Setdb2 (SET domain bifurcated histone lysine methyltransferase 2) - Rat Genome Database

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Gene: Setdb2 (SET domain bifurcated histone lysine methyltransferase 2) Rattus norvegicus
Analyze
Symbol: Setdb2
Name: SET domain bifurcated histone lysine methyltransferase 2
RGD ID: 2319564
Description: Predicted to enable histone methyltransferase activity (H3-K9 specific). Predicted to be involved in several processes, including heterochromatin organization; histone H3-K9 methylation; and regulation of gene expression. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SETDB2 (SET domain bifurcated histone lysine methyltransferase 2); INTERACTS WITH bisphenol A; paracetamol; 1,2-dichloroethane (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Also known as: histone-lysine N-methyltransferase SETDB2; LOC100361710; LOC102552532; LOC305931; PHD finger protein 11; SET domain bifurcated protein 2-Phf11-1 fusion protein-like; SET domain, bifurcated 2; uncharacterized LOC102552532
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21533,553,657 - 33,606,586 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1533,453,952 - 33,606,470 (-)Ensembl
Rnor_6.01538,699,135 - 39,745,035 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1539,693,842 - 39,705,208 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1539,712,861 - 39,742,103 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01543,514,812 - 43,566,347 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41538,485,801 - 38,537,934 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11538,521,117 - 38,546,769 (-)NCBI
Celera1533,261,262 - 33,313,067 (-)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromosome  (IEA)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:20404330   PMID:31904090  


Genomics

Comparative Map Data
Setdb2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21533,553,657 - 33,606,586 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1533,453,952 - 33,606,470 (-)Ensembl
Rnor_6.01538,699,135 - 39,745,035 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1539,693,842 - 39,705,208 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1539,712,861 - 39,742,103 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01543,514,812 - 43,566,347 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41538,485,801 - 38,537,934 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11538,521,117 - 38,546,769 (-)NCBI
Celera1533,261,262 - 33,313,067 (-)NCBICelera
Cytogenetic Map15p12NCBI
SETDB2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1349,444,374 - 49,495,003 (+)EnsemblGRCh38hg38GRCh38
GRCh381349,444,274 - 49,495,003 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371350,018,410 - 50,069,139 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361348,916,511 - 48,964,299 (+)NCBINCBI36hg18NCBI36
Build 341348,916,510 - 48,964,298NCBI
Celera1331,073,381 - 31,124,092 (+)NCBI
Cytogenetic Map13q14.2NCBI
HuRef1330,812,012 - 30,862,730 (+)NCBIHuRef
CHM1_11349,985,855 - 50,036,670 (+)NCBICHM1_1
Setdb2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391459,639,458 - 59,678,329 (-)NCBIGRCm39mm39
GRCm39 Ensembl1459,639,458 - 59,678,333 (-)Ensembl
GRCm381459,402,009 - 59,440,880 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1459,402,009 - 59,440,884 (-)EnsemblGRCm38mm10GRCm38
MGSCv371460,020,848 - 60,059,714 (-)NCBIGRCm37mm9NCBIm37
MGSCv361458,356,121 - 58,394,987 (-)NCBImm8
Celera1457,202,641 - 57,241,178 (-)NCBICelera
Cytogenetic Map14C3NCBI
Setdb2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554312,813,602 - 2,945,323 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554312,899,849 - 2,943,091 (+)NCBIChiLan1.0ChiLan1.0
SETDB2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11349,335,801 - 49,386,150 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1349,335,894 - 49,386,150 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01330,584,762 - 30,635,408 (+)NCBIMhudiblu_PPA_v0panPan3
SETDB2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1222,263,990 - 2,319,249 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl222,244,507 - 2,319,158 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha222,265,058 - 2,348,059 (-)NCBI
ROS_Cfam_1.0222,227,297 - 2,310,585 (-)NCBI
UMICH_Zoey_3.1222,135,665 - 2,218,647 (-)NCBI
UNSW_CanFamBas_1.0222,184,950 - 2,268,045 (-)NCBI
UU_Cfam_GSD_1.0222,203,337 - 2,286,353 (-)NCBI
LOC101978403
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945159,052,878 - 159,123,774 (+)NCBI
