Htt (huntingtin) - Rat Genome Database

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Gene: Htt (huntingtin) Rattus norvegicus
Analyze
Symbol: Htt
Name: huntingtin
RGD ID: 68337
Description: Enables signaling receptor binding activity. Involved in several processes, including mRNA transport; negative regulation of cysteine-type endopeptidase activity; and regulation of intracellular mRNA localization. Located in several cellular components, including neuronal cell body; neuronal ribonucleoprotein granule; and postsynaptic density. Used to study Huntington's disease. Biomarker of transient cerebral ischemia. Human ortholog(s) of this gene implicated in Huntington's disease and Parkinson's disease. Orthologous to human HTT (huntingtin); PARTICIPATES IN Huntington's disease pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Hd; HD protein homolog; Hdh; huntingtin (Huntington disease); Huntington disease gene homolog; huntington disease protein homolog
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
mRatBN7.21475,845,836 - 75,996,094 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1475,845,836 - 75,995,070 (-)Ensembl
Rnor_6.01481,105,139 - 81,254,637 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1481,105,139 - 81,254,637 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01481,793,632 - 81,942,093 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41481,490,322 - 81,636,856 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11481,492,926 - 81,639,072 (-)NCBI
Celera1474,771,910 - 74,919,669 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure morphogenesis  (ISO)
anterior/posterior pattern specification  (ISO)
associative learning  (ISO)
axo-dendritic transport  (ISO)
brain development  (ISO)
cell aging  (ISO)
central nervous system development  (IEP,ISO)
citrulline metabolic process  (ISO)
determination of adult lifespan  (ISO)
dopamine receptor signaling pathway  (ISO)
endoplasmic reticulum organization  (ISO)
endoplasmic reticulum to Golgi vesicle-mediated transport  (ISO)
endosomal transport  (ISO)
establishment of mitotic spindle orientation  (IEA,ISO)
gastrulation  (ISO)
Golgi organization  (IEA,ISO)
grooming behavior  (ISO)
hormone metabolic process  (ISO)
insulin secretion  (ISO)
iron ion homeostasis  (ISO)
lactate biosynthetic process from pyruvate  (ISO)
learning  (ISO)
learning or memory  (ISO)
locomotory behavior  (ISO)
microtubule-based transport  (IBA)
mitochondrial transport  (ISO)
mitochondrion organization  (ISO)
mRNA transport  (IMP)
negative regulation of apoptotic process  (ISO)
negative regulation of cysteine-type endopeptidase activity  (IMP)
negative regulation of extrinsic apoptotic signaling pathway  (IEA,ISO)
neural plate formation  (ISO)
neurogenesis  (ISO)
neuron development  (ISO)
olfactory lobe development  (ISO)
paraxial mesoderm formation  (ISO)
peptide hormone secretion  (ISO)
positive regulation of aggrephagy  (IEA,ISO)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of autophagy of mitochondrion  (IEA,ISO)
positive regulation of cilium assembly  (IEA,ISO)
positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity  (IEA,ISO)
positive regulation of lipophagy  (IEA,ISO)
positive regulation of motile cilium assembly  (ISO)
positive regulation of non-motile cilium assembly  (ISO)
postsynapse to nucleus signaling pathway  (ISO)
protein destabilization  (IEA,ISO)
protein localization to centrosome  (ISO)
protein localization to nucleus  (ISO)
quinolinate biosynthetic process  (ISO)
regulation of CAMKK-AMPK signaling cascade  (IEA,ISO)
regulation of cAMP-dependent protein kinase activity  (IEA,ISO)
regulation of gene expression  (ISO)
regulation of intracellular mRNA localization  (IMP)
regulation of neuron apoptotic process  (ISO)
regulation of phosphoprotein phosphatase activity  (IEA,ISO)
regulation of protein localization to nucleus  (ISO)
regulation of synaptic plasticity  (ISO)
response to calcium ion  (ISO)
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum  (IEA,ISO)
social behavior  (ISO)
spermatogenesis  (ISO)
striatum development  (ISO)
urea cycle  (ISO)
