Obscn (obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF) - Rat Genome Database

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Gene: Obscn (obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF) Rattus norvegicus
Analyze
Symbol: Obscn
Name: obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF
RGD ID: 631335
Description: Predicted to enable several functions, including cytoskeletal protein binding activity; phosphatidylinositol phosphate binding activity; and phosphatidylinositol-3,4-bisphosphate binding activity. Predicted to be involved in negative regulation of phosphatidylinositol 3-kinase signaling and protein autophosphorylation. Located in M band and Z disc. Orthologous to human OBSCN (obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: MODEL
Also known as: hypothetical LOC287353; LOC108352087; LOC287353; Obscnl; obscurin; obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF-like; obscurin-like; RGD1305774
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
mRatBN7.21043,774,113 - 43,919,718 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1043,789,293 - 43,919,723 (-)Ensembl
Rnor_6.01045,353,185 - 45,483,570 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1045,338,009 - 45,481,008 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01045,094,419 - 45,240,049 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41045,286,791 - 45,432,832 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1043,040,464 - 43,184,409 (-)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:11717165   PMID:15013951   PMID:15314079   PMID:16205939   PMID:17012262   PMID:18219491   PMID:18477606   PMID:18782775   PMID:19002483   PMID:19403693   PMID:19605563   PMID:22416964  
PMID:23392350   PMID:24516603   PMID:28826662  


Genomics

Comparative Map Data
Obscn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21043,774,113 - 43,919,718 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1043,789,293 - 43,919,723 (-)Ensembl
Rnor_6.01045,353,185 - 45,483,570 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1045,338,009 - 45,481,008 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01045,094,419 - 45,240,049 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41045,286,791 - 45,432,832 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1043,040,464 - 43,184,409 (-)NCBICelera
Cytogenetic Map10q22NCBI
OBSCN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1228,208,044 - 228,378,876 (+)EnsemblGRCh38hg38GRCh38
GRCh381228,208,044 - 228,378,876 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371228,395,745 - 228,566,577 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361226,462,484 - 226,633,198 (+)NCBINCBI36hg18NCBI36
Build 341224,702,595 - 224,855,685NCBI
Celera1201,585,880 - 201,756,652 (+)NCBI
Cytogenetic Map1q42.13NCBI
HuRef1198,910,669 - 199,081,449 (+)NCBIHuRef
CHM1_11229,668,122 - 229,838,939 (+)NCBICHM1_1
Obscn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391158,885,082 - 59,027,201 (-)NCBIGRCm39mm39
GRCm39 Ensembl1158,885,082 - 59,029,996 (-)Ensembl
GRCm381158,994,256 - 59,136,375 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1158,994,256 - 59,139,170 (-)EnsemblGRCm38mm10GRCm38
MGSCv371158,807,758 - 58,949,877 (-)NCBIGRCm37mm9NCBIm37
MGSCv361158,810,527 - 58,824,805 (-)NCBImm8
Celera1163,760,680 - 63,901,312 (-)NCBICelera
Cytogenetic Map11B1.3NCBI
Obscn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955581148,571 - 265,062 (-)NCBIChiLan1.0ChiLan1.0
OBSCN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11208,821,882 - 208,992,327 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1208,825,607 - 208,992,246 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01203,605,558 - 203,781,491 (+)NCBIMhudiblu_PPA_v0panPan3
OBSCN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.114664,404 - 782,376 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha14368,668 - 495,174 (+)NCBI
ROS_Cfam_1.014380,493 - 503,404 (-)NCBI
UMICH_Zoey_3.114566,842 - 694,225 (-)NCBI
UNSW_CanFamBas_1.014327,479 - 475,088 (-)NCBI
UU_Cfam_GSD_1.014337,710 - 460,914 (-)NCBI
LOC101962737
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721387,601,725 - 87,686,594 (-)NCBI
SpeTri2.0NW_004936864619 - 33,574 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OBSCN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl251,307,201 - 51,519,405 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1251,317,538 - 51,534,246 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2253,786,998 - 53,794,594 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OBSCN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1251,356,567 - 1,520,517 (-)NCBI
ChlSab1.1 Ensembl251,366,179 - 1,514,668 (-)Ensembl
Vero_WHO_p1.0NW_0236660551,236,221 - 1,403,869 (-)NCBI
Obscn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624937926,090 - 1,060,233 (+)NCBI

Position Markers
RH127871  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21043,789,403 - 43,789,605 (+)MAPPERmRatBN7.2
Rnor_6.01045,353,296 - 45,353,497NCBIRnor6.0
Rnor_5.01045,109,710 - 45,109,911UniSTSRnor5.0
RGSC_v3.41045,302,220 - 45,302,421UniSTSRGSC3.4
Celera1043,055,755 - 43,055,956UniSTS
RH 3.4 Map10501.6UniSTS
Cytogenetic Map10q22UniSTS
RH134278  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21043,773,999 - 43,774,199 (+)MAPPERmRatBN7.2
Rnor_6.01045,337,892 - 45,338,091NCBIRnor6.0
Rnor_5.01045,094,306 - 45,094,505UniSTSRnor5.0
RGSC_v3.41045,286,816 - 45,287,015UniSTSRGSC3.4
Celera1043,040,351 - 43,040,550UniSTS
RH 3.4 Map10489.3UniSTS
Cytogenetic Map10q22UniSTS
RH140532  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21043,790,935 - 43,791,040 (+)MAPPERmRatBN7.2
Rnor_6.01045,354,828 - 45,354,932NCBIRnor6.0
Rnor_5.01045,111,242 - 45,111,346UniSTSRnor5.0
RGSC_v3.41045,303,752 - 45,303,856UniSTSRGSC3.4
Celera1043,057,287 - 43,057,391UniSTS
RH 3.4 Map10502.6UniSTS
Cytogenetic Map10q22UniSTS
AA800048  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21043,791,878 - 43,792,014 (+)MAPPERmRatBN7.2
Rnor_6.01045,355,771 - 45,355,906NCBIRnor6.0
Rnor_5.01045,112,185 - 45,112,320UniSTSRnor5.0
RGSC_v3.41045,304,695 - 45,304,830UniSTSRGSC3.4
Celera1043,058,230 - 43,058,365UniSTS
RH 3.4 Map10501.59UniSTS
Cytogenetic Map10q22UniSTS


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
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
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
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
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
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
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
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
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
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103539226751793994Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
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

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:345
Count of miRNA genes:199
Interacting mature miRNAs:233
Transcripts:ENSRNOT00000033222, ENSRNOT00000058419
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 43 8 11 2 8
Low 11 9 7 9 31 13 8
Below cutoff 2 44 30 12 30 39 29 28 1

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_017597640 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087221 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087224 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087227 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087237 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087239 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087240 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087241 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087242 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005490245 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005490246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005490247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC099089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY167411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000220 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000078353   ⟹   ENSRNOP00000074671
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1045,338,062 - 45,480,999 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084697   ⟹   ENSRNOP00000069172
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1043,789,293 - 43,919,723 (-)Ensembl
Rnor_6.0 Ensembl1045,353,714 - 45,480,999 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087926   ⟹   ENSRNOP00000072721
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1045,338,009 - 45,481,008 (-)Ensembl
RefSeq Acc Id: XM_039087219   ⟹   XP_038943147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087220   ⟹   XP_038943148
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087221   ⟹   XP_038943149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087222   ⟹   XP_038943150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087223   ⟹   XP_038943151
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087224   ⟹   XP_038943152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087225   ⟹   XP_038943153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087226   ⟹   XP_038943154
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087227   ⟹   XP_038943155
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087228   ⟹   XP_038943156
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087229   ⟹   XP_038943157
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087230   ⟹   XP_038943158
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087231   ⟹   XP_038943159
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087232   ⟹   XP_038943160
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087234   ⟹   XP_038943162
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087235   ⟹   XP_038943163
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087236   ⟹   XP_038943164
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087237   ⟹   XP_038943165
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087238   ⟹   XP_038943166
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087239   ⟹   XP_038943167
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087240   ⟹   XP_038943168
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087241   ⟹   XP_038943169
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087242   ⟹   XP_038943170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087243   ⟹   XP_038943171
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087245   ⟹   XP_038943173
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087246   ⟹   XP_038943174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087247   ⟹   XP_038943175
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087248   ⟹   XP_038943176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087249   ⟹   XP_038943177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087250   ⟹   XP_038943178
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,919,716 (-)NCBI
RefSeq Acc Id: XM_039087251   ⟹   XP_038943179
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,789,293 - 43,919,717 (-)NCBI
RefSeq Acc Id: XM_039087252   ⟹   XP_038943180
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,789,293 - 43,919,717 (-)NCBI
RefSeq Acc Id: XM_039087253   ⟹   XP_038943181
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,838,934 (-)NCBI
RefSeq Acc Id: XM_039087254   ⟹   XP_038943182
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,840,706 (-)NCBI
RefSeq Acc Id: XM_039087256   ⟹   XP_038943184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,838,934 (-)NCBI
RefSeq Acc Id: XM_039087257   ⟹   XP_038943185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,774,113 - 43,838,934 (-)NCBI
RefSeq Acc Id: XM_039087258   ⟹   XP_038943186
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,789,293 - 43,919,716 (-)NCBI
RefSeq Acc Id: XR_005490245
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,837,698 - 43,919,718 (-)NCBI
RefSeq Acc Id: XR_005490246
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,833,087 - 43,919,718 (-)NCBI
RefSeq Acc Id: XR_005490247
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21043,832,527 - 43,919,718 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038943147 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943148 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943149 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943150 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943151 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943152 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943153 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943154 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943155 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943156 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943157 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943158 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943159 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943160 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943162 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943163 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943164 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943165 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943166 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943167 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943168 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943169 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943170 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943171 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943173 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943174 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943175 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943176 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943177 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943178 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943179 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943180 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943181 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943182 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943184 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943185 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943186 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAO34127 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000069172   ⟸   ENSRNOT00000084697
RefSeq Acc Id: ENSRNOP00000072721   ⟸   ENSRNOT00000087926
RefSeq Acc Id: ENSRNOP00000074671   ⟸   ENSRNOT00000078353
RefSeq Acc Id: XP_038943158   ⟸   XM_039087230
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038943166   ⟸   XM_039087238
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038943156   ⟸   XM_039087228
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038943153   ⟸   XM_039087225
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038943165   ⟸   XM_039087237
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038943154   ⟸   XM_039087226
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038943155   ⟸   XM_039087227
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038943157   ⟸   XM_039087229
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038943178   ⟸   XM_039087250
- Peptide Label: isoform X30
RefSeq Acc Id: XP_038943174   ⟸   XM_039087246
- Peptide Label: isoform X26
RefSeq Acc Id: XP_038943177   ⟸   XM_039087249
- Peptide Label: isoform X29
RefSeq Acc Id: XP_038943173   ⟸   XM_039087245
- Peptide Label: isoform X25
RefSeq Acc Id: XP_038943176   ⟸   XM_039087248
- Peptide Label: isoform X28
RefSeq Acc Id: XP_038943175   ⟸   XM_039087247
- Peptide Label: isoform X27
RefSeq Acc Id: XP_038943171   ⟸   XM_039087243
- Peptide Label: isoform X24
RefSeq Acc Id: XP_038943149   ⟸   XM_039087221
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038943170   ⟸   XM_039087242
- Peptide Label: isoform X23
RefSeq Acc Id: XP_038943168   ⟸   XM_039087240
- Peptide Label: isoform X21
RefSeq Acc Id: XP_038943163   ⟸   XM_039087235
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038943162   ⟸   XM_039087234
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038943152   ⟸   XM_039087224
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038943169   ⟸   XM_039087241
- Peptide Label: isoform X22
RefSeq Acc Id: XP_038943167   ⟸   XM_039087239
- Peptide Label: isoform X20
RefSeq Acc Id: XP_038943159   ⟸   XM_039087231
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038943148   ⟸   XM_039087220
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038943160   ⟸   XM_039087232
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038943151   ⟸   XM_039087223
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038943150   ⟸   XM_039087222
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038943164   ⟸   XM_039087236
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038943147   ⟸   XM_039087219
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943182   ⟸   XM_039087254
- Peptide Label: isoform X32
RefSeq Acc Id: XP_038943185   ⟸   XM_039087257
- Peptide Label: isoform X34
RefSeq Acc Id: XP_038943184   ⟸   XM_039087256
- Peptide Label: isoform X33
RefSeq Acc Id: XP_038943181   ⟸   XM_039087253
- Peptide Label: isoform X32
RefSeq Acc Id: XP_038943180   ⟸   XM_039087252
- Peptide Label: isoform X31
RefSeq Acc Id: XP_038943179   ⟸   XM_039087251
- Peptide Label: isoform X31
RefSeq Acc Id: XP_038943186   ⟸   XM_039087258
- Peptide Label: isoform X35
Protein Domains
DH   Fibronectin type-III   Ig-like   PH   Protein kinase   SH3

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:631335 AgrOrtholog
Ensembl Genes ENSRNOG00000058068 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069172 UniProtKB/TrEMBL
  ENSRNOP00000072721 UniProtKB/TrEMBL
  ENSRNOP00000074671 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078353 UniProtKB/TrEMBL
  ENSRNOT00000084697 UniProtKB/TrEMBL
  ENSRNOT00000087926 UniProtKB/TrEMBL
Gene3D-CATH 1.20.900.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro DBL_dom_sf UniProtKB/TrEMBL
  DH-domain UniProtKB/TrEMBL
  Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_I-set UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  IQ_motif_EF-hand-BS UniProtKB/TrEMBL
  Kinase-like_dom UniProtKB/TrEMBL
  Obscurin_SH3 UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Prot_kinase_dom UniProtKB/TrEMBL
  Protein_kinase_ATP_BS UniProtKB/TrEMBL
  Ser/Thr_kinase_AS UniProtKB/TrEMBL
  SH3-like_dom UniProtKB/TrEMBL
  SH3_domain UniProtKB/TrEMBL
  Tyr_kinase_AS UniProtKB/TrEMBL
NCBI Gene 338458 ENTREZGENE
Pfam fn3 UniProtKB/TrEMBL
  I-set UniProtKB/TrEMBL
  PF00612 UniProtKB/TrEMBL
  Pkinase UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
PhenoGen Obscn PhenoGen
PROSITE DH_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
  IG_LIKE UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  PROTEIN_KINASE_ATP UniProtKB/TrEMBL
  PROTEIN_KINASE_DOM UniProtKB/TrEMBL
  PROTEIN_KINASE_ST UniProtKB/TrEMBL
  PROTEIN_KINASE_TYR UniProtKB/TrEMBL
  PS50096 UniProtKB/TrEMBL
  SH3 UniProtKB/TrEMBL
SMART FN3 UniProtKB/TrEMBL
  IGc2 UniProtKB/TrEMBL
  IGv UniProtKB/TrEMBL
  RhoGEF UniProtKB/TrEMBL
  S_TKc UniProtKB/TrEMBL
  SM00015 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP DH-domain UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
  SSF49265 UniProtKB/TrEMBL
  SSF50044 UniProtKB/TrEMBL
  SSF56112 UniProtKB/TrEMBL
UniProt A0A0G2JUP3_RAT UniProtKB/TrEMBL
  A0A0G2K3P4_RAT UniProtKB/TrEMBL
  A0A0G2K8N1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Obscn  obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF  LOC108352087  obscurin-like  Data Merged 737654 PROVISIONAL
2016-08-02 LOC108352087  obscurin-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2015-11-06 Obscn  obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF  Obscnl  obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF-like  Data Merged 737654 APPROVED
2008-03-18 Obscnl  obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF-like  RGD1305774_predicted  hypothetical LOC287353 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1305774_predicted  hypothetical LOC287353 (predicted)  LOC287353_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287353_predicted  hypothetical LOC287353 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-02-11 Obscn  obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF      Symbol and Name status set to approved 625702 APPROVED