Nsd2 (nuclear receptor binding SET domain protein 2) - Rat Genome Database

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Gene: Nsd2 (nuclear receptor binding SET domain protein 2) Rattus norvegicus
Analyze
Symbol: Nsd2
Name: nuclear receptor binding SET domain protein 2
RGD ID: 1307955
Description: Predicted to enable chromatin binding activity; histone methyltransferase activity (H3-K36 specific); and sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to act upstream of or within several processes, including cardiac septum morphogenesis; histone lysine methylation; and regulation of nucleobase-containing compound metabolic process. Predicted to be located in nucleoplasm. Predicted to be active in chromatin and nucleus. Human ortholog(s) of this gene implicated in Wolf-Hirschhorn syndrome. Orthologous to human NSD2 (nuclear receptor binding SET domain protein 2); PARTICIPATES IN lysine degradation pathway; INTERACTS WITH 6-propyl-2-thiouracil; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: histone-lysine N-methyltransferase NSD2; LOC305456; LOC680537; probable histone-lysine N-methyltransferase NSD2; RGD1565590; similar to Wolf-Hirschhorn syndrome candidate 1 protein isoform 1; Whsc1; Wolf-Hirschhorn syndrome candidate 1; Wolf-Hirschhorn syndrome candidate 1 (human)
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
mRatBN7.21476,833,194 - 76,911,304 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1476,835,637 - 76,913,641 (-)Ensembl
Rnor_6.01482,119,210 - 82,196,501 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,119,210 - 82,171,480 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01482,803,450 - 82,885,540 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41482,528,213 - 82,580,192NCBIRGSC3.4rn4RGSC3.4
Celera1475,757,842 - 75,809,420 (-)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
berberine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
ciguatoxin CTX1B  (ISO)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
Enterolactone  (ISO)
entinostat  (ISO)
ethanol  (ISO)
fipronil  (EXP)
geraniol  (ISO)
glycerol 2-phosphate  (ISO)
L-ascorbic acid  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
lithium chloride  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
topotecan  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
xylitol  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:15632090   PMID:19483677   PMID:23241889   PMID:31040165  


