Tp53bp1 (tumor protein p53 binding protein 1) - Rat Genome Database

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Gene: Tp53bp1 (tumor protein p53 binding protein 1) Rattus norvegicus
Analyze
Symbol: Tp53bp1
Name: tumor protein p53 binding protein 1
RGD ID: 1308039
Description: Predicted to enable several functions, including DNA binding activity; histone binding activity; and p53 binding activity. Involved in cellular response to X-ray. Located in nucleus. Orthologous to human TP53BP1 (tumor protein p53 binding protein 1); PARTICIPATES IN ataxia telangiectasia-mutated (ATM) signaling pathway; histone modification pathway; non-homologous end joining pathway of double-strand break repair; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; all-trans-retinoic acid; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC296099; TP53-binding protein 1; transformation related protein 53 binding protein 1; Trp53bp1; tumor suppressor p53-binding protein 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
mRatBN7.23108,166,574 - 108,270,229 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3108,169,980 - 108,269,822 (-)Ensembl
Rnor_6.03113,160,030 - 113,259,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3113,160,000 - 113,231,790 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03119,697,122 - 119,799,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43107,994,425 - 108,071,133 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13107,897,216 - 107,968,850 (-)NCBI
Celera3107,073,150 - 107,144,062 (-)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
1H-pyrazole  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5'-phosphopyridoxal-6-azobenzene-2,4-disulfonic acid  (ISO)
acrolein  (ISO)
adenosine  (ISO)
adenosine 5'-monophosphate  (ISO)
ADP  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP)
alpha-pinene  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
ATP  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
biphenyl-4-amine  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
brefeldin A  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
GDP  (ISO)
geldanamycin  (ISO)
gemcitabine  (ISO)
GTP  (ISO)
guanosine  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
IDP  (ISO)
indometacin  (ISO)
inosine  (ISO)
ivermectin  (ISO)
mercury dichloride  (ISO)
methylmercury chloride  (ISO)
N-methyl-N-nitrosourea  (ISO)
nitric oxide  (ISO)
oxaliplatin  (ISO)
oxybenzone  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
pinocembrin  (ISO)
potassium chromate  (ISO)
propylparaben  (ISO)
rac-1,2-dichloropropane  (ISO)
resveratrol  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
torcetrapib  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
tungsten  (ISO)
UDP  (ISO)
UTP  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:8889548   PMID:9748285   PMID:11801725   PMID:11934988   PMID:14985081   PMID:15077110   PMID:15149599   PMID:15159415   PMID:15364958   PMID:17053789   PMID:17500065   PMID:17805299  
PMID:19001091   PMID:20362325   PMID:21746928   PMID:22373579   PMID:23209566   PMID:23241889   PMID:23333305   PMID:23333306   PMID:23345425   PMID:23760478   PMID:24001775   PMID:24217620  
PMID:24625528   PMID:28241136  


Genomics

Comparative Map Data
Tp53bp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23108,166,574 - 108,270,229 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl3108,169,980 - 108,269,822 (-)Ensembl
Rnor_6.03113,160,030 - 113,259,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3113,160,000 - 113,231,790 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03119,697,122 - 119,799,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43107,994,425 - 108,071,133 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13107,897,216 - 107,968,850 (-)NCBI
Celera3107,073,150 - 107,144,062 (-)NCBICelera
Cytogenetic Map3q35NCBI
TP53BP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1543,403,061 - 43,510,728 (-)EnsemblGRCh38hg38GRCh38
GRCh381543,403,061 - 43,510,640 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371543,695,259 - 43,802,838 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361541,486,699 - 41,590,028 (-)NCBINCBI36hg18NCBI36
Build 341541,486,698 - 41,590,028NCBI
Celera1520,470,061 - 20,573,379 (-)NCBI
Cytogenetic Map15q15.3NCBI
HuRef1520,547,443 - 20,650,644 (-)NCBIHuRef
CHM1_11543,818,081 - 43,921,400 (-)NCBICHM1_1
Trp53bp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392121,025,316 - 121,126,830 (-)NCBIGRCm39mm39
GRCm39 Ensembl2121,023,762 - 121,101,888 (-)Ensembl
GRCm382121,194,835 - 121,296,354 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2121,193,281 - 121,271,407 (-)EnsemblGRCm38mm10GRCm38
MGSCv372121,022,463 - 121,097,122 (-)NCBIGRCm37mm9NCBIm37
MGSCv362120,889,692 - 120,962,561 (-)NCBImm8
Celera2122,348,714 - 122,423,035 (-)NCBICelera
Cytogenetic Map2E5NCBI
Tp53bp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554169,962,897 - 10,035,278 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554169,962,736 - 10,035,433 (-)NCBIChiLan1.0ChiLan1.0
TP53BP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11540,519,012 - 40,626,845 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1540,519,012 - 40,626,741 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01522,364,696 - 22,472,499 (-)NCBIMhudiblu_PPA_v0panPan3
TP53BP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13010,263,650 - 10,362,646 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3010,263,650 - 10,336,134 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3010,322,230 - 10,419,975 (-)NCBI
ROS_Cfam_1.03010,399,747 - 10,497,632 (-)NCBI
ROS_Cfam_1.0 Ensembl3010,399,747 - 10,497,556 (-)Ensembl
UMICH_Zoey_3.13010,316,018 - 10,388,325 (-)NCBI
UNSW_CanFamBas_1.03010,437,331 - 10,535,512 (-)NCBI
UU_Cfam_GSD_1.03010,557,080 - 10,655,185 (-)NCBI
Tp53bp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864088,741,332 - 88,837,137 (-)NCBI
SpeTri2.0NW_0049364716,589,395 - 6,668,242 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TP53BP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1127,958,518 - 128,028,718 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11127,958,500 - 128,032,370 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21142,694,698 - 142,705,941 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TP53BP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12639,489,925 - 39,595,096 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2639,508,600 - 39,594,927 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666048101,414,132 - 101,524,417 (-)NCBIVero_WHO_p1.0
Tp53bp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480410,517,531 - 10,612,238 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Rat259  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23108,235,049 - 108,235,261 (+)MAPPERmRatBN7.2
Rnor_6.03113,223,783 - 113,223,994NCBIRnor6.0
Rnor_5.03119,763,585 - 119,763,796UniSTSRnor5.0
RGSC_v3.43108,063,213 - 108,063,425RGDRGSC3.4
RGSC_v3.43108,063,214 - 108,063,425UniSTSRGSC3.4
RGSC_v3.13107,961,584 - 107,961,796RGD
Celera3107,136,995 - 107,137,204UniSTS
SHRSP x BN Map352.9498UniSTS
SHRSP x BN Map352.9498RGD
Cytogenetic Map3q35UniSTS
BE108329  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23108,171,966 - 108,172,135 (+)MAPPERmRatBN7.2
Rnor_6.03113,162,019 - 113,162,187NCBIRnor6.0
Rnor_5.03119,701,820 - 119,701,988UniSTSRnor5.0
RGSC_v3.43108,001,450 - 108,001,618UniSTSRGSC3.4
Celera3107,075,139 - 107,075,307UniSTS
RH 3.4 Map3946.0UniSTS
Cytogenetic Map3q35UniSTS
AU049532  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23108,209,356 - 108,209,608 (+)MAPPERmRatBN7.2
Rnor_6.03113,198,095 - 113,198,346NCBIRnor6.0
Rnor_5.03119,737,896 - 119,738,147UniSTSRnor5.0
RGSC_v3.43108,037,526 - 108,037,777UniSTSRGSC3.4
Cytogenetic Map3q35UniSTS
RH68009  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23108,170,102 - 108,170,224 (+)MAPPERmRatBN7.2
Rnor_6.03113,160,155 - 113,160,276NCBIRnor6.0
Rnor_5.03119,699,956 - 119,700,077UniSTSRnor5.0
RGSC_v3.43107,999,586 - 107,999,707UniSTSRGSC3.4
Celera3107,073,275 - 107,073,396UniSTS
Cytogenetic Map3q35UniSTS
BI287966  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23108,206,847 - 108,207,097 (+)MAPPERmRatBN7.2
Rnor_6.03113,195,586 - 113,195,835NCBIRnor6.0
Rnor_5.03119,735,387 - 119,735,636UniSTSRnor5.0
RGSC_v3.43108,035,017 - 108,035,266UniSTSRGSC3.4
Celera3107,109,563 - 107,109,812UniSTS
RH 3.4 Map3948.2UniSTS
Cytogenetic Map3q35UniSTS
RH139947  
Rat AssemblyChrPosition (strand)SourceJBrowse
RH 3.4 Map3946.0UniSTS
Cytogenetic Map3q35UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)380800231114297550Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)396127817115665732Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1582216Bw65Body weight QTL 656.3body mass (VT:0001259)body weight (CMO:0000012)3102200529115665732Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:319
Count of miRNA genes:194
Interacting mature miRNAs:221
Transcripts:ENSRNOT00000019025, ENSRNOT00000033109, ENSRNOT00000067155
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 1 33 22 6 19 6 1 1 74 33 38 11 1
Low 2 10 35 35 35 7 10 2 3 7
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001371259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234865 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006234867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039104554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC116071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK840114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000019025   ⟹   ENSRNOP00000019025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3108,169,984 - 108,269,822 (-)Ensembl
Rnor_6.0 Ensembl3113,160,000 - 113,231,790 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106843   ⟹   ENSRNOP00000090164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3108,169,984 - 108,242,316 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107143   ⟹   ENSRNOP00000093681
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3108,169,980 - 108,243,008 (-)Ensembl
RefSeq Acc Id: NM_001371259   ⟹   NP_001358188
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,243,008 (-)NCBI
RefSeq Acc Id: XM_006234865   ⟹   XP_006234927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,264,268 (-)NCBI
Rnor_6.03113,160,030 - 113,252,655 (-)NCBI
Rnor_5.03119,697,122 - 119,799,485 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592214   ⟹   XP_017447703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,263,089 (-)NCBI
Rnor_6.03113,160,030 - 113,251,831 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017592215   ⟹   XP_017447704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,270,229 (-)NCBI
Rnor_6.03113,160,030 - 113,259,701 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104550   ⟹   XP_038960478
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,264,268 (-)NCBI
RefSeq Acc Id: XM_039104551   ⟹   XP_038960479
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,166,574 - 108,264,269 (-)NCBI
RefSeq Acc Id: XM_039104552   ⟹   XP_038960480
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,264,270 (-)NCBI
RefSeq Acc Id: XM_039104553   ⟹   XP_038960481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,179,399 - 108,264,274 (-)NCBI
RefSeq Acc Id: XM_039104554   ⟹   XP_038960482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23108,169,978 - 108,201,286 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006234927   ⟸   XM_006234865
- Peptide Label: isoform X1
- UniProtKB: F1M842 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447704   ⟸   XM_017592215
- Peptide Label: isoform X1
- UniProtKB: F1M842 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447703   ⟸   XM_017592214
- Peptide Label: isoform X1
- UniProtKB: F1M842 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019025   ⟸   ENSRNOT00000019025
RefSeq Acc Id: XP_038960479   ⟸   XM_039104551
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038960480   ⟸   XM_039104552
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038960478   ⟸   XM_039104550
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001358188   ⟸   NM_001371259
RefSeq Acc Id: XP_038960482   ⟸   XM_039104554
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038960481   ⟸   XM_039104553
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000090164   ⟸   ENSRNOT00000106843
RefSeq Acc Id: ENSRNOP00000093681   ⟸   ENSRNOT00000107143
Protein Domains
BRCT

Transcriptome

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

Promoters
RGD ID:13692358
Promoter ID:EPDNEW_R2877
Type:multiple initiation site
Name:Tp53bp1_1
Description:tumor protein p53 binding protein 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_6.03113,231,712 - 113,231,772EPDNEW

Strain Variation

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


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 119742900 119742901 C A snv ACI/EurMcwi (MCW), MHS/Gib (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), MNS/Gib (KNAW), HTX/Kyo (KyushuU), DOB/Oda (KyushuU), ZF (KyushuU), DA/BklArbNsi (KNAW), NIG-III/Hok (KyushuU)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 113203099 113203100 C A snv ACI/EurMcwi (MCW), ACI/N (MCW), ACI/EurMcwi (RGD), DA/OlaHsd (2019), ACI/EurMcwi (2019), ACI/N (2020), MHS/Gib (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308039 AgrOrtholog
Ensembl Genes ENSRNOG00000013837 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019025 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000090164 ENTREZGENE
  ENSRNOP00000093681 ENTREZGENE
Ensembl Transcript ENSRNOT00000019025 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000106843 ENTREZGENE
  ENSRNOT00000107143 ENTREZGENE
Gene3D-CATH 2.30.30.30 UniProtKB/TrEMBL
  3.40.50.10190 UniProtKB/TrEMBL
InterPro 53-BP1_Tudor UniProtKB/TrEMBL
  BRCT_dom UniProtKB/TrEMBL
  BRCT_dom_sf UniProtKB/TrEMBL
  Rib_L2_dom2 UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
NCBI Gene 296099 ENTREZGENE
Pfam 53-BP1_Tudor UniProtKB/TrEMBL
PhenoGen Tp53bp1 PhenoGen
PROSITE BRCT UniProtKB/TrEMBL
SMART BRCT UniProtKB/TrEMBL
Superfamily-SCOP BRCT UniProtKB/TrEMBL
UniProt F1M842 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tp53bp1  tumor protein p53 binding protein 1  Trp53bp1  transformation related protein 53 binding protein 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Trp53bp1  transformation related protein 53 binding protein 1   Trp53bp1_predicted  transformation related protein 53 binding protein 1 (predicted)  'predicted' is removed 2292626 APPROVED
2008-01-09 Trp53bp1_predicted  transformation related protein 53 binding protein 1 (predicted)  LOC688035  similar to transformation related protein 53 binding protein 1  Data Merged 1643240 APPROVED
2006-11-20 LOC688035  similar to transformation related protein 53 binding protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Trp53bp1_predicted  transformation related protein 53 binding protein 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED