Apcs (amyloid P component, serum) - Rat Genome Database

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Gene: Apcs (amyloid P component, serum) Rattus norvegicus
Analyze
Symbol: Apcs
Name: amyloid P component, serum
RGD ID: 68322
Description: Predicted to enable several functions, including complement component C1q complex binding activity; low-density lipoprotein particle binding activity; and virion binding activity. Involved in protein-containing complex assembly. Part of protein-containing complex. Human ortholog(s) of this gene implicated in amyloidosis. Orthologous to human APCS (amyloid P component, serum); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Sap; serum amyloid P-component
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
mRatBN7.21385,373,338 - 85,374,134 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1385,373,220 - 85,374,298 (-)Ensembl
Rnor_6.01391,426,621 - 91,427,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1391,426,479 - 91,427,575 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01395,938,118 - 95,938,914 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41389,112,845 - 89,113,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11389,301,610 - 89,302,610 (-)NCBI
Celera1384,980,649 - 84,981,445 (-)NCBICelera
Cytogenetic Map13q24NCBI
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
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,7-dimethylxanthine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
Actein  (EXP)
aflatoxin B1  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
carbon nanotube  (ISO)
carrageenan  (EXP)
cefaloridine  (EXP)
choline  (ISO)
chromium trinitrate  (ISO)
ciprofibrate  (ISO)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumarin  (EXP)
cyclosporin A  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
gemcitabine  (ISO)
heparin  (ISO)
L-ethionine  (EXP)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
mechlorethamine  (EXP)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
O-methyleugenol  (ISO)
omeprazole  (EXP)
p-toluidine  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP,ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
resveratrol  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
triadimefon  (ISO)
Tributyltin oxide  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valsartan  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

References

Additional References at PubMed
PMID:14519527   PMID:14607961   PMID:15769549   PMID:19056867   PMID:19372378   PMID:20551380   PMID:21630459   PMID:22306119   PMID:22396542   PMID:22516433   PMID:23376485   PMID:23533145  
PMID:23544079   PMID:23850452   PMID:27068509   PMID:27559042   PMID:29476059  


Genomics

Comparative Map Data
Apcs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21385,373,338 - 85,374,134 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1385,373,220 - 85,374,298 (-)Ensembl
Rnor_6.01391,426,621 - 91,427,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1391,426,479 - 91,427,575 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01395,938,118 - 95,938,914 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41389,112,845 - 89,113,641 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11389,301,610 - 89,302,610 (-)NCBI
Celera1384,980,649 - 84,981,445 (-)NCBICelera
Cytogenetic Map13q24NCBI
APCS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1159,587,826 - 159,588,865 (+)EnsemblGRCh38hg38GRCh38
GRCh381159,587,826 - 159,588,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371159,557,616 - 159,558,655 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361157,824,240 - 157,825,285 (+)NCBINCBI36hg18NCBI36
Build 341156,370,688 - 156,371,733NCBI
Celera1132,627,015 - 132,628,060 (+)NCBI
Cytogenetic Map1q23.2NCBI
HuRef1130,914,686 - 130,915,731 (+)NCBIHuRef
CHM1_11160,953,113 - 160,954,158 (+)NCBICHM1_1
Apcs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391172,721,528 - 172,722,621 (-)NCBIGRCm39mm39
GRCm39 Ensembl1172,721,528 - 172,722,608 (-)Ensembl
GRCm381172,893,961 - 172,895,054 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1172,893,961 - 172,895,041 (-)EnsemblGRCm38mm10GRCm38
MGSCv371174,824,092 - 174,825,185 (-)NCBIGRCm37mm9NCBIm37
MGSCv361174,730,637 - 174,731,718 (-)NCBImm8
Celera1175,741,973 - 175,743,066 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map180.33NCBI
Apcs
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546811,388,192 - 11,390,314 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546811,388,154 - 11,389,259 (+)NCBIChiLan1.0ChiLan1.0
APCS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11138,734,046 - 138,735,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1138,734,046 - 138,735,093 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01134,937,472 - 134,938,512 (+)NCBIMhudiblu_PPA_v0panPan3
Apcs
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050585,767,140 - 5,768,100 (+)NCBI
SpeTri2.0NW_004936740979,007 - 987,312 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APCS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl490,898,686 - 90,901,875 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1490,900,585 - 90,901,854 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2498,901,214 - 98,901,460 (-)NCBISscrofa10.2Sscrofa10.2susScr3
APCS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1204,360,955 - 4,363,810 (-)NCBI
ChlSab1.1 Ensembl204,358,654 - 4,362,095 (-)Ensembl
Vero_WHO_p1.0NW_0236660383,486,071 - 3,487,118 (-)NCBI
Apcs
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247941,689,619 - 1,690,700 (-)NCBI