Genomics

Comparative Map Data
Nsd2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21476,833,194 - 76,911,304 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1476,835,637 - 76,913,641 (-)Ensembl
Rnor_6.01482,119,210 - 82,196,501 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1482,119,210 - 82,171,480 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01482,803,450 - 82,885,540 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41482,528,213 - 82,580,192NCBIRGSC3.4rn4RGSC3.4
Celera1475,757,842 - 75,809,420 (-)NCBICelera
Cytogenetic Map14q21NCBI
NSD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl41,871,393 - 1,982,207 (+)EnsemblGRCh38hg38GRCh38
GRCh3841,871,393 - 1,982,207 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3741,873,120 - 1,983,919 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3641,842,921 - 1,953,728 (+)NCBINCBI36hg18NCBI36
Build 3441,908,238 - 1,948,753NCBI
Celera41,806,735 - 1,896,162 (+)NCBI
Cytogenetic Map4p16.3NCBI
HuRef41,835,879 - 1,925,293 (+)NCBIHuRef
CHM1_141,838,966 - 1,982,597 (+)NCBICHM1_1
Nsd2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39533,974,286 - 34,055,310 (+)NCBIGRCm39mm39
GRCm39 Ensembl533,978,069 - 34,055,319 (+)Ensembl
GRCm38533,820,676 - 33,897,966 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl533,820,725 - 33,897,975 (+)EnsemblGRCm38mm10GRCm38
MGSCv37534,185,761 - 34,240,615 (+)NCBIGRCm37mm9NCBIm37
MGSCv36534,137,582 - 34,212,733 (+)NCBImm8
Celera531,320,283 - 31,375,217 (+)NCBICelera
Cytogenetic Map5B2NCBI
Nsd2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555141,069,085 - 1,162,624 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555141,084,522 - 1,162,624 (+)NCBIChiLan1.0ChiLan1.0
NSD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.141,938,777 - 2,027,425 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl41,945,307 - 2,027,425 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v042,009,276 - 2,119,182 (+)NCBIMhudiblu_PPA_v0panPan3
NSD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1362,164,888 - 62,228,006 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl362,167,939 - 62,228,035 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha364,685,041 - 64,745,834 (-)NCBI
ROS_Cfam_1.0362,642,652 - 62,703,479 (-)NCBI
UMICH_Zoey_3.1362,136,547 - 62,197,103 (-)NCBI
UNSW_CanFamBas_1.0362,339,914 - 62,400,643 (-)NCBI
UU_Cfam_GSD_1.0362,698,946 - 62,759,731 (-)NCBI
Nsd2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528567,758,741 - 67,832,919 (-)NCBI
SpeTri2.0NW_00493647721,460,442 - 21,531,563 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NSD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8963,884 - 1,018,025 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18938,832 - 1,018,032 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28412,141 - 514,862 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NSD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12746,787,325 - 46,896,898 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2746,787,154 - 46,867,792 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660513,159,458 - 3,273,021 (-)NCBIVero_WHO_p1.0
Nsd2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475525,510,329 - 25,588,540 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH127704  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21476,835,714 - 76,835,917 (+)MAPPERmRatBN7.2
Rnor_6.01482,120,630 - 82,120,832NCBIRnor6.0
Rnor_5.01482,804,870 - 82,805,072UniSTSRnor5.0
RGSC_v3.41482,529,633 - 82,529,835UniSTSRGSC3.4
Celera1475,759,262 - 75,759,464UniSTS
Cytogenetic Map14q21UniSTS
BI290800  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21476,834,649 - 76,834,827 (+)MAPPERmRatBN7.2
Rnor_6.01482,119,565 - 82,119,742NCBIRnor6.0
Rnor_5.01482,803,805 - 82,803,982UniSTSRnor5.0
RGSC_v3.41482,528,568 - 82,528,745UniSTSRGSC3.4
Celera1475,758,197 - 75,758,374UniSTS
RH 3.4 Map14489.99UniSTS
Cytogenetic Map14q21UniSTS
RH140649  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21476,833,835 - 76,834,046 (+)MAPPERmRatBN7.2
Rnor_6.01482,118,751 - 82,118,961NCBIRnor6.0
Rnor_5.01482,802,991 - 82,803,201UniSTSRnor5.0
RGSC_v3.41482,527,754 - 82,527,964UniSTSRGSC3.4
Celera1475,757,383 - 75,757,593UniSTS
Cytogenetic Map14q21UniSTS
RH141045  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21476,859,206 - 76,859,410 (+)MAPPERmRatBN7.2
Rnor_6.01482,144,844 - 82,145,047NCBIRnor6.0
Rnor_5.01482,829,084 - 82,829,287UniSTSRnor5.0
RGSC_v3.41482,553,123 - 82,553,326UniSTSRGSC3.4
Celera1475,782,752 - 75,782,955UniSTS
Cytogenetic Map14q21UniSTS
BF390060  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21476,841,864 - 76,842,022 (+)MAPPERmRatBN7.2
Rnor_6.01482,126,780 - 82,126,937NCBIRnor6.0
Rnor_5.01482,811,020 - 82,811,177UniSTSRnor5.0
RGSC_v3.41482,535,783 - 82,535,940UniSTSRGSC3.4
Celera1475,765,412 - 75,765,569UniSTS
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:593
Count of miRNA genes:268
Interacting mature miRNAs:355
Transcripts:ENSRNOT00000021952
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 3 26 38 22 19 22 1 1 74 26 41 11 1
Low 17 19 19 19 7 10 9 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006251379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008770364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC133613 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000021952   ⟹   ENSRNOP00000021952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1476,835,637 - 76,913,641 (-)Ensembl
Rnor_6.0 Ensembl1482,119,210 - 82,171,480 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106566   ⟹   ENSRNOP00000082542
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1476,858,331 - 76,913,641 (-)Ensembl
RefSeq Acc Id: NM_001191552   ⟹   NP_001178481
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,834,295 - 76,885,843 (-)NCBI
Rnor_6.01482,119,210 - 82,171,480 (-)NCBI
Rnor_5.01482,803,450 - 82,885,540 (-)NCBI
Celera1475,757,842 - 75,809,420 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251372   ⟹   XP_006251434
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Rnor_5.01482,803,450 - 82,885,540 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251373   ⟹   XP_006251435
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Rnor_5.01482,803,450 - 82,885,540 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251376   ⟹   XP_006251438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Rnor_5.01482,803,450 - 82,885,540 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006251378   ⟹   XP_006251440
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Rnor_5.01482,803,450 - 82,885,540 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770364   ⟹   XP_008768586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599378   ⟹   XP_017454867
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599379   ⟹   XP_017454868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,910,699 (-)NCBI
Rnor_6.01482,120,552 - 82,196,501 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039092428   ⟹   XP_038948356
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092429   ⟹   XP_038948357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092430   ⟹   XP_038948358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092431   ⟹   XP_038948359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092432   ⟹   XP_038948360
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092433   ⟹   XP_038948361
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092434   ⟹   XP_038948362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092435   ⟹   XP_038948363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092436   ⟹   XP_038948364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092437   ⟹   XP_038948365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,304 (-)NCBI
RefSeq Acc Id: XM_039092438   ⟹   XP_038948366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,833,194 - 76,911,299 (-)NCBI
RefSeq Acc Id: XM_039092439   ⟹   XP_038948367
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21476,852,735 - 76,911,304 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178481   ⟸   NM_001191552
- Sequence:
RefSeq Acc Id: XP_006251440   ⟸   XM_006251378
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251435   ⟸   XM_006251373
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251438   ⟸   XM_006251376
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006251434   ⟸   XM_006251372
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768586   ⟸   XM_008770364
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454868   ⟸   XM_017599379
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017454867   ⟸   XM_017599378
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000021952   ⟸   ENSRNOT00000021952
RefSeq Acc Id: XP_038948361   ⟸   XM_039092433
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948358   ⟸   XM_039092430
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948364   ⟸   XM_039092436
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948357   ⟸   XM_039092429
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948362   ⟸   XM_039092434
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948365   ⟸   XM_039092437
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948359   ⟸   XM_039092431
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948363   ⟸   XM_039092435
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948356   ⟸   XM_039092428
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948360   ⟸   XM_039092432
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948366   ⟸   XM_039092438
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948367   ⟸   XM_039092439
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000082542   ⟸   ENSRNOT00000106566
Protein Domains
AWS   HMG box   PHD-type   Post-SET   PWWP   RING-type   SET

Transcriptome

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


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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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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_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 82132821 82132822 C G snv LEW/Crl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307955 AgrOrtholog
Ensembl Genes ENSRNOG00000038140 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021952 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021952 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
InterPro AWS UniProtKB/TrEMBL
  C5HCH UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  Post-SET_dom UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:680537 UniProtKB/TrEMBL
NCBI Gene 680537 ENTREZGENE
Pfam AWS UniProtKB/TrEMBL
  C5HCH UniProtKB/TrEMBL
  HMG_box UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
PhenoGen Nsd2 PhenoGen
PROSITE AWS UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/TrEMBL
  POST_SET UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
  ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART AWS UniProtKB/TrEMBL
  HMG UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PostSET UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  HMG-box UniProtKB/TrEMBL
UniProt D4A9J4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-11-29 Nsd2  nuclear receptor binding SET domain protein 2  Whsc1  Wolf-Hirschhorn syndrome candidate 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-02-04 Whsc1  Wolf-Hirschhorn syndrome candidate 1  Whsc1  Wolf-Hirschhorn syndrome candidate 1 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Whsc1  Wolf-Hirschhorn syndrome candidate 1 (human)  Whsc1_predicted  Wolf-Hirschhorn syndrome candidate 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 Whsc1_predicted  Wolf-Hirschhorn syndrome candidate 1 (predicted)  LOC682525  similar to Wolf-Hirschhorn syndrome candidate 1 protein isoform 1  Data Merged 1643240 APPROVED
2007-02-16 Whsc1_predicted  Wolf-Hirschhorn syndrome candidate 1 (predicted)  LOC680537  similar to Wolf-Hirschhorn syndrome candidate 1 protein isoform 1  Data Merged 737654 APPROVED
2006-11-20 LOC680537  similar to Wolf-Hirschhorn syndrome candidate 1 protein isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC682525  similar to Wolf-Hirschhorn syndrome candidate 1 protein isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Whsc1_predicted  Wolf-Hirschhorn syndrome candidate 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED