Nsd1 (nuclear receptor binding SET domain protein 1) - Rat Genome Database

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Gene: Nsd1 (nuclear receptor binding SET domain protein 1) Rattus norvegicus
Analyze
Symbol: Nsd1
Name: nuclear receptor binding SET domain protein 1
RGD ID: 1307748
Description: Predicted to enable several functions, including histone-lysine N-methyltransferase activity; nuclear receptor binding activity; and zinc ion binding activity. Predicted to be involved in histone methylation; negative regulation of transcription by RNA polymerase II; and positive regulation of transcription, DNA-templated. Predicted to act upstream of or within gastrulation with mouth forming second; regulation of RNA polymerase II regulatory region sequence-specific DNA binding activity; and regulation of protein modification process. Predicted to be active in chromatin and nucleus. Human ortholog(s) of this gene implicated in Sotos syndrome; Sotos syndrome 1; acute myeloid leukemia; microcephaly; and neuroblastoma. Orthologous to human NSD1 (nuclear receptor binding SET domain protein 1); PARTICIPATES IN histone modification pathway; lysine degradation pathway; INTERACTS WITH 17alpha-ethynylestradiol; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific; histone-lysine N-methyltransferase, H3 lysine-36 specific; LOC306764
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
mRatBN7.2179,311,963 - 9,426,373 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl179,315,237 - 9,425,358 (-)Ensembl
Rnor_6.0179,840,859 - 9,955,391 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl179,844,133 - 9,952,898 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01711,950,539 - 12,065,042 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,362,482 - 15,471,961 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11715,363,376 - 15,471,151 (-)NCBI
Celera179,393,607 - 9,502,492 (-)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9628876   PMID:11509567   PMID:12805229   PMID:15522233   PMID:18157086   PMID:20837538   PMID:21196496  


Genomics

Comparative Map Data
Nsd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2179,311,963 - 9,426,373 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl179,315,237 - 9,425,358 (-)Ensembl
Rnor_6.0179,840,859 - 9,955,391 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl179,844,133 - 9,952,898 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01711,950,539 - 12,065,042 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41715,362,482 - 15,471,961 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11715,363,376 - 15,471,151 (-)NCBI
Celera179,393,607 - 9,502,492 (-)NCBICelera
Cytogenetic Map17p14NCBI
NSD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5177,133,025 - 177,300,213 (+)EnsemblGRCh38hg38GRCh38
GRCh385177,131,835 - 177,300,213 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375176,560,016 - 176,727,214 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365176,493,532 - 176,655,369 (+)NCBINCBI36hg18NCBI36
Build 345176,494,690 - 176,655,367NCBI
Celera5171,774,148 - 171,941,231 (-)NCBI
Cytogenetic Map5q35.3NCBI
HuRef5171,481,615 - 171,647,948 (+)NCBIHuRef
CHM1_15175,992,834 - 176,160,257 (+)NCBICHM1_1
Nsd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391355,357,595 - 55,466,138 (+)NCBIGRCm39mm39
GRCm39 Ensembl1355,357,595 - 55,466,138 (+)Ensembl
GRCm381355,209,782 - 55,318,325 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1355,209,782 - 55,318,325 (+)EnsemblGRCm38mm10GRCm38
MGSCv371355,311,143 - 55,419,686 (+)NCBIGRCm37mm9NCBIm37
MGSCv361355,243,517 - 55,324,503 (+)NCBImm8
Celera1356,265,599 - 56,373,905 (+)NCBICelera
Cytogenetic Map13B1NCBI
Nsd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540829,413,595 - 29,542,768 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540829,416,393 - 29,547,444 (+)NCBIChiLan1.0ChiLan1.0
NSD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15179,499,866 - 179,666,351 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5179,499,865 - 179,666,351 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05172,431,968 - 172,602,174 (+)NCBIMhudiblu_PPA_v0panPan3
NSD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1436,058,351 - 36,214,254 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl436,063,134 - 36,210,999 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha436,025,606 - 36,179,354 (-)NCBI
ROS_Cfam_1.0436,424,511 - 36,576,907 (-)NCBI
UMICH_Zoey_3.1436,249,611 - 36,403,905 (-)NCBI
UNSW_CanFamBas_1.0436,435,795 - 36,591,251 (-)NCBI
UU_Cfam_GSD_1.0436,945,351 - 37,099,849 (-)NCBI
Nsd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213122,401,170 - 122,552,286 (+)NCBI
SpeTri2.0NW_0049365971,426,318 - 1,577,193 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NSD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl280,654,378 - 80,809,059 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1280,649,882 - 80,810,934 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2282,120,312 - 82,218,958 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NSD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12379,140,148 - 79,309,579 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2379,141,114 - 79,304,820 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607510,326,178 - 10,497,901 (+)NCBIVero_WHO_p1.0
Nsd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473312,781,693 - 12,929,861 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D17Rat101  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,348,318 - 9,348,531 (+)MAPPERmRatBN7.2
Rnor_6.0179,877,214 - 9,877,426NCBIRnor6.0
Rnor_5.01711,986,894 - 11,987,106UniSTSRnor5.0
RGSC_v3.41715,396,415 - 15,396,627UniSTSRGSC3.4
RGSC_v3.41715,396,414 - 15,396,627RGDRGSC3.4
RGSC_v3.11715,396,415 - 15,396,627RGD
Celera179,426,695 - 9,426,903UniSTS
RH 3.4 Map1777.9RGD
RH 3.4 Map1777.9UniSTS
RH 2.0 Map1741.5RGD
SHRSP x BN Map178.3RGD
Cytogenetic Map17p14UniSTS
RH137723  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,332,331 - 9,332,526 (+)MAPPERmRatBN7.2
Rnor_6.0179,861,228 - 9,861,422NCBIRnor6.0
Rnor_5.01711,970,908 - 11,971,102UniSTSRnor5.0
RGSC_v3.41715,379,577 - 15,379,771UniSTSRGSC3.4
Celera179,410,703 - 9,410,897UniSTS
RH 3.4 Map1776.4UniSTS
Cytogenetic Map17p14UniSTS
RH136183  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,317,647 - 9,317,847 (+)MAPPERmRatBN7.2
Rnor_6.0179,846,544 - 9,846,743NCBIRnor6.0
Rnor_5.01711,956,224 - 11,956,423UniSTSRnor5.0
RGSC_v3.41715,364,893 - 15,365,092UniSTSRGSC3.4
Celera179,396,018 - 9,396,217UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1581553Pur14Proteinuria QTL 145.30.0001total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)17797996816317111Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:174
Count of miRNA genes:122
Interacting mature miRNAs:151
Transcripts:ENSRNOT00000060928
Prediction methods:Miranda, Pita, 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 40 52 36 19 36 8 8 74 35 38 11 8
Low 3 5 5 5 3 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001107337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006253627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095619 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095622 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095623 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC095305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ217063 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000060928   ⟹   ENSRNOP00000057648
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,315,237 - 9,423,870 (-)Ensembl
Rnor_6.0 Ensembl179,844,133 - 9,952,898 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105851   ⟹   ENSRNOP00000084557
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,315,237 - 9,423,040 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107527   ⟹   ENSRNOP00000077028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,315,237 - 9,425,358 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113096   ⟹   ENSRNOP00000078952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,421,716 - 9,424,152 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118233   ⟹   ENSRNOP00000094644
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl179,315,237 - 9,424,476 (-)Ensembl
RefSeq Acc Id: NM_001107337   ⟹   NP_001100807
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,315,237 - 9,423,870 (-)NCBI
Rnor_6.0179,844,133 - 9,952,898 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
RGSC_v3.41715,362,482 - 15,471,961 (-)RGD
Celera179,393,607 - 9,502,492 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253620   ⟹   XP_006253682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,424,454 (-)NCBI
Rnor_6.0179,840,859 - 9,953,422 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253621   ⟹   XP_006253683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,425,180 (-)NCBI
Rnor_6.0179,840,859 - 9,954,376 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253622   ⟹   XP_006253684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,424,134 (-)NCBI
