Nectin1 (nectin cell adhesion molecule 1) - Rat Genome Database

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Gene: Nectin1 (nectin cell adhesion molecule 1) Rattus norvegicus
Analyze
Symbol: Nectin1
Name: nectin cell adhesion molecule 1
RGD ID: 620791
Description: Enables carbohydrate binding activity and virion binding activity. Involved in axon guidance; regulation of synapse assembly; and viral entry into host cell. Located in dendrite and growth cone membrane. Human ortholog(s) of this gene implicated in cleft lip; cleft lip-palate-ectodermal dysplasia syndrome; cleft palate; and ectodermal dysplasia. Orthologous to human NECTIN1 (nectin cell adhesion molecule 1); INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: HveC; nectin; nectin); nectin-1; poliovirus receptor-related 1 (herpesvirus entry mediator C; poliovirus receptor-related 1 (herpesvirus entry mediator C, nectin); poliovirus receptor-related protein 1; Pvrl1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Nectin1Tn(sb-T2/Bart3)2.284Mcwi  
Genetic Models: F344-Nectin1Tn(sb-T2/Bart3)2.284Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2844,101,776 - 44,164,863 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl844,101,776 - 44,189,787 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx849,600,140 - 49,663,198 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0847,878,811 - 47,941,870 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0845,746,411 - 45,809,474 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0848,094,233 - 48,198,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl848,094,673 - 48,157,305 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0846,714,981 - 46,777,484 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4846,739,657 - 46,799,051 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1846,807,104 - 46,807,754 (+)NCBI
Celera843,690,971 - 43,754,034 (+)NCBICelera
Cytogenetic Map8q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-amino-4,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alendronic acid  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
buta-1,3-diene  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP,ISO)
capsaicin  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper(II) sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
dimethylarsinic acid  (ISO)
dioxygen  (ISO)
diquat  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
iron dichloride  (ISO)
leflunomide  (ISO)
methapyrilene  (ISO)
methoxychlor  (EXP)
methylarsonic acid  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-Nitrosopyrrolidine  (ISO)
ochratoxin A  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
PCB138  (EXP)
rac-lactic acid  (ISO)
raloxifene  (EXP)
rotenone  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
thioacetamide  (EXP)
trichloroethene  (EXP)
troglitazone  (ISO)
valproic acid  (EXP)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Temporal and spatial localization of nectin-1 and l-afadin during synaptogenesis in hippocampal neurons. Lim ST, etal., J Comp Neurol. 2008 Mar 10;507(2):1228-44.
3. Nectin: an adhesion molecule involved in formation of synapses. Mizoguchi A, etal., J Cell Biol. 2002 Feb 4;156(3):555-65. Epub 2002 Feb 4.
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. Evaluation of cell survival, DNA double strand breaks, and DNA synthesis during concurrent camptothecin and X-radiation treatments. Ng CE, etal., Int J Cancer 2001 Oct 20;96(5):277-85.
6. Contacts between the commissural axons and the floor plate cells are mediated by nectins. Okabe N, etal., Dev Biol. 2004 Sep 15;273(2):244-56.
7. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Entry of herpes simplex virus type 1 into primary sensory neurons in vitro is mediated by Nectin-1/HveC. Richart SM, etal., J Virol. 2003 Mar;77(5):3307-11.
11. Mutations of PVRL1, encoding a cell-cell adhesion molecule/herpesvirus receptor, in cleft lip/palate-ectodermal dysplasia. Suzuki K, etal., Nat Genet. 2000 Aug;25(4):427-30.
12. Interneurite affinity is regulated by heterophilic nectin interactions in concert with the cadherin machinery. Togashi H, etal., J Cell Biol. 2006 Jul 3;174(1):141-51. Epub 2006 Jun 26.
Additional References at PubMed
PMID:10225955   PMID:11090177   PMID:11277703   PMID:12011057   PMID:12438620   PMID:12515806   PMID:12826663   PMID:15728677   PMID:18703497   PMID:21982860   PMID:22512338   PMID:22902367  
PMID:23418609   PMID:23533177  


Genomics

Comparative Map Data
Nectin1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2844,101,776 - 44,164,863 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl844,101,776 - 44,189,787 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx849,600,140 - 49,663,198 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0847,878,811 - 47,941,870 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0845,746,411 - 45,809,474 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0848,094,233 - 48,198,499 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl848,094,673 - 48,157,305 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0846,714,981 - 46,777,484 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4846,739,657 - 46,799,051 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1846,807,104 - 46,807,754 (+)NCBI
Celera843,690,971 - 43,754,034 (+)NCBICelera
Cytogenetic Map8q22NCBI
NECTIN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811119,638,098 - 119,729,200 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11119,623,408 - 119,729,200 (-)EnsemblGRCh38hg38GRCh38
GRCh3711119,508,808 - 119,599,910 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611119,014,018 - 119,104,645 (-)NCBINCBI36Build 36hg18NCBI36
Build 3411119,050,309 - 119,104,645NCBI
Celera11116,669,897 - 116,760,980 (-)NCBICelera
Cytogenetic Map11q23.3NCBI
HuRef11115,451,054 - 115,541,412 (-)NCBIHuRef
CHM1_111119,396,685 - 119,487,290 (-)NCBICHM1_1
T2T-CHM13v2.011119,660,108 - 119,752,026 (-)NCBIT2T-CHM13v2.0
Nectin1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39943,655,251 - 43,718,758 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl943,655,281 - 43,743,955 (+)EnsemblGRCm39 Ensembl
GRCm38943,737,075 - 43,807,461 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl943,743,984 - 43,832,658 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl943,743,984 - 43,807,461 (+)EnsemblGRCm38mm10GRCm38
MGSCv37943,552,659 - 43,615,544 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36943,495,571 - 43,558,456 (+)NCBIMGSCv36mm8
Celera941,000,673 - 41,063,599 (+)NCBICelera
Cytogenetic Map9A5.1NCBI
cM Map924.42NCBI
Nectin1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541220,682,861 - 20,745,069 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541220,683,007 - 20,745,069 (-)NCBIChiLan1.0ChiLan1.0
NECTIN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan111121,443,077 - 121,535,702 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v011114,497,177 - 114,565,338 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111118,425,181 - 118,493,090 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11118,401,321 - 118,493,090 (-)Ensemblpanpan1.1panPan2
NECTIN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1514,228,197 - 14,292,825 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl514,228,197 - 14,315,060 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha514,282,464 - 14,346,907 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0514,172,083 - 14,236,744 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl514,170,280 - 14,258,980 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1514,310,592 - 14,375,074 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0514,214,689 - 14,278,846 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0514,254,410 - 14,319,094 (+)NCBIUU_Cfam_GSD_1.0
Nectin1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947101,579,611 - 101,680,935 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365424,539,931 - 4,602,344 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365424,501,081 - 4,602,338 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NECTIN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl946,789,726 - 46,891,304 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1946,823,552 - 46,891,564 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2951,881,267 - 51,894,114 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NECTIN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11111,046,310 - 111,116,906 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1111,046,333 - 111,116,698 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604314,924,098 - 14,989,691 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nectin1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478414,997,424 - 15,059,761 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478414,997,533 - 15,058,971 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nectin1
289 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:74
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000008614
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82613018771130187Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)82613018771130187Rat
1359021Bp271Blood pressure QTL 2711.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82664491246711092Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82720571554998217Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
1331804Cm30Cardiac mass QTL 303.77443heart mass (VT:0007028)heart wet weight (CMO:0000069)82824291253961020Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)82824291273242912Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
2302278Gluco36Glucose level QTL 364.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)82950266550095447Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)82950266570386295Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815458482492Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83084815461290444Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83084815461290444Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83084815461290444Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83084815482460899Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83084815482460899Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83084815482460899Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83084815482460899Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83085640475856404Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83173772976737729Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83555193880551938Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83558203280582032Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84071306682925667Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84186687675097878Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84186701070386132Rat
5684993Bmd84Bone mineral density QTL 844.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)84269268450095447Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat

Markers in Region
BE121372  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2844,155,182 - 44,155,389 (+)MAPPERmRatBN7.2
Rnor_6.0848,147,637 - 48,147,842NCBIRnor6.0
Rnor_5.0846,767,806 - 46,768,011UniSTSRnor5.0
RGSC_v3.4846,792,374 - 46,792,579UniSTSRGSC3.4
Celera843,744,356 - 43,744,561UniSTS
RH 3.4 Map8422.2UniSTS
Cytogenetic Map8q22UniSTS
BI274299  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2844,154,917 - 44,155,135 (+)MAPPERmRatBN7.2
Rnor_6.0848,147,372 - 48,147,589NCBIRnor6.0
Rnor_5.0846,767,541 - 46,767,758UniSTSRnor5.0
RGSC_v3.4846,792,109 - 46,792,326UniSTSRGSC3.4
Celera843,744,091 - 43,744,308UniSTS
RH 3.4 Map8422.9UniSTS
Cytogenetic Map8q22UniSTS
AW529741  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2844,157,691 - 44,157,863 (+)MAPPERmRatBN7.2
Rnor_6.0848,150,144 - 48,150,315NCBIRnor6.0
Rnor_5.0846,770,313 - 46,770,484UniSTSRnor5.0
RGSC_v3.4846,794,882 - 46,795,053UniSTSRGSC3.4
Celera843,746,864 - 43,747,035UniSTS
RH 3.4 Map8424.0UniSTS
Cytogenetic Map8q22UniSTS


Genetic Models
This gene Nectin1 is modified in the following models/strains:
F344-Nectin1Tn(sb-T2/Bart3)2.284Mcwi    


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 12 12 12 66 25 25 3
Low 2 39 45 29 19 29 5 7 8 10 16 8 5
Below cutoff 4 3 4 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008614   ⟹   ENSRNOP00000008614
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl844,101,776 - 44,164,863 (+)Ensembl
Rnor_6.0 Ensembl848,094,673 - 48,157,305 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119575   ⟹   ENSRNOP00000078728
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl844,101,776 - 44,189,787 (+)Ensembl
RefSeq Acc Id: NM_001100476   ⟹   NP_001093946
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2844,101,776 - 44,164,863 (+)NCBI
Rnor_6.0848,094,233 - 48,157,315 (+)NCBI
Celera843,690,971 - 43,754,034 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001093946 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD26534 (Get FASTA)   NCBI Sequence Viewer  
  AIZ76578 (Get FASTA)   NCBI Sequence Viewer  
  EDL95269 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000008614
  ENSRNOP00000008614.6
  ENSRNOP00000078728.1
Reference Protein Sequences
RefSeq Acc Id: NP_001093946   ⟸   NM_001100476
- Peptide Label: precursor
- UniProtKB: F1LNP8 (UniProtKB/TrEMBL),   A6J3U6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008614   ⟸   ENSRNOT00000008614
RefSeq Acc Id: ENSRNOP00000078728   ⟸   ENSRNOT00000119575
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LNP8-F1-model_v2 AlphaFold F1LNP8 1-515 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620791 AgrOrtholog
BioCyc Gene G2FUF-30747 BioCyc
Ensembl Genes ENSRNOG00000006403 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008614 ENTREZGENE
  ENSRNOT00000008614.8 UniProtKB/TrEMBL
  ENSRNOT00000119575.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro CD80_C2-set UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  Nectin-1_Ig1 UniProtKB/TrEMBL
  Nectin-1_Ig2 UniProtKB/TrEMBL
KEGG Report rno:192183 UniProtKB/TrEMBL
NCBI Gene 192183 ENTREZGENE
PANTHER NECTIN-RELATED UniProtKB/TrEMBL
  PTHR23277:SF69 UniProtKB/TrEMBL
Pfam C2-set_2 UniProtKB/TrEMBL
  Ig_3 UniProtKB/TrEMBL
  V-set UniProtKB/TrEMBL
PhenoGen Nectin1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006403 RatGTEx
SMART IGc2 UniProtKB/TrEMBL
  IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A8I5ZLI7_RAT UniProtKB/TrEMBL
  A6J3U6 ENTREZGENE, UniProtKB/TrEMBL
  F1LNP8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Pvrl1  poliovirus receptor-related 1    poliovirus receptor-related 1 (herpesvirus entry mediator C; nectin)  Name updated 1299863 APPROVED
2002-08-07 Pvrl1  poliovirus receptor-related 1 (herpesvirus entry mediator C; nectin)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed at high levels in sensory neurons of the dorsal root ganglion compared to lower expression in motor neurons 704462