vesicle transport along microtubule  (IEA,ISO)
visual learning  (ISO)
vocal learning  (IEA,ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Boutell JM, etal., Hum Mol Genet. 1999 Sep;8(9):1647-55.
2. DiFiglia M, etal., Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):17204-9. Epub 2007 Oct 16.
3. Gabery S, etal., Eur J Neurosci. 2012 Sep;36(6):2789-800. doi: 10.1111/j.1460-9568.2012.08193.x. Epub 2012 Jun 25.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Goffredo D, etal., J Biol Chem 2002 Oct 18;277(42):39594-8.
7. KEGG
8. Kim M, etal., Exp Neurol 2003 Sep;183(1):109-15.
9. Kumar U Brain Res Mol Brain Res 2004 Sep 10;128(1):39-47.
10. Li SH, etal., J Neurosci. 1998 Feb 15;18(4):1261-9.
11. Liu W, etal., J Huntingtons Dis. 2013;2(4):491-500. doi: 10.3233/JHD-130079.
12. Lu J, etal., Biochem Biophys Res Commun. 2015 Sep 4;464(4):988-93. doi: 10.1016/j.bbrc.2015.07.007. Epub 2015 Jul 17.
13. Ma B, etal., Sci Rep. 2011;1:140. Epub 2011 Nov 3.
14. Mangiarini L, etal., Cell 1996 Nov 1;87(3):493-506.
15. Marcora E and Kennedy MB, Hum Mol Genet. 2010 Nov 15;19(22):4373-84. Epub 2010 Aug 25.
16. Mazurová Y, etal., Biomed Res Int. 2014;2014:291531. doi: 10.1155/2014/291531. Epub 2014 Aug 3.
17. MGD data from the GO Consortium
18. Miller LC, etal., J Biol Chem 2003 Dec 26;278(52):53072-81. Epub 2003 Oct 21.
19. Nasir J, etal., Cell 1995 Jun 2;81(5):811-23.
20. NCBI rat LocusLink and RefSeq merged data July 26, 2002
21. Norremolle A, etal., Hum Mol Genet. 1993 Sep;2(9):1475-6.
22. Okano A, etal., Brain Res 2003 Mar 28;967(1-2):210-25.
23. OMIM Disease Annotation Pipeline
24. Pipeline to import KEGG annotations from KEGG into RGD
25. RGD automated data pipeline
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. Ross CA and Tabrizi SJ, Lancet Neurol. 2011 Jan;10(1):83-98. doi: 10.1016/S1474-4422(10)70245-3.
29. Saudou F and Humbert S, Neuron. 2016 Mar 2;89(5):910-26. doi: 10.1016/j.neuron.2016.02.003.
30. Savas JN, etal., J Biol Chem. 2010 Apr 23;285(17):13142-53. doi: 10.1074/jbc.M110.114561. Epub 2010 Feb 25.
31. Schmitt I, etal., Hum Mol Genet 1995 Jul;4(7):1173-82.
32. Strong TV, etal., Nat Genet 1993 Nov;5(3):259-65.
33. Tang TS, etal., Neuron. 2003 Jul 17;39(2):227-39.
34. von Hörsten S, etal., Hum Mol Genet. 2003 Mar 15;12(6):617-24.
35. Zhang Y, etal., EMBO J. 2006 Dec 13;25(24):5896-906. Epub 2006 Nov 23.
Additional References at PubMed
PMID:7477378   PMID:7550343   PMID:7618107   PMID:7647777   PMID:7662892   PMID:7748555   PMID:8757264   PMID:9398841   PMID:9668110   PMID:9806905   PMID:10037472   PMID:10078572  
PMID:10082833   PMID:10196365   PMID:10196373   PMID:10699173   PMID:10739639   PMID:10778856   PMID:10801775   PMID:10823891   PMID:10932179   PMID:11030759   PMID:11062468   PMID:11092755  
PMID:11152661   PMID:11567051   PMID:11701969   PMID:11870213   PMID:12115678   PMID:12223581   PMID:12466534   PMID:12783847   PMID:12926013   PMID:15064418   PMID:15242649   PMID:15340079  
PMID:15615787   PMID:15654337   PMID:15837803   PMID:15935052   PMID:16109169   PMID:16256944   PMID:16330479   PMID:16403806   PMID:16476778   PMID:16624677   PMID:16697652   PMID:16978870  
PMID:17213233   PMID:17251428   PMID:17284197   PMID:17442827   PMID:17565993   PMID:17704510   PMID:17708681   PMID:17715336   PMID:17947297   PMID:18573880   PMID:18595722   PMID:18606820  
PMID:18844975   PMID:18922795   PMID:19240033   PMID:19240112   PMID:19247483   PMID:19270310   PMID:19352548   PMID:19487684   PMID:19491400   PMID:19498170   PMID:20515468   PMID:20644995  
PMID:20696378   PMID:21179468   PMID:21482444   PMID:21562226   PMID:21768291   PMID:21791172   PMID:21832090   PMID:21909508   PMID:21985783   PMID:22119730   PMID:22234237   PMID:22266730  
PMID:22543707   PMID:22815947   PMID:22854022   PMID:22956852   PMID:23137697   PMID:23275563   PMID:23955097   PMID:24248062   PMID:24352657   PMID:25446099   PMID:25686248   PMID:25738228  
PMID:25848931   PMID:26264729   PMID:26436900   PMID:27271685   PMID:27751235   PMID:28494017   PMID:28821645   PMID:29415038   PMID:30143534   PMID:30185623   PMID:32757223  


