Pbrm1 (polybromo 1) - Rat Genome Database

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Gene: Pbrm1 (polybromo 1) Rattus norvegicus
Analyze
Symbol: Pbrm1
Name: polybromo 1
RGD ID: 1565549
Description: Predicted to enable chromatin binding activity. Predicted to be involved in ATP-dependent chromatin remodeling and negative regulation of cell population proliferation. Predicted to act upstream of or within blastocyst formation; heart development; and placenta development. Predicted to be located in kinetochore and nucleoplasm. Predicted to be part of RSC-type complex. Human ortholog(s) of this gene implicated in renal cell carcinoma. Orthologous to human PBRM1 (polybromo 1); PARTICIPATES IN altered SWI/SNF family mediated chromatin remodeling pathway; histone modification pathway; pancreatic cancer pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; chloroprene.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC306254; RGD1565549; similar to polybromo-1
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
mRatBN7.2166,213,507 - 6,312,895 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl166,213,300 - 6,311,780 (+)Ensembl
Rnor_6.0167,103,714 - 7,202,899 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl167,103,998 - 7,200,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0167,032,357 - 7,131,462 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4166,456,202 - 6,550,030 (+)NCBIRGSC3.4rn4RGSC3.4
Celera168,876,544 - 8,975,777 (-)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Audenet F, etal., BJU Int. 2012 Jun;109(12):1864-70. doi: 10.1111/j.1464-410X.2011.10661.x. Epub 2011 Oct 28.
2. Churi CR, etal., PLoS One. 2014 Dec 23;9(12):e115383. doi: 10.1371/journal.pone.0115383. eCollection 2014.
3. Du M, etal., Lung Cancer. 2018 Jun;120:113-121. doi: 10.1016/j.lungcan.2018.04.008. Epub 2018 Apr 12.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Hargreaves DC and Crabtree GR, Cell Res. 2011 Mar;21(3):396-420. doi: 10.1038/cr.2011.32. Epub 2011 Mar 1.
6. Mehrotra A, etal., J Cell Physiol. 2013 Dec;228(12):2337-42. doi: 10.1002/jcp.24404.
7. Misumi K, etal., Histopathology. 2017 Apr;70(5):766-774. doi: 10.1111/his.13127. Epub 2017 Jan 18.
8. RGD automated data pipeline
9. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. RGD automated import pipeline for gene-chemical interactions
11. RGD comprehensive gene curation
12. Sanchez R, etal., Biochim Biophys Acta. 2014 Aug;1839(8):676-685. doi: 10.1016/j.bbagrm.2014.03.011. Epub 2014 Mar 28.
13. Shain AH and Pollack JR, PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.
14. Shu XS, etal., J Pathol. 2018 Jan;244(1):36-48. doi: 10.1002/path.4986. Epub 2017 Nov 27.
15. Wilson BG and Roberts CW, Nat Rev Cancer. 2011 Jun 9;11(7):481-92. doi: 10.1038/nrc3068.
16. Yang Z, etal., Mol Psychiatry. 2020 Jan;25(1):48-66. doi: 10.1038/s41380-019-0592-0. Epub 2019 Nov 13.
17. Zhou H, etal., NPJ Precis Oncol. 2020 Mar 16;4:6. doi: 10.1038/s41698-020-0112-3. eCollection 2020.
Additional References at PubMed
PMID:14519686   PMID:15601824   PMID:21248752   PMID:24335282   PMID:27869233  


Genomics

Comparative Map Data
Pbrm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2166,213,507 - 6,312,895 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl166,213,300 - 6,311,780 (+)Ensembl
Rnor_6.0167,103,714 - 7,202,899 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl167,103,998 - 7,200,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0167,032,357 - 7,131,462 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4166,456,202 - 6,550,030 (+)NCBIRGSC3.4rn4RGSC3.4
Celera168,876,544 - 8,975,777 (-)NCBICelera
Cytogenetic Map16p16NCBI
PBRM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl352,545,352 - 52,685,917 (-)EnsemblGRCh38hg38GRCh38
GRCh38352,545,367 - 52,685,913 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37352,579,383 - 52,719,929 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36352,554,423 - 52,694,892 (-)NCBINCBI36hg18NCBI36
Celera352,558,739 - 52,698,578 (-)NCBI
Cytogenetic Map3p21.1NCBI
HuRef352,641,983 - 52,781,706 (-)NCBIHuRef
CHM1_1352,531,687 - 52,671,935 (-)NCBICHM1_1
Pbrm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391430,741,095 - 30,843,549 (+)NCBIGRCm39mm39
GRCm39 Ensembl1430,741,095 - 30,843,549 (+)Ensembl
GRCm381431,019,138 - 31,121,592 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1431,019,138 - 31,121,592 (+)EnsemblGRCm38mm10GRCm38
MGSCv371431,832,324 - 31,934,778 (+)NCBIGRCm37mm9NCBIm37
MGSCv361429,848,147 - 29,950,601 (+)NCBImm8
Celera1427,276,955 - 27,380,012 (+)NCBICelera
Cytogenetic Map14BNCBI
Pbrm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554302,536,086 - 2,670,617 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554302,536,086 - 2,671,094 (-)NCBIChiLan1.0ChiLan1.0
PBRM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1353,715,342 - 53,854,267 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl353,718,051 - 53,850,146 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0352,487,083 - 52,626,418 (-)NCBIMhudiblu_PPA_v0panPan3
PBRM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12037,110,437 - 37,231,676 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2037,110,766 - 37,229,203 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2037,092,491 - 37,213,642 (+)NCBI
ROS_Cfam_1.02037,463,772 - 37,581,266 (+)NCBI
UMICH_Zoey_3.12036,824,752 - 36,945,835 (+)NCBI
UNSW_CanFamBas_1.02037,233,387 - 37,354,437 (+)NCBI
UU_Cfam_GSD_1.02037,510,917 - 37,632,467 (+)NCBI
Pbrm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118170,244,058 - 170,337,482 (-)NCBI
SpeTri2.0NW_0049364733,382,618 - 3,476,049 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PBRM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1334,689,721 - 34,820,957 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11334,689,718 - 34,821,117 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21337,897,740 - 38,020,410 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PBRM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12213,914,023 - 14,059,221 (-)NCBI
ChlSab1.1 Ensembl2213,913,285 - 14,055,254 (-)Ensembl
Vero_WHO_p1.0NW_023666041152,840,917 - 152,986,296 (+)NCBI
Pbrm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248224,529,350 - 4,666,714 (+)NCBI

Position Markers
RH132622  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2166,311,662 - 6,311,849 (+)MAPPERmRatBN7.2
Rnor_6.0167,201,667 - 7,201,853NCBIRnor6.0
Rnor_5.0167,130,230 - 7,130,416UniSTSRnor5.0
RGSC_v3.4166,548,798 - 6,548,984UniSTSRGSC3.4
Celera168,877,590 - 8,877,776UniSTS
Cytogenetic Map16p16UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1619639137Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16122477621Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16126727669Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16126727669Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16126727669Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16285170915884239Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16338015021361552Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760916039848Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16422773017696785Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:424
Count of miRNA genes:136
Interacting mature miRNAs:148
Transcripts:ENSRNOT00000016581, ENSRNOT00000016592, ENSRNOT00000016599, ENSRNOT00000017492
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 36 48 32 19 32 8 8 74 34 38 11 8
Low 7 9 9 9 3 1 3
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006222138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252686 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006252696 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771193 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771194 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771195 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771197 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771201 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771209 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771212 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771237 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017587540 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017587541 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600284 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600287 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600289 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600294 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095103 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095105 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095106 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095112 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095113 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095121 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095133 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095134 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC095672 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC121615 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016581   ⟹   ENSRNOP00000016581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl166,213,792 - 6,310,484 (+)Ensembl
Rnor_6.0 Ensembl167,103,998 - 7,200,362 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094186   ⟹   ENSRNOP00000079535
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl166,213,836 - 6,311,780 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096494   ⟹   ENSRNOP00000096705
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl166,213,300 - 6,311,780 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104141   ⟹   ENSRNOP00000092107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl166,213,746 - 6,311,780 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109995   ⟹   ENSRNOP00000081368
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl166,213,820 - 6,311,780 (+)Ensembl
RefSeq Acc Id: XM_006252686   ⟹   XP_006252748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,779 - 6,312,895 (+)NCBI
Rnor_6.0167,103,989 - 7,202,899 (+)NCBI
Rnor_5.0167,032,357 - 7,131,462 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252696   ⟹   XP_006252758
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,779 - 6,312,895 (+)NCBI
Rnor_6.0167,103,989 - 7,202,899 (+)NCBI
Rnor_5.0167,032,357 - 7,131,462 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600279   ⟹   XP_017455768
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
Rnor_6.0167,103,714 - 7,202,899 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600281   ⟹   XP_017455770
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
Rnor_6.0167,105,889 - 7,202,899 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600283   ⟹   XP_017455772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
Rnor_6.0167,105,889 - 7,202,899 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600286   ⟹   XP_017455775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
Rnor_6.0167,105,889 - 7,202,899 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600287   ⟹   XP_017455776
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,312,895 (+)NCBI
Rnor_6.0167,105,889 - 7,202,899 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095101   ⟹   XP_038951029
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095102   ⟹   XP_038951030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,779 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095103   ⟹   XP_038951031
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,509 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095104   ⟹   XP_038951032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,779 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095105   ⟹   XP_038951033
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095106   ⟹   XP_038951034
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095108   ⟹   XP_038951036
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095109   ⟹   XP_038951037
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095110   ⟹   XP_038951038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,779 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095111   ⟹   XP_038951039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095112   ⟹   XP_038951040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095113   ⟹   XP_038951041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095114   ⟹   XP_038951042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,514 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095116   ⟹   XP_038951044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,514 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095117   ⟹   XP_038951045
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095118   ⟹   XP_038951046
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095119   ⟹   XP_038951047
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095120   ⟹   XP_038951048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095121   ⟹   XP_038951049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095122   ⟹   XP_038951050
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095123   ⟹   XP_038951051
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,507 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095124   ⟹   XP_038951052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095126   ⟹   XP_038951054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095127   ⟹   XP_038951055
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,312,895 (+)NCBI
RefSeq Acc Id: XM_039095128   ⟹   XP_038951056
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095129   ⟹   XP_038951057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095130   ⟹   XP_038951058
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095131   ⟹   XP_038951059
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095132   ⟹   XP_038951060
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095133   ⟹   XP_038951061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
RefSeq Acc Id: XM_039095134   ⟹   XP_038951062
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,213,508 - 6,310,160 (+)NCBI
Protein Sequences
Protein RefSeqs XP_006252748 (Get FASTA)   NCBI Sequence Viewer  
  XP_006252758 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455768 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455770 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455772 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455775 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455776 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951029 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951030 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951031 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951032 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951033 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951034 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951036 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951037 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951038 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951039 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951040 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951041 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951042 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951044 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951045 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951046 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951047 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951048 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951049 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951050 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951051 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951052 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951054 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951055 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951056 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951057 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951058 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951059 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951060 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951061 (Get FASTA)   NCBI Sequence Viewer  
  XP_038951062 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006252748   ⟸   XM_006252686
- Peptide Label: isoform X1
- UniProtKB: D3ZT52 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252758   ⟸   XM_006252696
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017455768   ⟸   XM_017600279
- Peptide Label: isoform X1
- UniProtKB: D3ZT52 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455770   ⟸   XM_017600281
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017455772   ⟸   XM_017600283
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017455775   ⟸   XM_017600286
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017455776   ⟸   XM_017600287
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: ENSRNOP00000016581   ⟸   ENSRNOT00000016581
RefSeq Acc Id: XP_038951029   ⟸   XM_039095101
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951046   ⟸   XM_039095118
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038951034   ⟸   XM_039095106
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951036   ⟸   XM_039095108
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038951039   ⟸   XM_039095111
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038951033   ⟸   XM_039095105
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951047   ⟸   XM_039095119
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038951041   ⟸   XM_039095113
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038951051   ⟸   XM_039095123
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038951049   ⟸   XM_039095121
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038951048   ⟸   XM_039095120
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038951055   ⟸   XM_039095127
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038951040   ⟸   XM_039095112
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038951045   ⟸   XM_039095117
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038951037   ⟸   XM_039095109
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038951056   ⟸   XM_039095128
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038951052   ⟸   XM_039095124
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038951058   ⟸   XM_039095130
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038951061   ⟸   XM_039095133
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038951054   ⟸   XM_039095126
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038951050   ⟸   XM_039095122
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038951057   ⟸   XM_039095129
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038951059   ⟸   XM_039095131
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038951062   ⟸   XM_039095134
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038951060   ⟸   XM_039095132
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038951031   ⟸   XM_039095103
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951042   ⟸   XM_039095114
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038951044   ⟸   XM_039095116
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038951032   ⟸   XM_039095104
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951030   ⟸   XM_039095102
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951038   ⟸   XM_039095110
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000096705   ⟸   ENSRNOT00000096494
RefSeq Acc Id: ENSRNOP00000092107   ⟸   ENSRNOT00000104141
RefSeq Acc Id: ENSRNOP00000079535   ⟸   ENSRNOT00000094186
RefSeq Acc Id: ENSRNOP00000081368   ⟸   ENSRNOT00000109995
Protein Domains
BAH   Bromo   HMG box

