F11r (F11 receptor) - Rat Genome Database
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Gene: F11r (F11 receptor) Rattus norvegicus
Analyze
Symbol: F11r
Name: F11 receptor
RGD ID: 621842
Description: Predicted to have PDZ domain binding activity; integrin binding activity; and protein homodimerization activity. Involved in cell differentiation; positive regulation of blood pressure; and response to radiation. Localizes to cytoplasmic vesicle and slit diaphragm. Biomarker of hypertension; peptic esophagitis; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in hypertension. Orthologous to human F11R (F11 receptor); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: JAM-1; JAM-A; Jam1; junctional adhesion molecule 1; junctional adhesion molecule A
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
mRatBN7.21383,873,797 - 83,897,388 (+)NCBI
Rnor_6.0 Ensembl1389,826,254 - 89,850,612 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01389,826,272 - 89,850,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01394,453,478 - 94,477,357 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,369,918 - 87,393,508 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11387,558,801 - 87,582,389 (+)NCBI
Celera1383,504,334 - 83,527,924 (+)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol 3-benzoate  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (EXP,ISO)
carbonyl sulfide  (EXP)
cisplatin  (ISO)
clofibrate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
luteolin  (EXP)
LY294002  (ISO)
methamphetamine  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
N-[3,5-bis(trifluoromethyl)phenyl]-5-chloro-2-hydroxybenzamide  (ISO)
N-nitrosodiethylamine  (ISO)
ochratoxin A  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
p-cresol  (ISO)
paracetamol  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
poly(I:C)  (ISO)
potassium iodide  (EXP)
quercitrin  (ISO)
rac-lactic acid  (ISO)
riddelliine  (EXP)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
tetrachloromethane  (ISO)
topotecan  (EXP)
tributylstannane  (ISO)
trichostatin A  (ISO)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Bonnomet A, etal., Oncogene. 2012 Aug 16;31(33):3741-53. doi: 10.1038/onc.2011.540. Epub 2011 Nov 28.
2. Brooks TA, etal., Brain Res. 2006 Nov 20;1120(1):172-82. Epub 2006 Sep 27.
3. Cera MR, etal., J Clin Invest. 2004 Sep;114(5):729-38.
4. Ebnet K, etal., EMBO J. 2001 Jul 16;20(14):3738-48.
5. Ebnet K, etal., J Biol Chem. 2000 Sep 8;275(36):27979-88.
6. Fukasawa H, etal., J Am Soc Nephrol. 2009 Jul;20(7):1491-503. doi: 10.1681/ASN.2008101117. Epub 2009 May 28.
7. Gao XF, etal., Zhonghua Nan Ke Xue. 2010 Jan;16(1):10-3.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. Hou Y, etal., Ann Rheum Dis. 2010 Jan;69(1):249-54. doi: 10.1136/ard.2008.102624. Epub .
10. Huang P, etal., Exp Neurol. 2012 Oct;237(2):453-63. doi: 10.1016/j.expneurol.2012.07.017. Epub 2012 Jul 31.
11. Liu W, etal., Cell. 2011 Jun 24;145(7):1088-101. doi: 10.1016/j.cell.2011.05.015.
12. Martin-Padura I, etal., J Cell Biol 1998 Jul 13;142(1):117-27.
13. McSherry EA, etal., Int J Cancer. 2009 Sep 15;125(6):1343-51. doi: 10.1002/ijc.24498.
14. MGD data from the GO Consortium
15. Murakami M, etal., PLoS One. 2011;6(6):e21242. doi: 10.1371/journal.pone.0021242. Epub 2011 Jun 17.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. Ong KL, etal., J Intern Med. 2008 Mar;263(3):322-32. Epub 2007 Dec 6.
18. Ostermann G, etal., Arterioscler Thromb Vasc Biol. 2005 Apr;25(4):729-35. Epub 2005 Jan 27.
19. RGD automated import pipeline for gene-chemical interactions
20. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
21. Waki H, etal., Hypertension. 2007 Jun;49(6):1321-7. Epub 2007 Apr 9.
22. Xia W, etal., J Biol Chem. 2006 Jun 16;281(24):16799-813. Epub 2006 Apr 13.
23. Yoshikumi Y, etal., Endocr J. 2008 Aug;55(4):757-65. Epub 2008 May 28.
Additional References at PubMed
PMID:11812992   PMID:14749337   PMID:15344881   PMID:15489334   PMID:15494378   PMID:16396499   PMID:18357461   PMID:18514073   PMID:19199708   PMID:20458337   PMID:22918977   PMID:23376485  
PMID:23885123   PMID:25438062   PMID:25468996   PMID:25753039   PMID:25916097   PMID:26985018  


