Ap2b1 (adaptor related protein complex 2 subunit beta 1) - Rat Genome Database

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Gene: Ap2b1 (adaptor related protein complex 2 subunit beta 1) Rattus norvegicus
Analyze
Symbol: Ap2b1
Name: adaptor related protein complex 2 subunit beta 1
RGD ID: 71048
Description: Enables clathrin binding activity. Involved in several processes, including clathrin coat assembly; negative regulation of neuron death; and positive regulation of endocytosis. Part of clathrin coat. Biomarker of middle cerebral artery infarction. Orthologous to human AP2B1 (adaptor related protein complex 2 subunit beta 1); PARTICIPATES IN clathrin-dependent synaptic vesicle endocytosis; endocytosis pathway; Huntington's disease pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: adapter-related protein complex 2 beta subunit; adapter-related protein complex 2 subunit beta; adaptor protein complex AP-2 subunit beta; adaptor-related protein complex 2 subunit beta; adaptor-related protein complex 2, beta 1 subunit; AP-1 complex subunit beta-1-like; AP-2 complex subunit beta; AP-2 complex subunit beta-like; AP105B; beta adaptin; beta-2-adaptin; beta-adaptin; beta2-adaptin; clathrin assembly protein complex 2 beta large chain; LOC100912146; LOC103690090; plasma membrane adaptor HA2/AP2 adaptin beta subunit
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
mRatBN7.21068,099,397 - 68,205,023 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1068,099,547 - 68,205,013 (+)Ensembl
Rnor_6.01070,516,462 - 70,621,973 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1070,520,206 - 70,621,977 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,035,406 - 71,067,828 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01071,068,935 - 71,083,997 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41071,386,233 - 71,488,000 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11071,399,684 - 71,502,555 (+)NCBI
Celera1067,045,800 - 67,146,677 (+)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9694653   PMID:11382783   PMID:12086608   PMID:12234931   PMID:12477932   PMID:15533940   PMID:15728179   PMID:16903783   PMID:19509056   PMID:19946888   PMID:21499258   PMID:21700703  
PMID:22871113   PMID:23676497   PMID:24217640   PMID:25807483   PMID:26514267   PMID:29476059   PMID:30053369   PMID:32357304  


Genomics

Candidate Gene Status
Ap2b1 is a candidate Gene for QTL Bp302
Comparative Map Data
Ap2b1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21068,099,397 - 68,205,023 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1068,099,547 - 68,205,013 (+)Ensembl
Rnor_6.01070,516,462 - 70,621,973 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1070,520,206 - 70,621,977 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01071,035,406 - 71,067,828 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01071,068,935 - 71,083,997 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41071,386,233 - 71,488,000 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11071,399,684 - 71,502,555 (+)NCBI
Celera1067,045,800 - 67,146,677 (+)NCBICelera
Cytogenetic Map10q26NCBI
AP2B1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1735,578,046 - 35,726,413 (+)EnsemblGRCh38hg38GRCh38
GRCh381735,587,265 - 35,726,413 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371733,914,341 - 34,053,432 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361730,938,395 - 31,077,549 (+)NCBINCBI36hg18NCBI36
Build 341730,938,405 - 31,077,541NCBI
Celera1730,824,398 - 30,963,574 (+)NCBI
Cytogenetic Map17q12NCBI
HuRef1730,099,253 - 30,238,599 (+)NCBIHuRef
CHM1_11733,978,907 - 34,118,050 (+)NCBICHM1_1
Ap2b1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391183,189,545 - 83,295,861 (+)NCBIGRCm39mm39
GRCm39 Ensembl1183,189,850 - 83,295,861 (+)Ensembl
GRCm381183,298,719 - 83,405,035 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1183,299,024 - 83,405,035 (+)EnsemblGRCm38mm10GRCm38
MGSCv371183,116,199 - 83,218,537 (+)NCBIGRCm37mm9NCBIm37
MGSCv361183,118,892 - 83,221,230 (+)NCBImm8
Celera1192,894,853 - 92,999,587 (+)NCBICelera
Cytogenetic Map11CNCBI
Ap2b1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495548110,064,220 - 10,175,627 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495548110,061,021 - 10,175,070 (+)NCBIChiLan1.0ChiLan1.0
AP2B1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11721,363,115 - 21,501,720 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1721,363,121 - 21,501,721 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01721,070,132 - 21,208,610 (-)NCBIMhudiblu_PPA_v0panPan3
AP2B1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1937,946,761 - 38,078,074 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl937,946,788 - 38,078,041 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha937,170,891 - 37,302,120 (-)NCBI
ROS_Cfam_1.0938,758,380 - 38,889,742 (-)NCBI
UMICH_Zoey_3.1937,541,221 - 37,673,744 (-)NCBI
UNSW_CanFamBas_1.0937,826,684 - 37,958,055 (-)NCBI
UU_Cfam_GSD_1.0937,914,210 - 38,045,500 (-)NCBI
Ap2b1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560236,949,807 - 37,069,908 (-)NCBI
SpeTri2.0NW_0049364905,156 - 127,666 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AP2B1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1239,787,533 - 39,940,780 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11239,803,105 - 39,940,801 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
AP2B1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11629,061,662 - 29,198,942 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1629,061,568 - 29,201,464 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666075774,355 - 913,998 (-)NCBIVero_WHO_p1.0
Ap2b1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248753,085,518 - 3,206,930 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D10Mco43  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,193,870 - 68,193,987 (+)MAPPERmRatBN7.2
Rnor_6.01070,610,873 - 70,610,989NCBIRnor6.0
Rnor_5.01071,072,897 - 71,073,013UniSTSRnor5.0
Rnor_5.01070,244,698 - 70,244,814UniSTSRnor5.0
RGSC_v3.41071,476,899 - 71,477,016RGDRGSC3.4
RGSC_v3.41071,476,900 - 71,477,016UniSTSRGSC3.4
RGSC_v3.11071,490,756 - 71,490,873RGD
Celera1067,135,547 - 67,135,663UniSTS
Cytogenetic Map10q26UniSTS
D10Chm192  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,127,447 - 68,127,614 (+)MAPPERmRatBN7.2
mRatBN7.21068,127,447 - 68,127,673 (+)MAPPERmRatBN7.2
Rnor_6.01070,544,457 - 70,544,680NCBIRnor6.0
Rnor_6.01070,544,457 - 70,544,621NCBIRnor6.0
Rnor_5.01070,178,283 - 70,178,448NCBIRnor5.0
Rnor_5.01071,059,656 - 71,059,821NCBIRnor5.0
Rnor_5.01071,059,656 - 71,059,880NCBIRnor5.0
Rnor_5.01070,178,283 - 70,178,507NCBIRnor5.0
RGSC_v3.41071,410,484 - 71,410,707UniSTSRGSC3.4
RGSC_v3.41071,410,484 - 71,410,648UniSTSRGSC3.4
Celera1067,070,051 - 67,070,274UniSTS
Celera1067,070,051 - 67,070,215UniSTS
Cytogenetic Map10q26UniSTS
D10Chm187  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,109,898 - 68,110,141 (+)MAPPERmRatBN7.2
Rnor_6.01070,526,913 - 70,527,155NCBIRnor6.0
Rnor_5.01071,042,113 - 71,042,355UniSTSRnor5.0
Rnor_5.01070,160,740 - 70,160,982UniSTSRnor5.0
RGSC_v3.41071,392,940 - 71,393,182UniSTSRGSC3.4
Celera1067,052,507 - 67,052,749UniSTS
Cytogenetic Map10q26UniSTS
D10Chm146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,128,848 - 68,129,068 (+)MAPPERmRatBN7.2
Rnor_6.01070,545,856 - 70,546,075NCBIRnor6.0
Rnor_5.01071,061,056 - 71,061,275UniSTSRnor5.0
Rnor_5.01070,179,683 - 70,179,902UniSTSRnor5.0
RGSC_v3.41071,411,883 - 71,412,102UniSTSRGSC3.4
Celera1067,071,450 - 67,071,669UniSTS
Cytogenetic Map10q26UniSTS
D10Chm189  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,116,834 - 68,117,007 (+)MAPPERmRatBN7.2
Rnor_6.01070,533,845 - 70,534,017NCBIRnor6.0
Rnor_5.01071,049,045 - 71,049,217UniSTSRnor5.0
Rnor_5.01070,167,672 - 70,167,844UniSTSRnor5.0
RGSC_v3.41071,399,872 - 71,400,044UniSTSRGSC3.4
Celera1067,059,439 - 67,059,611UniSTS
Cytogenetic Map10q26UniSTS
D10Chm191  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,127,046 - 68,127,237 (+)MAPPERmRatBN7.2
Rnor_6.01070,544,056 - 70,544,246NCBIRnor6.0
Rnor_5.01071,059,256 - 71,059,446UniSTSRnor5.0
Rnor_5.01070,177,883 - 70,178,073UniSTSRnor5.0
RGSC_v3.41071,410,083 - 71,410,273UniSTSRGSC3.4
Celera1067,069,650 - 67,069,840UniSTS
Cytogenetic Map10q26UniSTS
D10Chm188  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,113,349 - 68,113,592 (+)MAPPERmRatBN7.2
Rnor_6.01070,530,364 - 70,530,602NCBIRnor6.0
Rnor_5.01071,045,564 - 71,045,802UniSTSRnor5.0
Rnor_5.01070,164,191 - 70,164,429UniSTSRnor5.0
RGSC_v3.41071,396,391 - 71,396,629UniSTSRGSC3.4
Celera1067,055,958 - 67,056,196UniSTS
Cytogenetic Map10q26UniSTS
D10Chm147  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,164,560 - 68,164,786 (+)MAPPERmRatBN7.2
Rnor_6.01070,581,568 - 70,581,793NCBIRnor6.0
Rnor_5.01070,215,393 - 70,215,618UniSTSRnor5.0
RGSC_v3.41071,447,595 - 71,447,820UniSTSRGSC3.4
Celera1067,107,082 - 67,107,307UniSTS
Cytogenetic Map10q26UniSTS
D10Chm190  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,123,812 - 68,124,057 (+)MAPPERmRatBN7.2
Rnor_6.01070,540,823 - 70,541,067NCBIRnor6.0
Rnor_5.01071,056,023 - 71,056,267UniSTSRnor5.0
Rnor_5.01070,174,650 - 70,174,894UniSTSRnor5.0
RGSC_v3.41071,406,850 - 71,407,094UniSTSRGSC3.4
Celera1067,066,417 - 67,066,661UniSTS
Cytogenetic Map10q26UniSTS
D10Chm120  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,166,668 - 68,166,913 (+)MAPPERmRatBN7.2
Rnor_6.01070,583,676 - 70,583,920NCBIRnor6.0
Rnor_5.01070,217,501 - 70,217,745UniSTSRnor5.0
RGSC_v3.41071,449,703 - 71,449,947UniSTSRGSC3.4
Celera1067,109,190 - 67,109,434UniSTS
Cytogenetic Map10q26UniSTS
D10Chm245  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,127,092 - 68,127,339 (+)MAPPERmRatBN7.2
Rnor_6.01070,544,102 - 70,544,348NCBIRnor6.0
Rnor_5.01071,059,302 - 71,059,548UniSTSRnor5.0
Rnor_5.01070,177,929 - 70,178,175UniSTSRnor5.0
RGSC_v3.41071,410,129 - 71,410,375UniSTSRGSC3.4
Celera1067,069,696 - 67,069,942UniSTS
Cytogenetic Map10q26UniSTS
D10Mco87  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,113,381 - 68,113,682 (+)MAPPERmRatBN7.2
Rnor_6.01070,530,396 - 70,530,692NCBIRnor6.0
Rnor_5.01071,045,596 - 71,045,892UniSTSRnor5.0
Rnor_5.01070,164,223 - 70,164,519UniSTSRnor5.0
RGSC_v3.41071,396,423 - 71,396,719UniSTSRGSC3.4
Celera1067,055,990 - 67,056,286UniSTS
Cytogenetic Map10q26UniSTS
D11Pas17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,145,471 - 68,145,631 (+)MAPPERmRatBN7.2
Rnor_6.01070,562,479 - 70,562,638NCBIRnor6.0
Rnor_5.01070,196,306 - 70,196,465UniSTSRnor5.0
RGSC_v3.41071,428,506 - 71,428,665UniSTSRGSC3.4
Celera1067,088,073 - 67,088,232UniSTS
Cytogenetic Map10q26UniSTS
RH127319  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,204,818 - 68,204,998 (+)MAPPERmRatBN7.2
mRatBN7.2134,290,540 - 34,290,720 (+)MAPPERmRatBN7.2
Rnor_6.0136,952,089 - 36,952,268NCBIRnor6.0
Rnor_6.01070,621,773 - 70,621,952NCBIRnor6.0
Rnor_5.01071,083,796 - 71,083,976NCBIRnor5.0
Rnor_5.01070,255,601 - 70,255,781NCBIRnor5.0
Rnor_5.0138,345,959 - 38,346,139NCBIRnor5.0
RGSC_v3.4174,457,158 - 4,457,337UniSTSRGSC3.4
RGSC_v3.41071,487,800 - 71,487,979UniSTSRGSC3.4
Celera1067,146,477 - 67,146,656UniSTS
Celera132,877,739 - 32,877,918UniSTS
Cytogenetic Map10q26UniSTS
AU046825  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,173,055 - 68,173,147 (+)MAPPERmRatBN7.2
Rnor_6.01070,590,060 - 70,590,151NCBIRnor6.0
Rnor_5.01070,223,885 - 70,223,976UniSTSRnor5.0
RGSC_v3.41071,456,087 - 71,456,178UniSTSRGSC3.4
Celera1067,115,574 - 67,115,665UniSTS
Cytogenetic Map10q26UniSTS
Ap2b1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,202,609 - 68,202,943 (-)MAPPERmRatBN7.2
mRatBN7.2134,292,605 - 34,292,939 (-)MAPPERmRatBN7.2
mRatBN7.21068,202,609 - 68,202,943 (+)MAPPERmRatBN7.2
mRatBN7.2134,292,605 - 34,292,939 (+)MAPPERmRatBN7.2
Rnor_6.01070,619,564 - 70,619,897NCBIRnor6.0
Rnor_6.0136,954,154 - 36,954,487NCBIRnor6.0
RGSC_v3.4174,459,223 - 4,459,556UniSTSRGSC3.4
RGSC_v3.41071,485,591 - 71,485,924UniSTSRGSC3.4
Celera1067,144,268 - 67,144,601UniSTS
Celera132,879,804 - 32,880,137UniSTS
Cytogenetic Map17p14UniSTS
Cytogenetic Map10q26UniSTS
UniSTS:259407  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,292,682 - 34,293,258 (+)MAPPERmRatBN7.2
Rnor_6.0136,954,231 - 36,954,806NCBIRnor6.0
Rnor_5.0138,348,102 - 38,348,677UniSTSRnor5.0
RGSC_v3.4174,459,300 - 4,459,875UniSTSRGSC3.4
Celera132,879,881 - 32,880,456UniSTS
Cytogenetic Map17p14UniSTS
Cytogenetic Map10q26UniSTS
Ap2b1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21068,202,612 - 68,202,943 (+)MAPPERmRatBN7.2
mRatBN7.2134,292,605 - 34,292,936 (+)MAPPERmRatBN7.2
Rnor_6.01070,619,567 - 70,619,897NCBIRnor6.0
Rnor_6.0136,954,154 - 36,954,484NCBIRnor6.0
RGSC_v3.4174,459,223 - 4,459,553UniSTSRGSC3.4
RGSC_v3.41071,485,594 - 71,485,924UniSTSRGSC3.4
Celera132,879,804 - 32,880,134UniSTS
Celera1067,144,271 - 67,144,601UniSTS
Cytogenetic Map10q26UniSTS
Cytogenetic Map17p14UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106134527681714865Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106134541382564856Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106592723382565079Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)106631944768164786Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)106631944768164786Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)106631944768164786Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)106631944768164786Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
631565Hcuc4Hepatic copper content QTL 44.15hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)106694181373452992Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
1579917Bp282Blood pressure QTL 2820.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106740031668164786Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106750210873579767Rat
2292440Bp312Blood pressure QTL 312arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106775004968164786Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1550
Count of miRNA genes:323
Interacting mature miRNAs:429
Transcripts:ENSRNOT00000013363, ENSRNOT00000013629
Prediction methods:Microtar, Miranda, 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 43 57 41 19 41 5 8 74 35 41 11 5
Low 3 3 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000085799   ⟹   ENSRNOP00000072290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1068,099,547 - 68,198,552 (+)Ensembl
Rnor_6.0 Ensembl1070,520,279 - 70,620,151 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088198   ⟹   ENSRNOP00000070905
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1068,103,192 - 68,205,013 (+)Ensembl
Rnor_6.0 Ensembl1070,520,206 - 70,621,965 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000090446   ⟹   ENSRNOP00000073619
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1068,115,639 - 68,205,013 (+)Ensembl
Rnor_6.0 Ensembl1070,520,254 - 70,621,977 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117903   ⟹   ENSRNOP00000084537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1068,115,135 - 68,198,665 (+)Ensembl
RefSeq Acc Id: NM_080583   ⟹   NP_542150
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,103,192 - 68,205,019 (+)NCBI
Rnor_6.01070,520,206 - 70,621,973 (+)NCBI
Rnor_5.01071,035,406 - 71,067,828 (+)NCBI
Rnor_5.01071,068,935 - 71,083,997 (+)NCBI
RGSC_v3.41071,386,233 - 71,488,000 (+)RGD
Celera1067,045,800 - 67,146,677 (+)RGD
Sequence:
RefSeq Acc Id: XM_008767935   ⟹   XP_008766157
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,103,185 - 68,205,023 (+)NCBI
Rnor_6.01070,519,469 - 70,621,973 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767936   ⟹   XP_008766158
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,099,544 - 68,205,023 (+)NCBI
Rnor_6.01070,516,585 - 70,621,973 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767937   ⟹   XP_008766159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,099,397 - 68,205,023 (+)NCBI
Rnor_6.01070,516,462 - 70,621,973 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767938   ⟹   XP_008766160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,099,559 - 68,205,023 (+)NCBI
Rnor_6.01070,516,573 - 70,621,973 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008767939   ⟹   XP_008766161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,103,171 - 68,204,223 (+)NCBI
Rnor_6.01070,519,470 - 70,619,606 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596973   ⟹   XP_017452462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21068,099,408 - 68,205,023 (+)NCBI
Rnor_6.01070,516,483 - 70,621,973 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_542150   ⟸   NM_080583
- UniProtKB: P62944 (UniProtKB/Swiss-Prot),   Q3ZB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766159   ⟸   XM_008767937
- Peptide Label: isoform X1
- UniProtKB: P62944 (UniProtKB/Swiss-Prot),   Q3ZB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766160   ⟸   XM_008767938
- Peptide Label: isoform X1
- UniProtKB: P62944 (UniProtKB/Swiss-Prot),   Q3ZB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766158   ⟸   XM_008767936
- Peptide Label: isoform X1
- UniProtKB: P62944 (UniProtKB/Swiss-Prot),   Q3ZB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766157   ⟸   XM_008767935
- Peptide Label: isoform X1
- UniProtKB: P62944 (UniProtKB/Swiss-Prot),   Q3ZB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766161   ⟸   XM_008767939
- Peptide Label: isoform X2
- UniProtKB: P62944 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017452462   ⟸   XM_017596973
- Peptide Label: isoform X1
- UniProtKB: P62944 (UniProtKB/Swiss-Prot),   Q3ZB97 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073619   ⟸   ENSRNOT00000090446
RefSeq Acc Id: ENSRNOP00000072290   ⟸   ENSRNOT00000085799
RefSeq Acc Id: ENSRNOP00000070905   ⟸   ENSRNOT00000088198
RefSeq Acc Id: ENSRNOP00000084537   ⟸   ENSRNOT00000117903
Protein Domains
Alpha_adaptinC2   B2-adapt-app_C

Transcriptome

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

Promoters
RGD ID:13697531
Promoter ID:EPDNEW_R8053
Type:initiation region
Name:Ap2b1_1
Description:adaptor-related protein complex 2, beta 1 subunit
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_6.01070,520,266 - 70,520,326EPDNEW

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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)
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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)
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:71048 AgrOrtholog
Ensembl Genes ENSRNOG00000061543 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000070905 UniProtKB/Swiss-Prot
  ENSRNOP00000072290 UniProtKB/Swiss-Prot
  ENSRNOP00000073619 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000085799 UniProtKB/Swiss-Prot
  ENSRNOT00000088198 UniProtKB/Swiss-Prot
  ENSRNOT00000090446 UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.1150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.310.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7929959 IMAGE-MGC_LOAD
InterPro AP_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP_complex_bsu_1_2_4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Armadillo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B-adaptin_app_sub_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Clathrin/coatomer_adapt-like_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Clathrin_a/b/g-adaptin_app_Ig UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Clathrin_app_Ig-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Clathrin_b-adaptin_app_Ig-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Coatomer/calthrin_app_sub_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBP_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:140670 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:124574 IMAGE-MGC_LOAD
NCBI Gene 140670 ENTREZGENE
PANTHER PTHR11134 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Adaptin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Alpha_adaptinC2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B2-adapt-app_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB AP2B1 RGD
PhenoGen Ap2b1 PhenoGen
PIRSF AP_complex_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Alpha_adaptinC2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  B2-adapt-app_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49348 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55711 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt AP2B1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q3ZB97 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary P21851 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Ap2b1  adaptor related protein complex 2 subunit beta 1  LOC103690090  AP-2 complex subunit beta-like  Data Merged 737654 PROVISIONAL
2018-05-03 Ap2b1  adaptor related protein complex 2 subunit beta 1  Ap2b1  adaptor-related protein complex 2, beta 1 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Ap2b1  adaptor-related protein complex 2, beta 1 subunit  LOC100912146  AP-1 complex subunit beta-1-like  Data Merged 737654 PROVISIONAL
2014-08-25 LOC103690090  AP-2 complex subunit beta-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2012-07-05 LOC100912146  AP-1 complex subunit beta-1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-07-09 Ap2b1  adaptor-related protein complex 2, beta 1 subunit      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function component of the adaptor complexes which link clathrin to receptors in coated vesicles; clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration 724707