Transcriptome

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

Promoters
RGD ID:13699926
Promoter ID:EPDNEW_R10446
Type:initiation region
Name:Pbrm1_1
Description:polybromo 1
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_6.0167,103,999 - 7,104,059EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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)
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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)
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)
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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)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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)
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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)
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/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
WKY/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
WKY/NCrl (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
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)
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
WN/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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565549 AgrOrtholog
Ensembl Genes ENSRNOG00000028227 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016581 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016581 UniProtKB/TrEMBL
Gene3D-CATH 1.20.920.10 UniProtKB/TrEMBL
  2.30.30.490 UniProtKB/TrEMBL
InterPro BAH_dom UniProtKB/TrEMBL
  BAH_sf UniProtKB/TrEMBL
  Bromodomain UniProtKB/TrEMBL
  Bromodomain-like_sf UniProtKB/TrEMBL
  Bromodomain_CS UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  PBRM1_BD5 UniProtKB/TrEMBL
  Rsc/polybromo UniProtKB/TrEMBL
KEGG Report rno:306254 UniProtKB/TrEMBL
NCBI Gene 306254 ENTREZGENE
PANTHER PTHR16062 UniProtKB/TrEMBL
Pfam BAH UniProtKB/TrEMBL
  Bromodomain UniProtKB/TrEMBL
  HMG_box UniProtKB/TrEMBL
PhenoGen Pbrm1 PhenoGen
PRINTS BROMODOMAIN UniProtKB/TrEMBL
PROSITE BAH UniProtKB/TrEMBL
  BROMODOMAIN_1 UniProtKB/TrEMBL
  BROMODOMAIN_2 UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/TrEMBL
SMART BAH UniProtKB/TrEMBL
  BROMO UniProtKB/TrEMBL
  HMG UniProtKB/TrEMBL
Superfamily-SCOP Bromodomain UniProtKB/TrEMBL
  HMG-box UniProtKB/TrEMBL
UniProt D3ZT52 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Pbrm1  polybromo 1  RGD1565549_predicted  similar to polybromo-1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565549_predicted  similar to polybromo-1 (predicted)  LOC306254  similar to polybromo-1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC306254  similar to polybromo-1      Symbol and Name status set to provisional 70820 PROVISIONAL