Genomics

Comparative Map Data
Htt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21475,845,836 - 75,996,094 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1475,845,836 - 75,995,070 (-)Ensembl
Rnor_6.01481,105,139 - 81,254,637 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1481,105,139 - 81,254,637 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01481,793,632 - 81,942,093 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41481,490,322 - 81,636,856 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11481,492,926 - 81,639,072 (-)NCBI
Celera1474,771,910 - 74,919,669 (-)NCBICelera
Cytogenetic Map14q21NCBI
HTT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl43,041,363 - 3,243,957 (+)EnsemblGRCh38hg38GRCh38
GRCh3843,074,681 - 3,243,960 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3743,076,408 - 3,245,687 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3643,046,206 - 3,215,485 (+)NCBINCBI36hg18NCBI36
Build 3443,113,411 - 3,282,656NCBI
Celera42,987,658 - 3,157,211 (+)NCBI
Cytogenetic Map4p16.3NCBI
HuRef43,014,819 - 3,184,168 (+)NCBIHuRef
CHM1_143,074,471 - 3,243,442 (+)NCBICHM1_1
Htt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39534,919,084 - 35,069,878 (+)NCBIGRCm39mm39
GRCm39 Ensembl534,919,084 - 35,069,878 (+)Ensembl
GRCm38534,761,721 - 34,912,534 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl534,761,740 - 34,912,534 (+)EnsemblGRCm38mm10GRCm38
MGSCv37535,104,389 - 35,252,045 (+)NCBIGRCm37mm9NCBIm37
MGSCv36535,078,597 - 35,226,253 (+)NCBImm8
Celera532,235,862 - 32,383,257 (+)NCBICelera
Cytogenetic Map5B2NCBI
cM Map517.92NCBI
Htt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555141,906,502 - 2,038,889 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555141,906,189 - 2,042,357 (+)NCBIChiLan1.0ChiLan1.0
HTT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.143,116,810 - 3,287,644 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl43,128,718 - 3,283,730 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v043,215,081 - 3,388,587 (+)NCBIMhudiblu_PPA_v0panPan3
HTT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1361,076,934 - 61,221,462 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl361,079,904 - 61,330,290 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha363,660,661 - 63,805,148 (-)NCBI
ROS_Cfam_1.0361,552,532 - 61,697,091 (-)NCBI
UMICH_Zoey_3.1361,044,140 - 61,188,581 (-)NCBI
UNSW_CanFamBas_1.0361,248,468 - 61,393,186 (-)NCBI
UU_Cfam_GSD_1.0361,608,204 - 61,752,888 (-)NCBI
LOC101966195
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528566,741,409 - 66,966,567 (-)NCBI
SpeTri2.0NW_00493647720,443,101 - 20,577,167 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HTT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl81,809,785 - 1,934,024 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.181,809,768 - 1,934,002 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.281,461,795 - 1,586,182 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap8pNCBI
HTT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12745,493,467 - 45,657,690 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2745,497,352 - 45,657,621 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660511,852,227 - 1,977,171 (-)NCBIVero_WHO_p1.0
Htt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475524,602,955 - 24,729,584 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
Hdh  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21475,994,849 - 75,994,990 (+)MAPPERmRatBN7.2
Rnor_6.01481,254,417 - 81,254,557NCBIRnor6.0
Rnor_5.01481,941,873 - 81,942,013UniSTSRnor5.0
RGSC_v3.41481,636,636 - 81,636,776UniSTSRGSC3.4
Celera1474,919,449 - 74,919,589UniSTS
Cytogenetic Map14q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:230
Count of miRNA genes:164
Interacting mature miRNAs:188
Transcripts:ENSRNOT00000058166
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 16 22 6 19 6 74 26 37 10
Low 2 27 35 35 35 8 11 9 4 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058166   ⟹   ENSRNOP00000054971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1475,845,836 - 75,995,070 (-)Ensembl
Rnor_6.0 Ensembl1481,105,139 - 81,254,637 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095135   ⟹   ENSRNOP00000093649
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1475,845,836 - 75,995,070 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099389   ⟹   ENSRNOP00000085805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1475,845,836 - 75,995,070 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116192   ⟹   ENSRNOP00000076581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1475,845,836 - 75,980,506 (-)Ensembl
RefSeq Acc Id: NM_024357   ⟹   NP_077333
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,845,836 - 75,995,070 (-)NCBI
Rnor_6.01481,105,139 - 81,254,637 (-)NCBI
Rnor_5.01481,793,632 - 81,942,093 (-)NCBI
RGSC_v3.41481,490,322 - 81,636,856 (-)RGD
Celera1474,771,910 - 74,919,669 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251230   ⟹   XP_006251292
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,848,945 - 75,996,082 (-)NCBI
Rnor_6.01481,105,152 - 81,254,618 (-)NCBI
Rnor_5.01481,793,632 - 81,942,093 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251232   ⟹   XP_006251294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,857,949 - 75,996,090 (-)NCBI
Rnor_6.01481,117,239 - 81,254,619 (-)NCBI
Rnor_5.01481,793,632 - 81,942,093 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770274   ⟹   XP_008768496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,848,945 - 75,979,645 (-)NCBI
Rnor_6.01481,105,152 - 81,238,805 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091787   ⟹   XP_038947715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,848,945 - 75,996,083 (-)NCBI
RefSeq Acc Id: XM_039091788   ⟹   XP_038947716
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,848,945 - 75,996,083 (-)NCBI
RefSeq Acc Id: XM_039091789   ⟹   XP_038947717
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21475,865,766 - 75,996,094 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_077333   ⟸   NM_024357
- UniProtKB: G3V9P7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251292   ⟸   XM_006251230
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251294   ⟸   XM_006251232
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008768496   ⟸   XM_008770274
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000054971   ⟸   ENSRNOT00000058166
RefSeq Acc Id: XP_038947716   ⟸   XM_039091788
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038947715   ⟸   XM_039091787
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038947717   ⟸   XM_039091789
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000076581   ⟸   ENSRNOT00000116192
RefSeq Acc Id: ENSRNOP00000093649   ⟸   ENSRNOT00000095135
RefSeq Acc Id: ENSRNOP00000085805   ⟸   ENSRNOT00000099389