SpeTri2.0NW_0049365652,536,623 - 2,607,824 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SETDB2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1118,252,527 - 18,297,826 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11118,252,525 - 18,298,234 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21118,568,628 - 18,613,159 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SETDB2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1327,359,571 - 27,410,910 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl327,360,150 - 27,411,466 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605716,475,108 - 16,525,745 (-)NCBIVero_WHO_p1.0


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:267
Count of miRNA genes:80
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000036781, ENSRNOT00000071919, ENSRNOT00000074587
Prediction methods:Microtar, Miranda, Rnahybrid
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 2 10 47 32 28 32 64 20 43 11
Low 4 76 66 49 10 49 16 21 84 50 39 11 16
Below cutoff 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_002725109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006221967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769140 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008769153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599892 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017604919 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093876 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093877 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093879 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093883 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039093888 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_224248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005493987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC093383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000270 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000015412   ⟹   ENSRNOP00000015412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,555,041 - 33,570,571 (-)Ensembl
Rnor_6.0 Ensembl1539,693,842 - 39,705,208 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000036781   ⟹   ENSRNOP00000036240
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,563,394 - 33,606,470 (-)Ensembl
Rnor_6.0 Ensembl1539,712,861 - 39,742,103 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071919   ⟹   ENSRNOP00000065027
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,530,525 - 33,606,470 (-)Ensembl
Rnor_6.0 Ensembl1539,712,861 - 39,742,103 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000074587   ⟹   ENSRNOP00000066366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,574,035 - 33,606,470 (-)Ensembl
Rnor_6.0 Ensembl1539,712,861 - 39,742,103 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094078   ⟹   ENSRNOP00000084411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,488,292 - 33,606,470 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095736   ⟹   ENSRNOP00000092797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,453,952 - 33,549,188 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110448   ⟹   ENSRNOP00000084130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,526,409 - 33,549,188 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112465   ⟹   ENSRNOP00000091454
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,453,952 - 33,473,651 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000120126   ⟹   ENSRNOP00000086164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,526,409 - 33,547,555 (-)Ensembl
RefSeq Acc Id: XM_039093875   ⟹   XP_038949803
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,553,657 - 33,606,488 (-)NCBI
RefSeq Acc Id: XM_039093876   ⟹   XP_038949804
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,606,586 (-)NCBI
RefSeq Acc Id: XM_039093877   ⟹   XP_038949805
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,597,378 (-)NCBI
RefSeq Acc Id: XM_039093879   ⟹   XP_038949807
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,600,097 (-)NCBI
RefSeq Acc Id: XM_039093880   ⟹   XP_038949808
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,589,123 (-)NCBI
RefSeq Acc Id: XM_039093881   ⟹   XP_038949809
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,574,344 - 33,606,483 (-)NCBI
RefSeq Acc Id: XM_039093882   ⟹   XP_038949810
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,566,468 - 33,606,484 (-)NCBI
RefSeq Acc Id: XM_039093883   ⟹   XP_038949811
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,581,609 (-)NCBI
RefSeq Acc Id: XM_039093884   ⟹   XP_038949812
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,579,838 - 33,606,485 (-)NCBI
RefSeq Acc Id: XM_039093885   ⟹   XP_038949813
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,583,135 (-)NCBI
RefSeq Acc Id: XM_039093886   ⟹   XP_038949814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,574,166 (-)NCBI
RefSeq Acc Id: XM_039093887   ⟹   XP_038949815
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,579,751 (-)NCBI
RefSeq Acc Id: XM_039093888   ⟹   XP_038949816
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,555,263 - 33,579,747 (-)NCBI
RefSeq Acc Id: XR_005493987
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21533,564,766 - 33,606,483 (-)NCBI
Reference Sequences
RefSeq Acc Id: ENSRNOP00000036240   ⟸   ENSRNOT00000036781
RefSeq Acc Id: ENSRNOP00000065027   ⟸   ENSRNOT00000071919
RefSeq Acc Id: ENSRNOP00000066366   ⟸   ENSRNOT00000074587
RefSeq Acc Id: ENSRNOP00000015412   ⟸   ENSRNOT00000015412
RefSeq Acc Id: XP_038949803   ⟸   XM_039093875
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949804   ⟸   XM_039093876
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038949807   ⟸   XM_039093879
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949805   ⟸   XM_039093877
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038949808   ⟸   XM_039093880
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038949813   ⟸   XM_039093885
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038949811   ⟸   XM_039093883
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038949815   ⟸   XM_039093887
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038949816   ⟸   XM_039093888
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038949814   ⟸   XM_039093886
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038949810   ⟸   XM_039093882
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038949809   ⟸   XM_039093881
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038949812   ⟸   XM_039093884
- Peptide Label: isoform X7
RefSeq Acc Id: ENSRNOP00000084411   ⟸   ENSRNOT00000094078
RefSeq Acc Id: ENSRNOP00000086164   ⟸   ENSRNOT00000120126
RefSeq Acc Id: ENSRNOP00000092797   ⟸   ENSRNOT00000095736
RefSeq Acc Id: ENSRNOP00000091454   ⟸   ENSRNOT00000112465
RefSeq Acc Id: ENSRNOP00000084130   ⟸   ENSRNOT00000110448
Protein Domains
MBD   PHD-type   Pre-SET   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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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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:2319564 AgrOrtholog
Ensembl Genes ENSRNOG00000021680 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000053915 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000015412 UniProtKB/TrEMBL
  ENSRNOP00000036240 UniProtKB/TrEMBL
  ENSRNOP00000065027 UniProtKB/TrEMBL
  ENSRNOP00000066366 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015412 UniProtKB/TrEMBL
  ENSRNOT00000036781 UniProtKB/TrEMBL
  ENSRNOT00000071919 UniProtKB/TrEMBL
  ENSRNOT00000074587 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro DNA-bd_integrase-typ UniProtKB/TrEMBL
  EPHD UniProtKB/TrEMBL
  Methyl_CpG_DNA-bd UniProtKB/TrEMBL
  Pre-SET_dom UniProtKB/TrEMBL
  SET_dom UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
NCBI Gene 100361710 ENTREZGENE
Pfam MBD UniProtKB/TrEMBL
  Pre-SET UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
PhenoGen Setdb2 PhenoGen
PROSITE EPHD UniProtKB/TrEMBL
  MBD UniProtKB/TrEMBL
  PRE_SET UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
SMART MBD UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  PreSET UniProtKB/TrEMBL
  SET UniProtKB/TrEMBL
Superfamily-SCOP DNA-binding_integrase-type UniProtKB/TrEMBL
  SSF57903 UniProtKB/TrEMBL
UniProt D3ZDZ9_RAT UniProtKB/TrEMBL
  F1LQ59_RAT UniProtKB/TrEMBL
  M0R6H5_RAT UniProtKB/TrEMBL
  M0RA29_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Setdb2  SET domain bifurcated histone lysine methyltransferase 2  LOC102552532  uncharacterized LOC102552532  Data Merged 737654 PROVISIONAL
2019-01-04 Setdb2  SET domain bifurcated histone lysine methyltransferase 2  Setdb2  SET domain, bifurcated 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-17 LOC102552532  uncharacterized LOC102552532      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-08-22 LOC100361710  SET domain bifurcated protein 2-Phf11-1 fusion protein-like  Setdb2  SET domain, bifurcated 2  Data Merged 737654 APPROVED
2012-08-22 Setdb2  SET domain, bifurcated 2  LOC100361710  SET domain bifurcated protein 2-Phf11-1 fusion protein-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100361710  SET domain bifurcated protein 2-Phf11-1 fusion protein-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Setdb2  SET domain, bifurcated 2   Setdb2_predicted  SET domain, bifurcated 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Setdb2_predicted  SET domain, bifurcated 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED