Unc5c (unc-5 netrin receptor C) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Unc5c (unc-5 netrin receptor C) Rattus norvegicus
Analyze
Symbol: Unc5c
Name: unc-5 netrin receptor C
RGD ID: 735109
Description: Predicted to enable netrin receptor activity involved in chemorepulsion; protein kinase binding activity; and tubulin binding activity. Predicted to be involved in chemorepulsion of axon; dorsal root ganglion development; and netrin-activated signaling pathway. Predicted to act upstream of or within nervous system development; positive regulation of apoptotic process; and regulation of cell migration. Predicted to be located in several cellular components, including filopodium; growth cone; and lamellipodium. Orthologous to human UNC5C (unc-5 netrin receptor C); INTERACTS WITH 17alpha-ethynylestradiol; 6-propyl-2-thiouracil; androgen antagonist.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: netrin receptor UNC5C; protein unc-5 homolog C; unc-5 homolog 3; unc-5 homolog C; unc-5 homolog C (C. elegans)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Unc5chob   Unc5ccvd  
Genetic Models: HOB-Unc5chob/Snk HOB/Snk F344.CVD-Unc5ccvd/Kyo
Is Marker For: Strains:   HOB/Snk   HOB-Unc5chob/Snk   CVD/Opu   F344.CVD-Unc5ccvd/Kyo  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22230,180,353 - 230,535,219 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2230,180,951 - 230,535,217 (+)Ensembl
Rnor_6.02247,045,813 - 247,397,483 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2247,248,407 - 247,397,483 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02265,573,406 - 265,926,229 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42239,365,109 - 239,721,231 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12239,351,848 - 239,707,971 (+)NCBI
Celera2222,239,483 - 222,591,078 (+)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
axon  (ISO,ISS)
cell surface  (IEA)
dendrite  (IEA,ISO,ISS)
filopodium  (IEA,ISO,ISS)
growth cone  (IEA,ISO,ISS)
integral component of membrane  (IEA)
lamellipodium  (IEA,ISO,ISS)
neuronal cell body  (IEA,ISO,ISS)
plasma membrane  (IEA,ISO,ISS)
synapse  (IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:1401878   PMID:9126743   PMID:9389662   PMID:9550145   PMID:10818148   PMID:10964959   PMID:11387206   PMID:18077458   PMID:18479186   PMID:22685302   PMID:23144223   PMID:25419706  
PMID:27068745   PMID:28483977  


Genomics

Comparative Map Data
Unc5c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22230,180,353 - 230,535,219 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2230,180,951 - 230,535,217 (+)Ensembl
Rnor_6.02247,045,813 - 247,397,483 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2247,248,407 - 247,397,483 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02265,573,406 - 265,926,229 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42239,365,109 - 239,721,231 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12239,351,848 - 239,707,971 (+)NCBI
Celera2222,239,483 - 222,591,078 (+)NCBICelera
Cytogenetic Map2q44NCBI
UNC5C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl495,162,504 - 95,549,206 (-)EnsemblGRCh38hg38GRCh38
GRCh38495,162,504 - 95,549,210 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37496,083,655 - 96,470,124 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36496,308,712 - 96,689,185 (-)NCBINCBI36hg18NCBI36
Build 34496,446,866 - 96,827,340NCBI
Celera493,380,311 - 93,766,978 (-)NCBI
Cytogenetic Map4q22.3NCBI
HuRef491,820,282 - 92,206,879 (-)NCBIHuRef
CHM1_1496,060,693 - 96,447,078 (-)NCBICHM1_1
Unc5c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393141,171,325 - 141,540,685 (+)NCBIGRCm39mm39
GRCm39 Ensembl3141,170,977 - 141,540,685 (+)Ensembl
GRCm383141,465,564 - 141,834,924 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3141,465,216 - 141,834,924 (+)EnsemblGRCm38mm10GRCm38
MGSCv373141,128,528 - 141,497,886 (+)NCBIGRCm37mm9NCBIm37
MGSCv363141,402,951 - 141,772,309 (+)NCBImm8
Celera3147,889,997 - 148,247,699 (+)NCBICelera
Cytogenetic Map3H1NCBI
cM Map365.57NCBI
Unc5c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554055,797,590 - 5,950,544 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554055,791,286 - 6,049,952 (-)NCBIChiLan1.0ChiLan1.0
UNC5C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1498,198,831 - 98,589,857 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl498,205,554 - 98,587,888 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0487,527,262 - 87,921,351 (-)NCBIMhudiblu_PPA_v0panPan3
UNC5C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13217,981,286 - 18,333,111 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3217,987,464 - 18,333,602 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3223,609,404 - 23,959,891 (+)NCBI
ROS_Cfam_1.03218,164,222 - 18,513,849 (-)NCBI
ROS_Cfam_1.0 Ensembl3218,167,485 - 18,513,818 (-)Ensembl
UMICH_Zoey_3.13218,134,124 - 18,485,245 (-)NCBI
UNSW_CanFamBas_1.03217,955,873 - 18,306,960 (-)NCBI
UU_Cfam_GSD_1.03221,584,814 - 21,936,742 (+)NCBI
Unc5c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530123,396,564 - 23,746,350 (+)NCBI
SpeTri2.0NW_0049366872,600,635 - 2,951,407 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UNC5C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8124,149,968 - 124,530,603 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18124,149,364 - 124,533,755 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
UNC5C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1743,405,666 - 43,786,436 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603721,777,546 - 22,164,042 (-)NCBIVero_WHO_p1.0
Unc5c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475723,145,200 - 23,537,812 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D2Rat296  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22230,469,531 - 230,469,773 (+)MAPPERmRatBN7.2
Rnor_6.02247,331,943 - 247,332,273NCBIRnor6.0
Rnor_5.02265,860,605 - 265,860,935UniSTSRnor5.0
RGSC_v3.42239,654,588 - 239,654,790RGDRGSC3.4
RGSC_v3.42239,654,589 - 239,654,790UniSTSRGSC3.4
RGSC_v3.12239,641,328 - 239,641,530RGD
Celera2222,525,569 - 222,525,770UniSTS
SHRSP x BN Map298.7698UniSTS
SHRSP x BN Map298.7698RGD
Cytogenetic Map2q44UniSTS
RH138265  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22230,533,052 - 230,533,210 (+)MAPPERmRatBN7.2
Rnor_6.02247,395,319 - 247,395,476NCBIRnor6.0
Rnor_5.02265,924,063 - 265,924,220UniSTSRnor5.0
RGSC_v3.42239,719,067 - 239,719,224UniSTSRGSC3.4
Celera2222,588,914 - 222,589,071UniSTS
RH 3.4 Map21581.1UniSTS
Cytogenetic Map2q44UniSTS
AU049740  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22230,203,710 - 230,203,853 (+)MAPPERmRatBN7.2
Rnor_6.02247,068,459 - 247,068,601NCBIRnor6.0
Rnor_5.02265,596,052 - 265,596,194UniSTSRnor5.0
RGSC_v3.42239,387,756 - 239,387,898UniSTSRGSC3.4
Celera2222,262,140 - 222,262,282UniSTS
Cytogenetic Map2q44UniSTS
Unc5c  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22230,534,393 - 230,534,816 (+)MAPPERmRatBN7.2
Rnor_6.02247,396,660 - 247,397,082NCBIRnor6.0
Rnor_5.02265,925,404 - 265,925,826UniSTSRnor5.0
RGSC_v3.42239,720,408 - 239,720,830UniSTSRGSC3.4
Celera2222,590,255 - 222,590,677UniSTS
Cytogenetic Map2q44UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
631563Hcuc3Hepatic copper content QTL 33.87hepatic copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2199341726234244620Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2189599258234599258Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2189599258234599258Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat


Related Rat Strains
The following Strains have been annotated to Unc5c


Genetic Models
This gene Unc5c is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:74
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000050330
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 4 8 2 3 2 48 12 13 2
Low 2 28 17 7 16 7 6 6 26 21 24 9 6
Below cutoff 1 11 27 27 27 2 4 2 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050330   ⟹   ENSRNOP00000050380
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,436,411 - 230,535,217 (+)Ensembl
Rnor_6.0 Ensembl2247,299,433 - 247,391,299 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082287   ⟹   ENSRNOP00000068741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,383,654 - 230,535,217 (+)Ensembl
Rnor_6.0 Ensembl2247,248,407 - 247,397,483 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000093785   ⟹   ENSRNOP00000095040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,448,646 - 230,535,217 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106798   ⟹   ENSRNOP00000090774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,180,951 - 230,535,217 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000108186   ⟹   ENSRNOP00000089543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,180,951 - 230,535,217 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116804   ⟹   ENSRNOP00000087486
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,434,570 - 230,535,217 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000120185   ⟹   ENSRNOP00000088490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2230,181,214 - 230,535,217 (+)Ensembl
RefSeq Acc Id: NM_199407   ⟹   NP_955439
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,181,064 - 230,535,217 (+)NCBI
Rnor_6.02247,045,813 - 247,397,483 (+)NCBI
Rnor_5.02265,573,406 - 265,926,229 (+)NCBI
RGSC_v3.42239,365,109 - 239,721,231 (+)RGD
Celera2222,239,483 - 222,591,078 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233402   ⟹   XP_006233464
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,180,358 - 230,535,219 (+)NCBI
Rnor_6.02247,045,865 - 247,396,687 (+)NCBI
Rnor_5.02265,573,406 - 265,926,229 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102727   ⟹   XP_038958655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,409,416 - 230,535,219 (+)NCBI
RefSeq Acc Id: XM_039102728   ⟹   XP_038958656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,433,704 - 230,535,219 (+)NCBI
RefSeq Acc Id: XM_039102729   ⟹   XP_038958657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,434,701 - 230,535,219 (+)NCBI
RefSeq Acc Id: XM_039102730   ⟹   XP_038958658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22230,180,353 - 230,503,747 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_955439   ⟸   NM_199407
- Peptide Label: precursor
- UniProtKB: Q761X5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006233464   ⟸   XM_006233402
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000068741   ⟸   ENSRNOT00000082287
RefSeq Acc Id: ENSRNOP00000050380   ⟸   ENSRNOT00000050330
RefSeq Acc Id: XP_038958658   ⟸   XM_039102730
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038958655   ⟸   XM_039102727
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038958656   ⟸   XM_039102728
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038958657   ⟸   XM_039102729
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000088490   ⟸   ENSRNOT00000120185
RefSeq Acc Id: ENSRNOP00000087486   ⟸   ENSRNOT00000116804
RefSeq Acc Id: ENSRNOP00000095040   ⟸   ENSRNOT00000093785
RefSeq Acc Id: ENSRNOP00000089543   ⟸   ENSRNOT00000108186
RefSeq Acc Id: ENSRNOP00000090774   ⟸   ENSRNOT00000106798
Protein Domains
Death   Ig-like   Ig-like C2-type   TSP type-1   ZU5

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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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
F344/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
FHH/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
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)
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)
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)
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
FXLE18/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
GH/OmrMcwi (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)
GK/FarMcwi (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
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)
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
HXB2/IpcvMcwi (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
HXB20/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
HXB31/IpcvMcwi (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
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)
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
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)
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)
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
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)
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
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)
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
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)
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: 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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 265880369 265880370 G A snv ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), WAG/Rij (KNAW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BBDP/WorN (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/NCrl (KNAW), F344/NHsd (KNAW), FHL/EurMcwi (KNAW), LE/Stm (Illumina) (KNAW), LE/Stm (SOLiD) (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), SBN/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), F344/NRrrc (Illumina) (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL), NIG-III/Hok (KyushuU), F344/DuCrlCrlj (KyushuU), LE/Stm (KyushuU), HTX/Kyo (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), HWY/Slc (KyushuU), LEC/Tj (KyushuU), F344/Jcl (KyushuU), ZFDM (KyushuU), FHH/EurMcwi (KNAW), COP/CrCrl (MCW & UW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 230489115 230489116 G A snv ACI/EurMcwi (2019), WKY/N (2020), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB4/IpcvMcwi (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), ACI/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 247351625 247351626 G A snv CDR, WKY/N (2020), ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), SBN/Ygl (MCW), SS/JrHsdMcwi (MCW), ACI/N (MCW), F344/NRrrc (MCW), WKY/N (MCW), ACI/EurMcwi (RGD), BBDP/Wor (RGD), F344/NCrl (RGD), FHH/EurMcwi (RGD), FHL/EurMcwi (RGD), LE/Stm (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), LH/MavRrrc (RGD), LL/MavRrrc (RGD), MNS/Gib (RGD), SBN/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), WKY/NHsd (RGD), ACI/EurMcwi (2019), ACI/N (2020), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FHH/EurMcwi (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB4/IpcvMcwi (2020), LEW/Crl (2019), LEXF11/Stm (2020), LEXF1A/Stm (2019), LEXF1C/Stm (2019), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF4/Stm (2020), LE/Stm (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LEXF10A/StmMcwi (2020), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), SS/JrHsdMcwi (2019), WAG/RijCrl (2020), WKY/NCrl (2019), CDS


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
2 239674406 239674407 G A snv ACI/EurMcwi (MCW), F344/NHsd (ICAHN), FHL/EurMcwi (MCW), SS/JrHsdMcwi (MCW), SHR/OlaIpcv (ICL), FHH/EurMcwi (MDC), SHRSP/Gcrc (MDC), SS/JrHsdMcwi (MDC), ACI/N (KNAW), F344/NRrrc (KNAW), LE/Stm (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), ACI/EurMcwi (ICL), BBDP/WorN (ICL), F344/NCrl (ICL), FHH/EurMcwi (ICL), FHL/EurMcwi (ICL), LE/Stm (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), MNS/Gib (ICL), SBN/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), WAG/Rij (ICL), WKY/NCrl (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735109 AgrOrtholog
Ensembl Genes ENSRNOG00000029071 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000050380 UniProtKB/TrEMBL
  ENSRNOP00000068741 UniProtKB/TrEMBL
  ENSRNOP00000087486 ENTREZGENE
  ENSRNOP00000088490 ENTREZGENE
  ENSRNOP00000089543 ENTREZGENE
  ENSRNOP00000090774 ENTREZGENE
Ensembl Transcript ENSRNOT00000050330 UniProtKB/TrEMBL
  ENSRNOT00000082287 UniProtKB/TrEMBL
  ENSRNOT00000106798 ENTREZGENE
  ENSRNOT00000108186 ENTREZGENE
  ENSRNOT00000116804 ENTREZGENE
  ENSRNOT00000120185 ENTREZGENE
Gene3D-CATH 1.10.533.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.20.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro DEATH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Death_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Death_UNC5C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UNC5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UPA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:362049 UniProtKB/Swiss-Prot
NCBI Gene 362049 ENTREZGENE
PANTHER PTHR12582 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Death UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UPA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Unc5c PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZU5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47986 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF82895 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JTK0_RAT UniProtKB/TrEMBL
  F1LM73_RAT UniProtKB/TrEMBL
  Q761X5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-06-26 Unc5c  unc-5 netrin receptor C  Unc5c  unc-5 homolog C (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Unc5c  unc-5 homolog C (C. elegans)      Symbol and Name status set to approved 1299863 APPROVED