Position Markers
RH127703  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21385,373,421 - 85,373,616 (+)MAPPERmRatBN7.2
Rnor_6.01391,426,705 - 91,426,899NCBIRnor6.0
Rnor_5.01395,938,202 - 95,938,396UniSTSRnor5.0
RGSC_v3.41389,112,929 - 89,113,123UniSTSRGSC3.4
Celera1384,980,733 - 84,980,927UniSTS
RH 3.4 Map13565.0UniSTS
Cytogenetic Map13q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat
1302791Stl29Serum triglyceride level QTL 293.30.0011blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)138473078886800898Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:19
Count of miRNA genes:18
Interacting mature miRNAs:19
Transcripts:ENSRNOT00000012092
Prediction methods: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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 23 23 17
Medium 12 10 10 15 2 1
Low 3 20 8 12 8 5 5 6 8 9 7 5
Below cutoff 7 2 5 3 3 13 4 15 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_017170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209497 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ218545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438946 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438952 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438953 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438964 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JQ438965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M83177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X55761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000012092   ⟹   ENSRNOP00000012092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1385,373,220 - 85,374,298 (-)Ensembl
Rnor_6.0 Ensembl1391,426,479 - 91,427,575 (-)Ensembl
RefSeq Acc Id: NM_017170   ⟹   NP_058866
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21385,373,338 - 85,374,134 (-)NCBI
Rnor_6.01391,426,621 - 91,427,417 (-)NCBI
Rnor_5.01395,938,118 - 95,938,914 (-)NCBI
RGSC_v3.41389,112,845 - 89,113,641 (-)RGD
Celera1384,980,649 - 84,981,445 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_058866   ⟸   NM_017170
- Peptide Label: precursor
- UniProtKB: P23680 (UniProtKB/Swiss-Prot),   H6X320 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012092   ⟸   ENSRNOT00000012092
Protein Domains
Pentraxin (PTX)

Transcriptome

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

Promoters
RGD ID:13699035
Promoter ID:EPDNEW_R9560
Type:multiple initiation site
Name:Apcs_1
Description:amyloid P component, serum
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_6.01391,427,478 - 91,427,538EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (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
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (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)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
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
F344/NCrl (2019)
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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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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)
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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/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)
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
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)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (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
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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: 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:68322 AgrOrtholog
Ensembl Genes ENSRNOG00000009086 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012092 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012092 ENTREZGENE, UniProtKB/TrEMBL
InterPro ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pentaxin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pentraxin-related UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29339 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29339 ENTREZGENE
Pfam Pentaxin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Apcs PhenoGen
PRINTS PENTAXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE PTX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PTX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC229609
UniProt A0A0H2UHH2_RAT UniProtKB/TrEMBL
  H6X320 ENTREZGENE, UniProtKB/TrEMBL
  P23680 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q63539 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-25 Apcs  amyloid P component, serum  Apcs  serum amyloid P-component  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Apcs  serum amyloid P-component  Sap    Symbol updated 1299863 APPROVED
2002-06-10 Sap  serum amyloid P-component      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein 208 amino acids 68215
gene_regulation mRNA expression is increased following lipopolysaccharide treatment 68215