Transcriptome

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

Promoters
RGD ID:13699395
Promoter ID:EPDNEW_R9920
Type:multiple initiation site
Name:Htt_1
Description:huntingtin
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_6.01481,254,628 - 81,254,688EPDNEW

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)
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)
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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)
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)
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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)
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)
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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)
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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/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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 81818434 81818435 A T snv F344/DuCrlCrlj (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 81132389 81132390 A C snv LN/MavRrrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:68337 AgrOrtholog
Ensembl Genes ENSRNOG00000011073 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000054971 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058166 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Huntingtin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Huntingtin_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Huntingtin_middle-repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29424 UniProtKB/TrEMBL
NCBI Gene 29424 ENTREZGENE
PANTHER PTHR10170 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF3652 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Htt PhenoGen
PRINTS HUNTINGTIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V9P7 ENTREZGENE, UniProtKB/TrEMBL
  HD_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-06-27 Htt  huntingtin  Htt  huntingtin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-11 Htt  huntingtin  Hd  huntingtin (Huntington disease)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-18 Hd  huntingtin (Huntington disease)  Hdh  Huntington disease gene homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Hdh  Huntington disease gene homolog      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in neurons of the dentate gyrus and pyramidal neurons of the hippocampal formation, cerebellar granule cell layer, cerebellar Purkinje cells and pontine nuclei 68260