Dvl1 (dishevelled segment polarity protein 1) - Rat Genome Database

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Gene: Dvl1 (dishevelled segment polarity protein 1) Rattus norvegicus
Analyze
Symbol: Dvl1
Name: dishevelled segment polarity protein 1
RGD ID: 620632
Description: Enables protein kinase binding activity and small GTPase binding activity. Involved in several processes, including dendritic spine morphogenesis; positive regulation of excitatory postsynaptic potential; and positive regulation of neuron projection arborization. Located in several cellular components, including dendritic spine; growth cone; and postsynaptic density. Colocalizes with microtubule. Biomarker of myocardial infarction. Human ortholog(s) of this gene implicated in DiGeorge syndrome and autosomal dominant Robinow syndrome 2. Orthologous to human DVL1 (dishevelled segment polarity protein 1); PARTICIPATES IN Wnt signaling, canonical pathway; Wnt signaling pathway; Wnt signaling, non-canonical pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: dishevelled 1; dishevelled, dsh homolog 1; dishevelled, dsh homolog 1 (Drosophila); dishevelled-1; DSH homolog 1; dvl-1; segment polarity protein dishevelled homolog DVL-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
mRatBN7.25166,456,989 - 166,468,733 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5166,456,686 - 166,468,664 (+)Ensembl
Rnor_6.05173,295,948 - 173,308,014 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,296,270 - 173,307,945 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,771,577 - 176,783,630 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,705,951 - 172,717,626 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15172,716,445 - 172,728,121 (+)NCBI
Celera5164,657,716 - 164,669,383 (+)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axon extension  (ISO)
axon guidance  (ISO)
axonogenesis  (ISO)
canonical Wnt signaling pathway  (IBA,ISO)
cochlea morphogenesis  (ISO)
collateral sprouting  (ISO)
convergent extension involved in neural plate elongation  (ISO)
convergent extension involved in organogenesis  (ISO)
cytoplasmic microtubule organization  (ISO)
dendrite morphogenesis  (ISO)
dendritic spine morphogenesis  (IGI)
intracellular signal transduction  (IEA)
negative regulation of protein binding  (ISO)
negative regulation of protein kinase activity  (ISO)
negative regulation of protein phosphorylation  (ISO)
neural tube development  (ISO)
neuromuscular junction development  (ISO)
neurotransmitter secretion  (ISO)
planar cell polarity pathway involved in neural tube closure  (IBA,ISO)
positive regulation of excitatory postsynaptic potential  (IGI)
positive regulation of neuron projection arborization  (IGI)
positive regulation of neuron projection development  (ISO)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
postsynapse organization  (ISO)
prepulse inhibition  (ISO)
presynapse assembly  (ISO)
protein localization to microtubule  (ISO)
protein localization to nucleus  (ISO)
protein stabilization  (ISO)
receptor clustering  (ISO)
regulation of neurotransmitter levels  (ISO)
regulation of protein localization  (ISO)
regulation of protein phosphorylation  (ISO)
regulation of synaptic vesicle exocytosis  (ISO)
regulation of transcription, DNA-templated  (ISO)
skeletal muscle acetylcholine-gated channel clustering  (ISO)
social behavior  (ISO)
synapse organization  (ISO)
Wnt signaling pathway  (IGI,TAS)
Wnt signaling pathway, planar cell polarity pathway  (ISO)

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8817329   PMID:9271238   PMID:10330181   PMID:10409711   PMID:11113207   PMID:11742004   PMID:11742073   PMID:12138115   PMID:12165471   PMID:12556519   PMID:12805222   PMID:14648878  
PMID:14734535   PMID:14747478   PMID:14960015   PMID:14966280   PMID:15454084   PMID:15548427   PMID:16116426   PMID:16571627   PMID:16818724   PMID:17005174   PMID:17027228   PMID:17212654  
PMID:17239604   PMID:17558396   PMID:17593335   PMID:18093802   PMID:18716223   PMID:19008950   PMID:19020093   PMID:19388021   PMID:19625296   PMID:19643732   PMID:20177058   PMID:21189423  
PMID:21718540   PMID:21880741   PMID:22899650   PMID:23074275   PMID:23160799   PMID:24305805   PMID:25674206   PMID:26359454   PMID:26400647   PMID:29510185   PMID:32105766  


Genomics

Comparative Map Data
Dvl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25166,456,989 - 166,468,733 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5166,456,686 - 166,468,664 (+)Ensembl
Rnor_6.05173,295,948 - 173,308,014 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,296,270 - 173,307,945 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05176,771,577 - 176,783,630 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,705,951 - 172,717,626 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15172,716,445 - 172,728,121 (+)NCBI
Celera5164,657,716 - 164,669,383 (+)NCBICelera
Cytogenetic Map5q36NCBI
DVL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11,335,276 - 1,349,418 (-)EnsemblGRCh38hg38GRCh38
GRCh3811,335,278 - 1,349,418 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711,270,658 - 1,284,798 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611,260,521 - 1,274,358 (-)NCBINCBI36hg18NCBI36
Build 3411,310,581 - 1,324,438NCBI
Celera11,305,944 - 1,310,484 (+)NCBI
Cytogenetic Map1p36.33NCBI
HuRef1541,861 - 555,565 (-)NCBIHuRef
CHM1_111,257,686 - 1,271,561 (-)NCBICHM1_1
Dvl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394155,931,829 - 155,943,760 (+)NCBIGRCm39mm39
GRCm39 Ensembl4155,931,859 - 155,943,760 (+)Ensembl
GRCm384155,847,402 - 155,859,303 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4155,847,402 - 155,859,303 (+)EnsemblGRCm38mm10GRCm38
MGSCv374155,221,521 - 155,233,412 (+)NCBIGRCm37mm9NCBIm37
MGSCv364154,691,212 - 154,703,103 (+)NCBImm8
Celera4158,118,352 - 158,130,254 (+)NCBICelera
Cytogenetic Map4E2NCBI
cM Map487.61NCBI
Dvl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,464,313 - 9,469,984 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554869,464,390 - 9,469,984 (+)NCBIChiLan1.0ChiLan1.0
DVL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111,292,052 - 1,300,006 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11,292,052 - 1,301,008 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0192,469 - 106,748 (-)NCBIMhudiblu_PPA_v0panPan3
DVL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,507,803 - 56,519,382 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,507,739 - 56,519,491 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha556,584,127 - 56,595,703 (-)NCBI
ROS_Cfam_1.0556,710,022 - 56,721,601 (-)NCBI
UMICH_Zoey_3.1556,700,763 - 56,712,335 (-)NCBI
UNSW_CanFamBas_1.0556,593,044 - 56,604,611 (-)NCBI
UU_Cfam_GSD_1.0556,983,289 - 56,994,870 (-)NCBI
Dvl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505827,654,912 - 27,668,618 (-)NCBI
SpeTri2.0NW_0049367371,797,348 - 1,811,043 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DVL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,617,789 - 63,629,229 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,617,787 - 63,628,965 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2658,115,863 - 58,126,973 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DVL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120130,105,032 - 130,118,978 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20130,104,639 - 130,117,139 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605434,662,915 - 34,682,331 (+)NCBIVero_WHO_p1.0
Dvl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248188,267,111 - 8,283,755 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH141334  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,468,498 - 166,468,686 (+)MAPPERmRatBN7.2
Rnor_6.05173,307,780 - 173,307,967NCBIRnor6.0
Rnor_5.05176,783,396 - 176,783,583UniSTSRnor5.0
RGSC_v3.45172,717,461 - 172,717,648UniSTSRGSC3.4
Celera5164,669,218 - 164,669,405UniSTS
RH 3.4 Map51174.5UniSTS
Cytogenetic Map5q36UniSTS
AI406524  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,463,925 - 166,464,075 (+)MAPPERmRatBN7.2
Rnor_6.05173,303,207 - 173,303,356NCBIRnor6.0
Rnor_5.05176,778,823 - 176,778,972UniSTSRnor5.0
RGSC_v3.45172,712,888 - 172,713,037UniSTSRGSC3.4
Celera5164,664,645 - 164,664,794UniSTS
RH 3.4 Map51175.1UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:121
Count of miRNA genes:85
Interacting mature miRNAs:109
Transcripts:ENSRNOT00000026439
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 38 57 41 19 41 8 11 74 35 41 11 8
Low 5
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_031820 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006239598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008764391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593659 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110851 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC106940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC126156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF143545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF143546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH007910 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC062070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC090034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC160920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000026439   ⟹   ENSRNOP00000026439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,456,989 - 166,468,664 (+)Ensembl
Rnor_6.0 Ensembl5173,296,270 - 173,307,945 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107156   ⟹   ENSRNOP00000085309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,456,686 - 166,468,575 (+)Ensembl
RefSeq Acc Id: NM_031820   ⟹   NP_114008
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,456,989 - 166,468,664 (+)NCBI
Rnor_6.05173,296,270 - 173,307,945 (+)NCBI
Rnor_5.05176,771,577 - 176,783,630 (+)NCBI
RGSC_v3.45172,705,951 - 172,717,626 (+)RGD
Celera5164,657,716 - 164,669,383 (+)RGD
Sequence:
RefSeq Acc Id: XM_006239598   ⟹   XP_006239660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,456,990 - 166,468,733 (+)NCBI
Rnor_6.05173,295,949 - 173,308,014 (+)NCBI
Rnor_5.05176,771,577 - 176,783,630 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039110850   ⟹   XP_038966778
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,456,990 - 166,468,733 (+)NCBI
RefSeq Acc Id: XM_039110851   ⟹   XP_038966779
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,457,025 - 166,468,733 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_114008   ⟸   NM_031820
- UniProtKB: Q9WVB9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006239660   ⟸   XM_006239598
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000026439   ⟸   ENSRNOT00000026439
RefSeq Acc Id: XP_038966778   ⟸   XM_039110850
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038966779   ⟸   XM_039110851
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000085309   ⟸   ENSRNOT00000107156
Protein Domains
DEP   DIX   PDZ

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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)
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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)
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
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)
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
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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
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)
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
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)
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
M520/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
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 176780959 176780960 G C snv IS-Tlk/Kyo (KyushuU)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 172713396 172713397 G T snv LCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620632 AgrOrtholog
Ensembl Genes ENSRNOG00000019423 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000026439 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026439 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.30.42.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.20.380 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599217 IMAGE-MGC_LOAD
  IMAGE:7461890 IMAGE-MGC_LOAD
InterPro DEP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dishevelled_C-dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dishevelled_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dishevelled_protein_dom UniProtKB/Swiss-Prot
  DIX UniProtKB/Swiss-Prot
  DIX_dom_sf UniProtKB/Swiss-Prot
  Dsh/Dvl-rel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DVL-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:83721 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188669 IMAGE-MGC_LOAD
  MGC:72382 IMAGE-MGC_LOAD
NCBI Gene 83721 ENTREZGENE
PANTHER PTHR10878 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10878:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Dishevelled UniProtKB/Swiss-Prot
  DIX UniProtKB/Swiss-Prot
  Dsh_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot
PhenoGen Dvl1 PhenoGen
PRINTS DISHEVELLED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DIX UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
SMART DAX UniProtKB/Swiss-Prot
  DEP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PDZ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50156 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54236 UniProtKB/Swiss-Prot
UniProt B1H2A0_RAT UniProtKB/TrEMBL
  DVL1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9QUG5 UniProtKB/Swiss-Prot
  Q9WVB8 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-05 Dvl1  dishevelled segment polarity protein 1  Dvl1  dishevelled, dsh homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Dvl1  dishevelled, dsh homolog 1 (Drosophila)    dishevelled 1  Name updated 1299863 APPROVED
2002-08-07 Dvl1  dishevelled 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_other excluded as a candidate gene for brain ischemia in the stroke-prone spontaneously hypertensive rat (SHRSP) because sequences in stroke-prone and control rats are identical 634738