Bcor (BCL6 co-repressor) - Rat Genome Database

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Gene: Bcor (BCL6 co-repressor) Rattus norvegicus
Analyze
Symbol: Bcor
Name: BCL6 co-repressor
RGD ID: 1562735
Description: Predicted to enable several functions, including heat shock protein binding activity; histone deacetylase binding activity; and transcription corepressor activity. Predicted to contribute to ubiquitin-protein transferase activity. Predicted to be involved in several processes, including histone H2A monoubiquitination; negative regulation of biomineral tissue development; and negative regulation of histone methylation. Predicted to act upstream of or within blastocyst hatching and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of BCOR complex. Human ortholog(s) of this gene implicated in syndromic microphthalmia 1 and syndromic microphthalmia 2. Orthologous to human BCOR (BCL6 corepressor); INTERACTS WITH bisphenol A; resveratrol; vinclozolin.
Type: protein-coding
RefSeq Status: INFERRED
Also known as: BCL-6 corepressor; Bcl6 interacting corepressor; LOC317346; RGD1562735; similar to BCoR protein (BCL-6 corepressor)
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
mRatBN7.2X10,609,756 - 10,729,613 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX10,687,732 - 10,729,613 (+)Ensembl
Rnor_6.0X11,570,155 - 11,692,022 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX11,648,989 - 11,691,099 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X12,366,781 - 12,488,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X22,699,778 - 22,820,234 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX11,211,546 - 11,253,981 (+)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:10898795   PMID:12776190   PMID:15878880   PMID:16943429   PMID:17517692   PMID:19578371   PMID:25331958   PMID:27869233  


Genomics

Comparative Map Data
Bcor
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X10,609,756 - 10,729,613 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX10,687,732 - 10,729,613 (+)Ensembl
Rnor_6.0X11,570,155 - 11,692,022 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX11,648,989 - 11,691,099 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X12,366,781 - 12,488,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X22,699,778 - 22,820,234 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX11,211,546 - 11,253,981 (+)NCBICelera
Cytogenetic MapXq12NCBI
BCOR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX40,049,815 - 40,177,329 (-)EnsemblGRCh38hg38GRCh38
GRCh38X40,051,246 - 40,177,390 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X39,910,499 - 40,036,582 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X39,795,561 - 39,846,998 (-)NCBINCBI36hg18NCBI36
CeleraX44,049,354 - 44,175,356 (-)NCBI
Cytogenetic MapXp11.4NCBI
HuRefX37,648,006 - 37,771,447 (-)NCBIHuRef
CHM1_1X39,942,309 - 40,068,287 (-)NCBICHM1_1
Bcor
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X11,902,976 - 12,026,769 (-)NCBIGRCm39mm39
GRCm39 EnsemblX11,902,979 - 12,026,594 (-)Ensembl
GRCm38X12,036,737 - 12,160,516 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX12,036,740 - 12,160,355 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X11,613,863 - 11,737,481 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X11,193,696 - 11,237,013 (-)NCBImm8
CeleraX9,733,265 - 9,856,163 (-)NCBICelera
Cytogenetic MapXA1.1NCBI
Bcor
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555661,412,540 - 1,457,329 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555661,412,540 - 1,510,339 (-)NCBIChiLan1.0ChiLan1.0
BCOR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X40,203,565 - 40,328,788 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX40,202,235 - 40,249,986 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X32,497,931 - 32,624,307 (-)NCBIMhudiblu_PPA_v0panPan3
BCOR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X34,621,314 - 34,735,502 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX34,621,886 - 34,645,766 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX21,969,928 - 22,084,065 (-)NCBI
ROS_Cfam_1.0X34,669,641 - 34,783,826 (-)NCBI
UMICH_Zoey_3.1X34,749,439 - 34,863,578 (-)NCBI
UNSW_CanFamBas_1.0X34,721,876 - 34,836,005 (-)NCBI
UU_Cfam_GSD_1.0X34,764,590 - 34,878,770 (-)NCBI
Bcor
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X26,923,332 - 26,971,483 (-)NCBI
SpeTri2.0NW_0049365026,764,043 - 6,812,194 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BCOR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X35,768,013 - 35,891,013 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X39,823,458 - 39,946,360 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BCOR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X37,191,242 - 37,319,966 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX37,192,874 - 37,319,782 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660762,405,573 - 2,532,624 (-)NCBIVero_WHO_p1.0
Bcor
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476215,338,331 - 15,465,683 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
DXGot5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X10,618,413 - 10,618,539 (+)MAPPERmRatBN7.2
Rnor_6.0X11,578,842 - 11,578,965NCBIRnor6.0
Rnor_5.0X12,375,422 - 12,375,545UniSTSRnor5.0
RGSC_v3.4X22,708,282 - 22,708,405UniSTSRGSC3.4
RGSC_v3.4X22,708,281 - 22,708,405RGDRGSC3.4
RGSC_v3.1X22,761,600 - 22,761,723RGD
CeleraX11,142,153 - 11,142,278UniSTS
RH 3.4 MapX44.5UniSTS
RH 3.4 MapX44.5RGD
RH 2.0 Map2125.4RGD
Cytogenetic MapXq13UniSTS
RH91894  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X10,685,254 - 10,685,385 (+)MAPPERmRatBN7.2
Rnor_6.0X11,646,512 - 11,646,642NCBIRnor6.0
Rnor_5.0X12,444,190 - 12,444,320UniSTSRnor5.0
RGSC_v3.4X22,775,978 - 22,776,108UniSTSRGSC3.4
CeleraX11,209,073 - 11,209,203UniSTS
Cytogenetic MapXq13UniSTS
AU047974  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X10,635,771 - 10,636,028 (+)MAPPERmRatBN7.2
Rnor_6.0X11,596,186 - 11,596,442NCBIRnor6.0
Rnor_5.0X12,392,766 - 12,393,022UniSTSRnor5.0
RGSC_v3.4X22,725,626 - 22,725,882UniSTSRGSC3.4
CeleraX11,159,497 - 11,159,741UniSTS
Cytogenetic MapXq13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144797211374346Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:226
Count of miRNA genes:143
Interacting mature miRNAs:174
Transcripts:ENSRNOT00000041003
Prediction methods:Miranda, Pita, Pita,Targetscan, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 26 17 8 18 8 1 1 53 22 31 11 1
Low 1 17 40 33 1 33 7 10 21 13 10 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191586 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256664 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039099767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JACYVU010000350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041003   ⟹   ENSRNOP00000047677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX10,687,732 - 10,729,613 (+)Ensembl
Rnor_6.0 EnsemblX11,648,989 - 11,691,099 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105188   ⟹   ENSRNOP00000076883
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX10,687,732 - 10,729,613 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116761   ⟹   ENSRNOP00000086890
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX10,687,732 - 10,729,613 (+)Ensembl
RefSeq Acc Id: NM_001191586   ⟹   NP_001178515
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,687,732 - 10,729,613 (+)NCBI
Rnor_6.0X11,648,989 - 11,691,099 (+)NCBI
Rnor_5.0X12,366,781 - 12,488,777 (+)NCBI
CeleraX11,211,546 - 11,253,981 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099759   ⟹   XP_038955687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,640,621 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099760   ⟹   XP_038955688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,609,756 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099761   ⟹   XP_038955689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,688,362 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099762   ⟹   XP_038955690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,674,743 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099763   ⟹   XP_038955691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,685,194 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099764   ⟹   XP_038955692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,688,753 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099765   ⟹   XP_038955693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,687,821 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099766   ⟹   XP_038955694
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,687,821 - 10,729,061 (+)NCBI
RefSeq Acc Id: XM_039099767   ⟹   XP_038955695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X10,687,821 - 10,729,061 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001178515   ⟸   NM_001191586
- UniProtKB: D4A2J9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047677   ⟸   ENSRNOT00000041003
RefSeq Acc Id: XP_038955688   ⟸   XM_039099760
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955687   ⟸   XM_039099759
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955690   ⟸   XM_039099762
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955691   ⟸   XM_039099763
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955694   ⟸   XM_039099766
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955693   ⟸   XM_039099765
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955695   ⟸   XM_039099767
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038955689   ⟸   XM_039099761
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955692   ⟸   XM_039099764
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000076883   ⟸   ENSRNOT00000105188
RefSeq Acc Id: ENSRNOP00000086890   ⟸   ENSRNOT00000116761
Protein Domains
ANK_REP_REGION

Transcriptome

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

Promoters
RGD ID:13701714
Promoter ID:EPDNEW_R12238
Type:multiple initiation site
Name:Bcor_1
Description:BCL6 co-repressor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X11,648,965 - 11,649,025EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 12478141 12478142 G A snv ZF (KyushuU)
X 12487636 12487637 C T snv ZFDM (KyushuU), Crl:SD (UDEL), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MHS/Gib (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BUF/N (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHH/EurMcwi (KNAW), FHL/EurMcwi (KNAW), M520/N (KNAW), MNS/Gib (KNAW), SBH/Ygl (KNAW), SBN/Ygl (KNAW), F344/NRrrc (Illumina) (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), F344/Jcl (KyushuU), BDIX/NemOda (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZF (KyushuU), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 11689958 11689959 C T snv CDS, WN/N (2020), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (MCW), SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), Buf/N (MCW), F344/NRrrc (MCW), M520/N (MCW), WN/N (MCW), ACI/EurMcwi (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), MHS/Gib (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SBN/Ygl (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEXF4/Stm (2020), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), M520/NRrrcMcwi (2019), M520/N (2020), MWF/Hsd (2019), SR/JrHsd (2020), SS/JrHsdMcwi (2019), ACI/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562735 AgrOrtholog
Ensembl Genes ENSRNOG00000034240 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000047677 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041003 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/TrEMBL
  3.10.260.40 UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  BCOR UniProtKB/TrEMBL
  PUFD UniProtKB/TrEMBL
  PUFD_som_sf UniProtKB/TrEMBL
KEGG Report rno:317346 UniProtKB/TrEMBL
NCBI Gene 317346 ENTREZGENE
Pfam Ank_2 UniProtKB/TrEMBL
  BCOR UniProtKB/TrEMBL
  PUFD UniProtKB/TrEMBL
PhenoGen Bcor PhenoGen
PROSITE ANK_REP_REGION UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/TrEMBL
SMART ANK UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
UniProt D4A2J9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-01-05 Bcor  BCL6 co-repressor  Bcor  Bcl6 interacting corepressor   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Bcor  Bcl6 interacting corepressor   Bcor_predicted  Bcl6 interacting corepressor (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Bcor_predicted  Bcl6 interacting corepressor (predicted)  RGD1562735_predicted  similar to BCoR protein (BCL-6 corepressor) (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1562735_predicted  similar to BCoR protein (BCL-6 corepressor) (predicted)  LOC317346  similar to BCoR protein (BCL-6 corepressor)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317346  similar to BCoR protein (BCL-6 corepressor)      Symbol and Name status set to provisional 70820 PROVISIONAL