Rnor_6.0179,840,859 - 9,953,180 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253623   ⟹   XP_006253685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,424,099 (-)NCBI
Rnor_6.0179,840,859 - 9,953,134 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253624   ⟹   XP_006253686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,426,373 (-)NCBI
Rnor_6.0179,840,859 - 9,955,391 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006253627   ⟹   XP_006253689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,317,899 - 9,424,455 (-)NCBI
Rnor_6.0179,846,845 - 9,953,421 (-)NCBI
Rnor_5.01711,950,539 - 12,065,042 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771491   ⟹   XP_008769713
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,423,865 (-)NCBI
Rnor_6.0179,840,859 - 9,952,931 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039095618   ⟹   XP_038951546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,424,450 (-)NCBI
RefSeq Acc Id: XM_039095619   ⟹   XP_038951547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,425,180 (-)NCBI
RefSeq Acc Id: XM_039095620   ⟹   XP_038951548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,426,373 (-)NCBI
RefSeq Acc Id: XM_039095621   ⟹   XP_038951549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,424,097 (-)NCBI
RefSeq Acc Id: XM_039095622   ⟹   XP_038951550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,424,135 (-)NCBI
RefSeq Acc Id: XM_039095623   ⟹   XP_038951551
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,422,974 (-)NCBI
RefSeq Acc Id: XM_039095624   ⟹   XP_038951552
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,311,963 - 9,422,203 (-)NCBI
RefSeq Acc Id: XM_039095625   ⟹   XP_038951553
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2179,352,086 - 9,424,462 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100807   ⟸   NM_001107337
- UniProtKB: D4AA06 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253686   ⟸   XM_006253624
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253683   ⟸   XM_006253621
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253682   ⟸   XM_006253620
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253684   ⟸   XM_006253622
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253685   ⟸   XM_006253623
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253689   ⟸   XM_006253627
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_008769713   ⟸   XM_008771491
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000057648   ⟸   ENSRNOT00000060928
RefSeq Acc Id: XP_038951548   ⟸   XM_039095620
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951547   ⟸   XM_039095619
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951546   ⟸   XM_039095618
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951550   ⟸   XM_039095622
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951549   ⟸   XM_039095621
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951551   ⟸   XM_039095623
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951552   ⟸   XM_039095624
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038951553   ⟸   XM_039095625
- Peptide Label: isoform X6
RefSeq Acc Id: ENSRNOP00000078952   ⟸   ENSRNOT00000113096
RefSeq Acc Id: ENSRNOP00000084557   ⟸   ENSRNOT00000105851
RefSeq Acc Id: ENSRNOP00000094644   ⟸   ENSRNOT00000118233
RefSeq Acc Id: ENSRNOP00000077028   ⟸   ENSRNOT00000107527
Protein Domains
AWS   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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307748 AgrOrtholog
Ensembl Genes ENSRNOG00000016680 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000057648 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000060928 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro AWS UniProtKB/TrEMBL
  C5HCH 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:306764 UniProtKB/TrEMBL
NCBI Gene 306764 ENTREZGENE
Pfam AWS UniProtKB/TrEMBL
  C5HCH UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
PhenoGen Nsd1 PhenoGen
PROSITE AWS 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
  PHD UniProtKB/TrEMBL
  PostSET UniProtKB/TrEMBL
  PWWP UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt D4AA06 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Nsd1  nuclear receptor binding SET domain protein 1   Nsd1_predicted  nuclear receptor binding SET domain protein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Nsd1_predicted  nuclear receptor binding SET domain protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED