Nectin3 (nectin cell adhesion molecule 3) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Nectin3 (nectin cell adhesion molecule 3) Rattus norvegicus
Analyze
Symbol: Nectin3
Name: nectin cell adhesion molecule 3
RGD ID: 1309516
Description: Predicted to have cell adhesion molecule binding activity and protein homodimerization activity. Predicted to be involved in several processes, including camera-type eye morphogenesis; heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; and homophilic cell adhesion via plasma membrane adhesion molecules. Localizes to axon; dendrite; and synapse. Orthologous to human NECTIN3 (nectin cell adhesion molecule 3); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC288124; nectin-3; poliovirus receptor-related 3; poliovirus receptor-related protein 3; Pvrl3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21154,362,712 - 54,461,316 (+)NCBI
Rnor_6.0 Ensembl1157,897,879 - 57,993,548 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01157,897,879 - 57,995,193 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01162,049,050 - 62,146,379 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41155,843,801 - 55,940,634 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11155,901,379 - 55,946,114 (+)NCBI
Celera1153,897,883 - 53,994,695 (+)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium atom  (ISO)
chloroprene  (ISO)
choline  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dichloromethane  (EXP)
dicrotophos  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethylbenzene  (EXP)
flutamide  (EXP)
folic acid  (ISO)
glafenine  (EXP)
ketamine  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nimesulide  (EXP)
ouabain  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propiconazole  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
succimer  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

References

Additional References at PubMed
PMID:10744716   PMID:11827984   PMID:12438620   PMID:12515806   PMID:12740392   PMID:12759359   PMID:12826663   PMID:15328010   PMID:15660130   PMID:15728677   PMID:16249236   PMID:22512338  
PMID:22902367   PMID:23073828   PMID:23533177   PMID:23990464   PMID:25232752   PMID:27044745   PMID:27217376   PMID:28176461  


Genomics

Comparative Map Data
Nectin3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21154,362,712 - 54,461,316 (+)NCBI
Rnor_6.0 Ensembl1157,897,879 - 57,993,548 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01157,897,879 - 57,995,193 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01162,049,050 - 62,146,379 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41155,843,801 - 55,940,634 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11155,901,379 - 55,946,114 (+)NCBI
Celera1153,897,883 - 53,994,695 (+)NCBICelera
Cytogenetic Map11q21NCBI
NECTIN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3111,070,071 - 111,275,563 (+)EnsemblGRCh38hg38GRCh38
GRCh383111,071,764 - 111,201,444 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373110,790,663 - 110,913,017 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh373110,790,606 - 110,913,017 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363112,273,555 - 112,335,752 (+)NCBINCBI36hg18NCBI36
Build 343112,273,554 - 112,335,752NCBI
Celera3109,190,329 - 109,252,381 (+)NCBI
Cytogenetic Map3q13.13NCBI
HuRef3108,164,840 - 108,287,207 (+)NCBIHuRef
CHM1_13110,754,866 - 110,877,275 (+)NCBICHM1_1
Nectin3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391646,208,028 - 46,318,898 (-)NCBIGRCm39mm39
GRCm381646,387,665 - 46,498,535 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1646,387,706 - 46,498,525 (-)EnsemblGRCm38mm10GRCm38
MGSCv371646,395,118 - 46,497,080 (-)NCBIGRCm37mm9NCBIm37
MGSCv361646,314,342 - 46,416,301 (-)NCBImm8
Celera1646,777,549 - 46,846,805 (-)NCBICelera
Cytogenetic Map16B5NCBI
Nectin3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542711,606,909 - 11,724,004 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542711,639,942 - 11,731,910 (+)NCBIChiLan1.0ChiLan1.0
NECTIN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13115,148,481 - 115,278,563 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3115,148,481 - 115,270,507 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03108,223,380 - 108,354,079 (+)NCBIMhudiblu_PPA_v0panPan3
NECTIN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3315,911,411 - 15,933,307 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13315,868,813 - 16,173,158 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Nectin3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493683486,195 - 110,686 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NECTIN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13148,452,278 - 148,579,160 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113148,448,581 - 148,578,920 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213158,456,487 - 158,604,357 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NECTIN3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12269,597,729 - 69,719,397 (-)NCBI
ChlSab1.1 Ensembl2269,598,895 - 69,719,343 (-)Ensembl
Nectin3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473137,425,966 - 37,567,938 (-)NCBI

Position Markers
BF386882  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01157,937,717 - 57,937,867NCBIRnor6.0
Rnor_5.01162,088,888 - 62,089,038UniSTSRnor5.0
RGSC_v3.41155,899,485 - 55,899,635UniSTSRGSC3.4
Celera1153,953,547 - 53,953,697UniSTS
RH 3.4 Map4581.7UniSTS
Cytogenetic Map11q21UniSTS
RH12011  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01157,949,873 - 57,949,997NCBIRnor6.0
Rnor_5.01162,101,044 - 62,101,168UniSTSRnor5.0
RGSC_v3.41155,887,352 - 55,887,476UniSTSRGSC3.4
Celera1153,941,436 - 53,941,560UniSTS
Cytogenetic Map11q21UniSTS
RH133661  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01157,946,965 - 57,947,122NCBIRnor6.0
Rnor_5.01162,098,136 - 62,098,293UniSTSRnor5.0
RGSC_v3.41155,890,227 - 55,890,384UniSTSRGSC3.4
Celera1153,944,311 - 53,944,468UniSTS
RH 3.4 Map4621.62UniSTS
Cytogenetic Map11q21UniSTS
BE111876  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01157,943,025 - 57,943,196NCBIRnor6.0
Rnor_5.01162,094,196 - 62,094,367UniSTSRnor5.0
RGSC_v3.41155,894,153 - 55,894,324UniSTSRGSC3.4
Celera1153,948,237 - 53,948,408UniSTS
RH 3.4 Map4581.3UniSTS
Cytogenetic Map11q21UniSTS
RH137470  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01157,948,440 - 57,948,646NCBIRnor6.0
Rnor_5.01162,099,611 - 62,099,817UniSTSRnor5.0
RGSC_v3.41155,888,703 - 55,888,909UniSTSRGSC3.4
Celera1153,942,787 - 53,942,993UniSTS
Cytogenetic Map11q21UniSTS
PVRL3__5617  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01157,949,496 - 57,950,075NCBIRnor6.0
Rnor_5.01162,100,667 - 62,101,246UniSTSRnor5.0
RGSC_v3.41155,887,274 - 55,887,853UniSTSRGSC3.4
Celera1153,941,358 - 53,941,937UniSTS
Cytogenetic Map11q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)114444434769649708Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:48
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000002957
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 3 29 34 29 29 2 2 74 34 41 11 2
Low 14 23 12 19 12 6 8 1 6
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002957   ⟹   ENSRNOP00000002957
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1157,897,879 - 57,993,548 (-)Ensembl
RefSeq Acc Id: NM_001105883   ⟹   NP_001099353
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21154,364,487 - 54,461,316 (+)NCBI
Rnor_6.01157,897,879 - 57,993,548 (-)NCBI
Rnor_5.01162,049,050 - 62,146,379 (-)NCBI
RGSC_v3.41155,843,801 - 55,940,634 (+)RGD
Celera1153,897,883 - 53,994,695 (+)RGD
Sequence:
RefSeq Acc Id: XM_006248335   ⟹   XP_006248397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21154,364,278 - 54,413,560 (+)NCBI
Rnor_6.01157,948,112 - 57,993,586 (-)NCBI
Rnor_5.01162,049,050 - 62,146,379 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248338   ⟹   XP_006248400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01157,937,549 - 57,993,586 (-)NCBI
Rnor_5.01162,049,050 - 62,146,379 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088189   ⟹   XP_038944117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21154,362,712 - 54,413,560 (+)NCBI
RefSeq Acc Id: XR_001840409
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01157,937,650 - 57,995,193 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001840410
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01157,937,650 - 57,973,371 (-)NCBI
Sequence:
RefSeq Acc Id: XR_358269
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01157,937,650 - 57,993,586 (-)NCBI
Rnor_5.01162,049,050 - 62,146,379 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099353 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248397 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944117 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11119 (Get FASTA)   NCBI Sequence Viewer  
  EDM11121 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099353   ⟸   NM_001105883
- UniProtKB: D4A5C0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248400   ⟸   XM_006248338
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006248397   ⟸   XM_006248335
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000002957   ⟸   ENSRNOT00000002957
RefSeq Acc Id: XP_038944117   ⟸   XM_039088189
- Peptide Label: isoform X1
Protein Domains
Ig-like

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 (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 (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/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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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 (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
11 62049296 62049297 C T snv SBH/Ygl (KNAW), SBH/Ygl (MCW)
11 62090603 62090604 G A snv M520/N (KNAW), SS/Jr (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 57898125 57898126 C T snv SBH/Ygl (MCW), SBH/Ygl (RGD)
11 57939432 57939433 G A snv SS/Jr (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 55897920 55897921 C T snv SS/JrHsdMcwi (MDC), SS/Jr (ICL), SS/JrHsdMcwi (MCW)
11 55940388 55940389 G A snv SBH/Ygl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309516 AgrOrtholog
Ensembl Genes ENSRNOG00000002176 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002957 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002957 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro CD80_C2-set UniProtKB/TrEMBL
  Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  Nectin-3 UniProtKB/TrEMBL
KEGG Report rno:288124 UniProtKB/TrEMBL
NCBI Gene 288124 ENTREZGENE
PANTHER PTHR23277:SF12 UniProtKB/TrEMBL
Pfam C2-set_2 UniProtKB/TrEMBL
  V-set UniProtKB/TrEMBL
PhenoGen Nectin3 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
SMART SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt D4A5C0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Nectin3  nectin cell adhesion molecule 3  Pvrl3  poliovirus receptor-related 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pvrl3  poliovirus receptor-related 3   Pvrl3_predicted  poliovirus receptor-related 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pvrl3_predicted  poliovirus receptor-related 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED