cytosolic calcium ion concentration. Predicted to be located in cortical endoplasmic reticulum and plasma membrane. Predicted to be integral component of endoplasmic reticulum membrane. Predicted to be active in endoplasmic reticulum. Human ortholog(s) of this gene implicated in cholangiocarcinoma. Orthologous to human ASPH (aspartate beta-hydroxylase); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: aspartyl/asparaginyl beta-hydroxylase; junctate; junctin; LOC100910356; LOC312981; uncharacterized LOC100910356
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
mRatBN7.2522,603,879 - 22,814,107 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl522,603,486 - 22,813,876 (-)Ensembl
Rnor_6.0522,577,680 - 22,799,333 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl522,577,675 - 22,799,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0527,312,094 - 27,529,901 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4523,495,780 - 23,520,672 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1523,337,888 - 23,733,050 (-)NCBI
Celera521,856,777 - 22,069,140 (-)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
avobenzone  (ISO)
benzatropine  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
choline  (ISO)
chromium atom  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
clozapine  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
gentamycin  (EXP)
haloperidol  (ISO)
hydralazine  (ISO)
indometacin  (ISO)
isoflavones  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methyl methanesulfonate  (ISO)
methylparaben  (ISO)
nicotinic acid  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
PCB138  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
Soman  (EXP)
succimer  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
warfarin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

Additional References at PubMed
PMID:8530521   PMID:11773073   PMID:12477932   PMID:15302852   PMID:15798210   PMID:17400717   PMID:18387192   PMID:21062895   PMID:22123818   PMID:22586105   PMID:33450132  


Genomics

Comparative Map Data
Asph
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2522,603,879 - 22,814,107 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl522,603,486 - 22,813,876 (-)Ensembl
Rnor_6.0522,577,680 - 22,799,333 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl522,577,675 - 22,799,349 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0527,312,094 - 27,529,901 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4523,495,780 - 23,520,672 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1523,337,888 - 23,733,050 (-)NCBI
Celera521,856,777 - 22,069,140 (-)NCBICelera
Cytogenetic Map5q13NCBI
ASPH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl861,500,556 - 61,714,640 (-)EnsemblGRCh38hg38GRCh38
GRCh38861,500,556 - 61,714,609 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37862,413,115 - 62,627,151 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36862,578,374 - 62,789,560 (-)NCBINCBI36hg18NCBI36
Build 34862,699,648 - 62,764,919NCBI
Celera858,402,958 - 58,617,392 (-)NCBI
Cytogenetic Map8q12.3NCBI
HuRef857,901,587 - 58,116,117 (-)NCBIHuRef
CHM1_1862,465,102 - 62,679,146 (-)NCBICHM1_1
Asph
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3949,449,085 - 9,669,344 (-)NCBIGRCm39mm39
GRCm39 Ensembl49,448,069 - 9,669,344 (-)Ensembl
GRCm3849,449,085 - 9,669,344 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl49,448,069 - 9,669,344 (-)EnsemblGRCm38mm10GRCm38
MGSCv3749,376,232 - 9,596,309 (-)NCBIGRCm37mm9NCBIm37
MGSCv3649,376,232 - 9,596,231 (-)NCBImm8
Celera49,289,732 - 9,501,866 (-)NCBICelera
Cytogenetic Map4A1NCBI
Asph
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544417,121,559 - 17,318,295 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544417,116,060 - 17,320,966 (+)NCBIChiLan1.0ChiLan1.0
ASPH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1859,629,707 - 59,843,921 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl859,629,707 - 59,843,658 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0857,921,580 - 58,134,778 (-)NCBIMhudiblu_PPA_v0panPan3
ASPH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12911,812,275 - 12,022,755 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2911,814,554 - 12,022,680 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2912,127,227 - 12,309,441 (-)NCBI
ROS_Cfam_1.02911,908,475 - 12,120,515 (-)NCBI
ROS_Cfam_1.0 Ensembl2911,910,753 - 12,120,515 (-)Ensembl
UMICH_Zoey_3.12911,900,440 - 12,082,741 (-)NCBI
UNSW_CanFamBas_1.02912,036,855 - 12,218,830 (-)NCBI
UU_Cfam_GSD_1.02912,307,233 - 12,489,655 (-)NCBI
Asph
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530362,970,453 - 63,180,486 (-)NCBI
SpeTri2.0NW_00493649611,604,992 - 11,815,680 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ASPH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl471,903,359 - 72,107,046 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1471,902,891 - 72,107,047 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2478,382,152 - 78,505,768 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ASPH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1857,378,019 - 57,599,812 (-)NCBIChlSab1.1chlSab2
ChlSab1.1857,378,019 - 57,599,812 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl857,375,894 - 57,565,259 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603984,051,765 - 84,274,334 (+)NCBIVero_WHO_p1.0
Asph
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474430,190,625 - 30,420,501 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH133103  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,760,555 - 22,760,770 (+)MAPPERmRatBN7.2
Rnor_6.0522,745,859 - 22,746,073NCBIRnor6.0
Rnor_5.0527,476,382 - 27,476,596UniSTSRnor5.0
RGSC_v3.4523,495,888 - 23,496,102UniSTSRGSC3.4
Celera522,015,735 - 22,015,949UniSTS
RH 3.4 Map5133.71UniSTS
Cytogenetic Map5q13UniSTS
RH133181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,724,932 - 22,725,114 (+)MAPPERmRatBN7.2
Rnor_6.0522,710,265 - 22,710,446NCBIRnor6.0
Rnor_5.0527,440,703 - 27,440,884UniSTSRnor5.0
RGSC_v3.4523,459,744 - 23,459,925UniSTSRGSC3.4
Celera521,980,125 - 21,980,306UniSTS
RH 3.4 Map5133.8UniSTS
Cytogenetic Map5q13UniSTS
BE097198  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,772,063 - 22,772,218 (+)MAPPERmRatBN7.2
Rnor_6.0522,757,343 - 22,757,497NCBIRnor6.0
Rnor_5.0527,487,907 - 27,488,061UniSTSRnor5.0
RGSC_v3.4523,508,218 - 23,508,372UniSTSRGSC3.4
Celera522,027,279 - 22,027,433UniSTS
RH 3.4 Map5133.8UniSTS
Cytogenetic Map5q13UniSTS
BE106090  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,616,606 - 22,616,756 (+)MAPPERmRatBN7.2
Rnor_6.0522,592,828 - 22,592,977NCBIRnor6.0
Rnor_5.0527,324,933 - 27,325,082UniSTSRnor5.0
RGSC_v3.4523,349,236 - 23,349,385UniSTSRGSC3.4
Celera521,872,173 - 21,872,322UniSTS
RH 3.4 Map5130.8UniSTS
Cytogenetic Map5q13UniSTS
RH138910  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,770,107 - 22,770,236 (+)MAPPERmRatBN7.2
Rnor_6.0522,755,411 - 22,755,539NCBIRnor6.0
Rnor_5.0527,485,934 - 27,486,062UniSTSRnor5.0
RGSC_v3.4523,505,440 - 23,505,568UniSTSRGSC3.4
Celera522,025,287 - 22,025,415UniSTS
RH 3.4 Map5158.0UniSTS
Cytogenetic Map5q13UniSTS
RH139586  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,769,095 - 22,769,300 (+)MAPPERmRatBN7.2
Rnor_6.0522,754,399 - 22,754,603NCBIRnor6.0
Rnor_5.0527,484,922 - 27,485,126UniSTSRnor5.0
RGSC_v3.4523,504,428 - 23,504,632UniSTSRGSC3.4
Celera522,024,275 - 22,024,479UniSTS
RH 3.4 Map5133.8UniSTS
Cytogenetic Map5q13UniSTS
RH140434  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2522,769,095 - 22,769,246 (+)MAPPERmRatBN7.2
Rnor_6.0522,754,399 - 22,754,549NCBIRnor6.0
Rnor_5.0527,484,922 - 27,485,072UniSTSRnor5.0
RGSC_v3.4523,504,428 - 23,504,578UniSTSRGSC3.4
Celera522,024,275 - 22,024,425UniSTS
Cytogenetic Map5q13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:94
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000047805
Prediction methods:Miranda, 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 1 25 12 12 12 8 11 46 26 29 8 8
Low 2 18 45 29 19 29 28 9 12 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001098239 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006225199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237855 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237861 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237862 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237863 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006237864 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763572 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008763575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775895 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039109773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AJ865348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000047805   ⟹   ENSRNOP00000048656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl522,745,751 - 22,769,907 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076113   ⟹   ENSRNOP00000068228
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl522,748,839 - 22,769,932 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076167   ⟹   ENSRNOP00000068254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl522,748,985 - 22,769,919 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076204   ⟹   ENSRNOP00000068059
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,603,486 - 22,813,876 (-)Ensembl
Rnor_6.0 Ensembl522,581,310 - 22,799,349 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076426   ⟹   ENSRNOP00000068479
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,603,486 - 22,813,876 (-)Ensembl
Rnor_6.0 Ensembl522,577,675 - 22,799,090 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076507   ⟹   ENSRNOP00000067926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,723,822 - 22,784,518 (-)Ensembl
Rnor_6.0 Ensembl522,709,158 - 22,769,925 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077044   ⟹   ENSRNOP00000068402
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,723,822 - 22,813,876 (-)Ensembl
Rnor_6.0 Ensembl522,709,158 - 22,799,113 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000079432   ⟹   ENSRNOP00000075358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl522,746,780 - 22,765,429 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083779   ⟹   ENSRNOP00000072176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,603,486 - 22,784,518 (-)Ensembl
Rnor_6.0 Ensembl522,578,943 - 22,770,008 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096794   ⟹   ENSRNOP00000082455
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,768,913 - 22,813,876 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099512   ⟹   ENSRNOP00000083516
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,603,486 - 22,813,876 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106256   ⟹   ENSRNOP00000097341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,603,486 - 22,780,679 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113533   ⟹   ENSRNOP00000090443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,723,822 - 22,784,518 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118158   ⟹   ENSRNOP00000082407
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl522,603,486 - 22,813,876 (-)Ensembl
RefSeq Acc Id: NM_001098239   ⟹   NP_001091709
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,760,448 - 22,784,518 (-)NCBI
RefSeq Acc Id: XM_006237855   ⟹   XP_006237917
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,814,104 (-)NCBI
Rnor_6.0522,577,680 - 22,799,333 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237858   ⟹   XP_006237920
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,814,101 (-)NCBI
Rnor_6.0522,577,680 - 22,799,332 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237859   ⟹   XP_006237921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,786,294 (-)NCBI
Rnor_6.0522,577,680 - 22,771,612 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237860   ⟹   XP_006237922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,786,280 (-)NCBI
Rnor_6.0522,577,680 - 22,771,612 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237861   ⟹   XP_006237923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,814,103 (-)NCBI
Rnor_6.0522,577,680 - 22,799,333 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237862   ⟹   XP_006237924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,789,453 (-)NCBI
Rnor_6.0522,577,680 - 22,771,613 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237863   ⟹   XP_006237925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,760,432 - 22,814,070 (-)NCBI
Rnor_6.0522,745,735 - 22,799,333 (-)NCBI
Rnor_5.0527,312,094 - 27,529,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763575   ⟹   XP_008761797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,768,531 - 22,814,100 (-)NCBI
Rnor_6.0522,755,799 - 22,799,332 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109766   ⟹   XP_038965694
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,814,105 (-)NCBI
RefSeq Acc Id: XM_039109767   ⟹   XP_038965695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,814,103 (-)NCBI
RefSeq Acc Id: XM_039109768   ⟹   XP_038965696
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,789,452 (-)NCBI
RefSeq Acc Id: XM_039109769   ⟹   XP_038965697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,814,107 (-)NCBI
RefSeq Acc Id: XM_039109770   ⟹   XP_038965698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,786,286 (-)NCBI
RefSeq Acc Id: XM_039109771   ⟹   XP_038965699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,603,879 - 22,780,629 (-)NCBI
RefSeq Acc Id: XM_039109773   ⟹   XP_038965701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2522,723,822 - 22,814,104 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006237917   ⟸   XM_006237855
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006237923   ⟸   XM_006237861
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006237920   ⟸   XM_006237858
- Peptide Label: isoform X8
- UniProtKB: A0A096MKE0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237924   ⟸   XM_006237862
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_006237921   ⟸   XM_006237859
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006237922   ⟸   XM_006237860
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006237925   ⟸   XM_006237863
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_008761797   ⟸   XM_008763575
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: ENSRNOP00000075358   ⟸   ENSRNOT00000079432
RefSeq Acc Id: ENSRNOP00000068402   ⟸   ENSRNOT00000077044
RefSeq Acc Id: ENSRNOP00000048656   ⟸   ENSRNOT00000047805
RefSeq Acc Id: ENSRNOP00000072176   ⟸   ENSRNOT00000083779
RefSeq Acc Id: ENSRNOP00000068059   ⟸   ENSRNOT00000076204
RefSeq Acc Id: ENSRNOP00000068254   ⟸   ENSRNOT00000076167
RefSeq Acc Id: ENSRNOP00000068228   ⟸   ENSRNOT00000076113
RefSeq Acc Id: ENSRNOP00000068479   ⟸   ENSRNOT00000076426
RefSeq Acc Id: ENSRNOP00000067926   ⟸   ENSRNOT00000076507
RefSeq Acc Id: XP_038965697   ⟸   XM_039109769
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038965694   ⟸   XM_039109766
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038965695   ⟸   XM_039109767
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038965696   ⟸   XM_039109768
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965698   ⟸   XM_039109770
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038965699   ⟸   XM_039109771
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038965701   ⟸   XM_039109773
- Peptide Label: isoform X13
RefSeq Acc Id: NP_001091709   ⟸   NM_001098239
RefSeq Acc Id: ENSRNOP00000082407   ⟸   ENSRNOT00000118158
RefSeq Acc Id: ENSRNOP00000083516   ⟸   ENSRNOT00000099512
RefSeq Acc Id: ENSRNOP00000090443   ⟸   ENSRNOT00000113533
RefSeq Acc Id: ENSRNOP00000097341   ⟸   ENSRNOT00000106256
RefSeq Acc Id: ENSRNOP00000082455   ⟸   ENSRNOT00000096794
Protein Domains
Asp-B-Hydro_N   Asp_Arg_Hydrox

Transcriptome

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

Promoters
RGD ID:13693566
Promoter ID:EPDNEW_R4082
Type:multiple initiation site
Name:Asph_1
Description:aspartate-beta-hydroxylase
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_6.0522,799,091 - 22,799,151EPDNEW

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)
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)
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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)
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:1312000 AgrOrtholog
Ensembl Genes ENSRNOG00000007445 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000048656 UniProtKB/TrEMBL
  ENSRNOP00000067926 UniProtKB/TrEMBL
  ENSRNOP00000068059 UniProtKB/TrEMBL
  ENSRNOP00000068228 UniProtKB/TrEMBL
  ENSRNOP00000068254 UniProtKB/TrEMBL
  ENSRNOP00000068402 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068479 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072176 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000075358 UniProtKB/TrEMBL
  ENSRNOP00000082407 ENTREZGENE
  ENSRNOP00000082455 ENTREZGENE
Ensembl Transcript ENSRNOT00000047805 UniProtKB/TrEMBL
  ENSRNOT00000076113 UniProtKB/TrEMBL
  ENSRNOT00000076167 UniProtKB/TrEMBL
  ENSRNOT00000076204 UniProtKB/TrEMBL
  ENSRNOT00000076426 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076507 UniProtKB/TrEMBL
  ENSRNOT00000077044 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000079432 UniProtKB/TrEMBL
  ENSRNOT00000083779 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000096794 ENTREZGENE
  ENSRNOT00000118158 ENTREZGENE
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
  2.60.120.330 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7193538 IMAGE-MGC_LOAD
InterPro Asp-B-hydro/Triadin UniProtKB/TrEMBL
  Asp_Arg_Pro-Hydrxlase UniProtKB/TrEMBL
  ASPH UniProtKB/TrEMBL
  IPNS-like UniProtKB/TrEMBL
  TPR-like_helical_dom UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
MGC_CLONE MGC:94733 IMAGE-MGC_LOAD
NCBI Gene 312981 ENTREZGENE
PANTHER PTHR12366 UniProtKB/TrEMBL
Pfam Asp-B-Hydro_N UniProtKB/TrEMBL
  Asp_Arg_Hydrox UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Asph PhenoGen
PROSITE TPR UniProtKB/TrEMBL
SMART TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A096MIY8_RAT UniProtKB/TrEMBL
  A0A096MJA9_RAT UniProtKB/TrEMBL
  A0A096MJR0_RAT UniProtKB/TrEMBL
  A0A096MJT4_RAT UniProtKB/TrEMBL
  A0A096MK70_RAT UniProtKB/TrEMBL
  A0A096MKE0 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K2B5_RAT UniProtKB/TrEMBL
  A0A0G2KAD6_RAT UniProtKB/TrEMBL
  Q5U2Q8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Asph  aspartate-beta-hydroxylase  LOC100910356  uncharacterized LOC100910356  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100910356  uncharacterized LOC100910356      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Asph  aspartate-beta-hydroxylase   Asph_predicted  aspartate-beta-hydroxylase (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Asph_predicted  aspartate-beta-hydroxylase (predicted)      Symbol and Name status set to approved 70820 APPROVED