Hp (haptoglobin) - Rat Genome Database

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Gene: Hp (haptoglobin) Rattus norvegicus
Analyze
Symbol: Hp
Name: haptoglobin
RGD ID: 2825
Description: Enables hemoglobin binding activity and identical protein binding activity. Involved in several processes, including response to X-ray; response to growth hormone; and response to vitamin. Located in Golgi apparatus; blood microparticle; and endoplasmic reticulum. Used to study obesity and type 1 diabetes mellitus. Biomarker of several diseases, including artery disease (multiple); diabetes mellitus (multiple); hepatocellular adenoma; kidney failure (multiple); and middle cerebral artery infarction. Human ortholog(s) of this gene implicated in Plasmodium falciparum malaria; artery disease (multiple); gout; hemolytic anemia; and hyperglycemia. Orthologous to several human genes including HP (haptoglobin); INTERACTS WITH 1,1-dichloroethene; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ba1-647; liver regeneration-related protein LRRG173; zonulin
RGD Orthologs
Human
Mouse
Squirrel
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21937,539,626 - 37,544,178 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1937,539,627 - 37,544,523 (-)Ensembl
Rnor_6.01942,096,255 - 42,100,805 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1942,097,995 - 42,100,804 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01952,921,384 - 52,925,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41939,443,016 - 39,447,566 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11939,447,897 - 39,452,447 (-)NCBI
Celera1936,944,700 - 36,949,250 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute kidney failure  (IEP,ISO)
AIDS-Associated Nephropathy  (ISO)
allergic disease  (ISO)
alpha thalassemia  (ISO)
Anaphylaxis  (ISO)
anemia  (ISO)
Anhaptoglobinemia  (ISO)
arteriosclerosis  (ISO)
arthritis  (ISO)
asthma  (ISO)
atherosclerosis  (IEP,ISO)
autoimmune disease  (ISO)
beta thalassemia  (ISO)
Brain Injuries  (IEP)
Breast Neoplasms  (ISO)
cardiovascular system disease  (ISO)
Carotid Artery Injuries  (IEP)
Cerebral Hemorrhage  (ISO)
cholestasis  (IEP)
Chronic Hepatitis B  (ISO)
Chronic Hepatitis C  (ISO)
chronic kidney disease  (IEP)
chronic obstructive pulmonary disease  (ISO)
colitis  (IEP)
congestive heart failure  (IEP)
coronary artery disease  (ISO)
Coronary Disease  (ISO)
COVID-19  (ISO)
Diabetes Complications  (ISO)
diabetes mellitus  (ISO)
diabetic angiopathy  (ISO)
dilated cardiomyopathy  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
Dyslipidemias  (ISO)
Experimental Arthritis  (IEP)
Experimental Diabetes Mellitus  (IEP)
Experimental Liver Cirrhosis  (IEP)
Female Genital Neoplasms  (ISO)
Foodborne Diseases  (ISO)
gout  (ISO)
hemochromatosis  (ISO)
Hemolysis  (ISO)
hemolytic anemia  (ISO)
hemolytic-uremic syndrome  (ISO)
Hemorrhagic Shock  (IEP)
hepatitis B  (ISO)
hepatocellular adenoma  (IEP)
hepatocellular carcinoma  (ISO)
human immunodeficiency virus infectious disease  (ISO)
Hypercholesterolemia  (ISO)
hyperglycemia  (ISO)
hyperinsulinism  (ISO)
hypertension  (IEP,ISO)
Hypertensive Nephropathy  (IEP)
Hypoxia  (IEP)
Inflammation  (IEP)
inflammatory bowel disease  (ISO)
Intestinal Reperfusion Injury  (IEP)
iron deficiency anemia  (ISO)
Kawasaki disease  (ISO)
leukemia  (ISO)
liver cirrhosis  (ISO)
Liver Reperfusion Injury  (IEP)
lung cancer  (IEP)
malaria  (ISO)
Mammary Neoplasms, Experimental  (IDA)
Metabolic Syndrome  (IDA,ISO)
middle cerebral artery infarction  (IEP)
myocardial infarction  (ISO)
non-alcoholic fatty liver disease  (IEP,ISO)
obesity  (IDA,IEP,ISO)
obstructive sleep apnea  (ISO)
Pasteurellaceae Infections  (ISO)
pasteurellosis  (ISO)
Plasmodium falciparum malaria  (ISO)
Pneumococcal Pneumonia  (ISO)
pre-eclampsia  (ISO)
Pregnancy-Induced Hypertension  (ISO)
pulmonary embolism  (IEP,ISO)
pulmonary hypertension  (ISO)
retinal detachment  (ISO)
sarcoidosis  (ISO)
schizophrenia  (ISO)
severe acute respiratory syndrome  (ISO)
sickle cell anemia  (ISO)
Sickle Cell Trait  (ISO)
Starvation  (IEP)
Stroke  (ISO)
trypanosomiasis  (ISO)
tuberculosis  (ISO)
type 1 diabetes mellitus  (IDA,IEP,ISO)
type 2 diabetes mellitus  (IEP,ISO)
Venous Thrombosis  (ISO)
Wounds and Injuries  (IEP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-lariciresinol  (ISO)
(-)-lariciresinol  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
1,1-dichloroethene  (EXP,ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
3',5'-cyclic AMP  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
aflatoxin B1  (EXP,ISO)
alclofenac  (ISO)
aldehydo-D-glucose  (ISO)
ammonium chloride  (EXP)
ampicillin  (EXP)
andrographolide  (ISO)
azathioprine  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium atom  (ISO)
calciol  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (EXP,ISO)
chlordecone  (ISO)
chlorpyrifos  (ISO)
cisplatin  (EXP)
clofibrate  (EXP)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
D-penicillamine  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
diisopropyl fluorophosphate  (EXP)
dimethyl sulfoxide  (EXP)
doramapimod  (ISO)
doxorubicin  (EXP)
flutamide  (EXP)
furan  (EXP)
genistein  (EXP)
gentamycin  (EXP)
glucose  (ISO)
hexachlorobenzene  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
L-ascorbic acid  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lipopolysaccharide  (ISO)
menadione  (ISO)
methimazole  (ISO)
metronidazole  (EXP)
minocycline  (EXP)
morphine  (EXP)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodimethylamine  (EXP)
neomycin  (EXP)
nickel atom  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (EXP)
pirinixic acid  (EXP,ISO)
potassium bromate  (ISO)
potassium chromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
profenofos  (EXP)
progesterone  (ISO)
quartz  (EXP)
quercetin  (ISO)
sarin  (EXP)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenite  (EXP)
sodium fluoride  (EXP,ISO)
streptozocin  (ISO)
sulforaphane  (ISO)
T-2 toxin  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (EXP)
trichloroethene  (EXP)
Triptolide  (EXP)
triptonide  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (EXP)
warfarin  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
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Additional References at PubMed
PMID:11865981   PMID:12477932   PMID:15489334   PMID:16502470   PMID:17616219   PMID:17910034   PMID:19056867   PMID:19433579   PMID:19521970   PMID:19545490   PMID:19740759   PMID:20155810  
PMID:21805676   PMID:22254015   PMID:22516433   PMID:22664934   PMID:23012479   PMID:23117660   PMID:23376485   PMID:23533145   PMID:24006456   PMID:25645918  


Genomics

Candidate Gene Status
Hp is a candidate Gene for QTL Eau8
Comparative Map Data
Hp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21937,539,626 - 37,544,178 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1937,539,627 - 37,544,523 (-)Ensembl
Rnor_6.01942,096,255 - 42,100,805 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1942,097,995 - 42,100,804 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01952,921,384 - 52,925,934 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41939,443,016 - 39,447,566 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11939,447,897 - 39,452,447 (-)NCBI
Celera1936,944,700 - 36,949,250 (-)NCBICelera
Cytogenetic Map19q12NCBI
HP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1672,054,505 - 72,061,055 (+)EnsemblGRCh38hg38GRCh38
GRCh381672,054,505 - 72,061,055 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371672,088,404 - 72,094,954 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361670,646,009 - 70,652,458 (+)NCBINCBI36hg18NCBI36
Build 341670,646,008 - 70,652,458NCBI
Celera1656,402,627 - 56,409,074 (+)NCBI
Cytogenetic Map16q22.2NCBI
HuRef1657,855,340 - 57,861,787 (+)NCBIHuRef
CHM1_11673,501,856 - 73,508,303 (+)NCBICHM1_1
Hp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398110,301,760 - 110,305,804 (-)NCBIGRCm39mm39
GRCm39 Ensembl8110,301,760 - 110,305,804 (-)Ensembl
GRCm388109,575,128 - 109,579,172 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8109,575,128 - 109,579,172 (-)EnsemblGRCm38mm10GRCm38
MGSCv378112,099,028 - 112,103,072 (-)NCBIGRCm37mm9NCBIm37
MGSCv368112,464,257 - 112,468,192 (-)NCBImm8
Celera8113,800,405 - 113,804,474 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map857.11NCBI
LOC101976500
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934937,743,357 - 37,748,060 (+)NCBI
SpeTri2.0NW_00493647521,841,054 - 21,845,821 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1614,980,382 - 14,985,245 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2614,643,378 - 14,648,241 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap6p15-p14NCBI

Position Markers
D19Mgh5  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.01952,922,785 - 52,922,895NCBIRnor5.0
Rnor_5.01952,922,786 - 52,922,896NCBIRnor5.0
RGSC_v3.41939,446,055 - 39,446,164RGDRGSC3.4
RGSC_v3.41939,446,054 - 39,446,163UniSTSRGSC3.4
RGSC_v3.11939,450,936 - 39,451,045RGD
Celera1936,947,738 - 36,947,847UniSTS
RH 2.0 Map19457.6RGD
Cytogenetic Map19q12UniSTS
D19Arb2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21937,544,401 - 37,544,765 (-)MAPPERmRatBN7.2
Rnor_6.01942,095,668 - 42,096,031NCBIRnor6.0
Rnor_5.01952,920,797 - 52,921,160UniSTSRnor5.0
RGSC_v3.41939,447,789 - 39,448,152RGDRGSC3.4
RGSC_v3.41939,447,790 - 39,448,152UniSTSRGSC3.4
RGSC_v3.11939,452,670 - 39,453,033RGD
Celera1936,949,474 - 36,949,837UniSTS
FHH x ACI Map1930.2099UniSTS
FHH x ACI Map1930.2099RGD
Cytogenetic Map19q12UniSTS
D19Wox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21937,540,644 - 37,540,803 (-)MAPPERmRatBN7.2
Rnor_6.01942,099,630 - 42,099,786NCBIRnor6.0
Rnor_5.01952,924,759 - 52,924,915UniSTSRnor5.0
RGSC_v3.41939,444,034 - 39,444,191RGDRGSC3.4
RGSC_v3.41939,444,035 - 39,444,191UniSTSRGSC3.4
RGSC_v3.11939,448,915 - 39,449,072RGD
Celera1936,945,719 - 36,945,875UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)192753020737947399Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)192753020737947399Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)192753020737947399Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:169
Count of miRNA genes:93
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000020197, ENSRNOT00000050989
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 31 25 25
Medium 1 15 10 11 10 2 2 1 1 23 11 2
Low 3 42 17 6 8 6 6 9 73 34 18 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC111713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF476963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH002183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY325231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473972 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209684 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219547 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  K01933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000020197   ⟹   ENSRNOP00000020196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,539,627 - 37,542,488 (-)Ensembl
Rnor_6.0 Ensembl1942,097,995 - 42,100,804 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104067   ⟹   ENSRNOP00000089249
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,539,766 - 37,544,237 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115765   ⟹   ENSRNOP00000079870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,539,627 - 37,544,523 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118054   ⟹   ENSRNOP00000085960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,539,627 - 37,544,232 (-)Ensembl
RefSeq Acc Id: NM_012582   ⟹   NP_036714
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21937,539,626 - 37,544,178 (-)NCBI
Rnor_6.01942,096,255 - 42,100,805 (+)NCBI
Rnor_5.01952,921,384 - 52,925,934 (+)NCBI
RGSC_v3.41939,443,016 - 39,447,566 (-)RGD
Celera1936,944,700 - 36,949,250 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_036714   ⟸   NM_012582
- Peptide Label: precursor
- UniProtKB: P06866 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000020196   ⟸   ENSRNOT00000020197
RefSeq Acc Id: ENSRNOP00000079870   ⟸   ENSRNOT00000115765
RefSeq Acc Id: ENSRNOP00000089249   ⟸   ENSRNOT00000104067
RefSeq Acc Id: ENSRNOP00000085960   ⟸   ENSRNOT00000118054
Protein Domains
Peptidase S1   Sushi

Transcriptome

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

Promoters
RGD ID:13701135
Promoter ID:EPDNEW_R11659
Type:initiation region
Name:Hp_1
Description:haptoglobin
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_6.01942,097,982 - 42,098,042EPDNEW

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)
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
BXH2/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
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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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)
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/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)
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
FHH/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
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/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
FXLE18/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
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)
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
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)
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
HXB2/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
HXB20/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
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)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2825 AgrOrtholog
Ensembl Genes ENSRNOG00000014964 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020196 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020197 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.40.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7321960 IMAGE-MGC_LOAD
InterPro Haptoglobin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S1_PA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S1_PA_chymotrypsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_S1A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sushi_SCR_CCP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Trypsin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24464 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108751 IMAGE-MGC_LOAD
NCBI Gene 24464 ENTREZGENE
PANTHER PTHR24255:SF27 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Trypsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hp PhenoGen
PIRSF Haptoglobin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS CHYMOTRYPSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SUSHI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRYPSIN_DOM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Tryp_SPc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF50494 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57535 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC210914
UniProt A0A0H2UHM3_RAT UniProtKB/TrEMBL
  HPT_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5EBB4 UniProtKB/Swiss-Prot
  Q7TP23 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Hp  Haptoglobin      Symbol and Name status set to approved 70586 APPROVED