Genomics

Comparative Map Data
F11r
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21383,873,797 - 83,897,388 (+)NCBI
Rnor_6.0 Ensembl1389,826,254 - 89,850,612 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01389,826,272 - 89,850,151 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01394,453,478 - 94,477,357 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41387,369,918 - 87,393,508 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11387,558,801 - 87,582,389 (+)NCBI
Celera1383,504,334 - 83,527,924 (+)NCBICelera
Cytogenetic Map13q24NCBI
F11R
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1160,995,211 - 161,021,343 (-)EnsemblGRCh38hg38GRCh38
GRCh381160,995,211 - 161,021,152 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371160,965,001 - 160,990,942 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh371160,965,001 - 160,991,133 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361159,232,608 - 159,275,358 (-)NCBINCBI36hg18NCBI36
Build 341157,779,056 - 157,821,784NCBI
Celera1134,032,809 - 134,058,962 (-)NCBI
Cytogenetic Map1q23.3NCBI
HuRef1132,321,150 - 132,348,030 (-)NCBIHuRef
CHM1_11162,360,724 - 162,386,856 (-)NCBICHM1_1
F11r
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391171,265,129 - 171,292,161 (+)NCBIGRCm39mm39
GRCm381171,437,561 - 171,464,593 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1171,437,535 - 171,464,603 (+)EnsemblGRCm38mm10GRCm38
MGSCv371173,367,692 - 173,394,724 (+)NCBIGRCm37mm9NCBIm37
MGSCv361173,274,236 - 173,301,268 (+)NCBImm8
Celera1173,888,870 - 173,917,464 (+)NCBICelera
Cytogenetic Map1H3NCBI
cM Map179.43NCBI
F11r
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546812,765,874 - 12,785,929 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546812,764,968 - 12,785,956 (-)NCBIChiLan1.0ChiLan1.0
F11R
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11140,322,264 - 140,347,158 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1140,324,943 - 140,346,890 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01136,399,766 - 136,424,722 (-)NCBIMhudiblu_PPA_v0panPan3
F11R
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3821,451,952 - 21,454,959 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13821,433,819 - 21,456,722 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
F11r
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936903317,975 - 338,892 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
F11R
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl489,425,039 - 89,449,932 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1489,425,101 - 89,447,889 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2497,325,385 - 97,348,465 (-)NCBISscrofa10.2Sscrofa10.2susScr3
F11R
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1202,966,019 - 2,986,177 (+)NCBI
ChlSab1.1 Ensembl202,966,164 - 2,984,269 (+)Ensembl
F11r
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624794346,281 - 367,132 (+)NCBI

Position Markers
AU048745  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q32UniSTS
Cytogenetic Map13q24UniSTS
Cytogenetic Map6q32UniSTS
Cytogenetic Map17p12UniSTS
Cytogenetic Map16p14UniSTS
Cytogenetic Map13q26UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map7q11UniSTS
Cytogenetic Map8q24UniSTS
Cytogenetic Map5q21UniSTS
Cytogenetic Map4q24UniSTS
Cytogenetic Map2q11UniSTS
Cytogenetic Map1q54UniSTS
Cytogenetic Map1q36UniSTS
Cytogenetic Map18p11UniSTS
Cytogenetic Map13q13UniSTS
Cytogenetic Map10q24UniSTS
Cytogenetic Map8q31UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map13p13UniSTS
Cytogenetic Map1q21UniSTS
Cytogenetic Map11q23UniSTS
Cytogenetic Map10q31UniSTS
Cytogenetic Map16q12.2UniSTS
Cytogenetic Map3q24UniSTS
Cytogenetic Map5q36UniSTS
Cytogenetic Map3p13UniSTS
F11r  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01389,847,009 - 89,847,346NCBIRnor6.0
Rnor_6.01220,610,946 - 220,611,040NCBIRnor6.0
Rnor_5.01394,474,215 - 94,474,552UniSTSRnor5.0
Rnor_5.01227,541,910 - 227,542,004UniSTSRnor5.0
RGSC_v3.41387,390,385 - 87,390,722UniSTSRGSC3.4
RGSC_v3.41207,868,018 - 207,868,112UniSTSRGSC3.4
Celera1383,524,801 - 83,525,138UniSTS
Celera1200,074,132 - 200,074,226UniSTS
Cytogenetic Map1q43UniSTS
Cytogenetic Map13q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133950130093652524Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134567662990676629Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)135108098996080989Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135156924896569248Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)135157782490675199Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)136500824591629354Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)137456837892916783Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)137456837892916783Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)137456837892916783Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)138040355991629354Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:341
Count of miRNA genes:216
Interacting mature miRNAs:245
Transcripts:ENSRNOT00000006141
Prediction methods:Microtar, Miranda, Rnahybrid
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 37 53 41 15 41 1 1 6 35 40 11 1
Low 6 4 4 7 10 68 1 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006141   ⟹   ENSRNOP00000006141
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1389,826,254 - 89,850,612 (+)Ensembl
RefSeq Acc Id: NM_053796   ⟹   NP_446248
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21383,873,797 - 83,897,388 (+)NCBI
Rnor_6.01389,826,272 - 89,850,151 (+)NCBI
Rnor_5.01394,453,478 - 94,477,357 (+)NCBI
RGSC_v3.41387,369,918 - 87,393,508 (+)RGD
Celera1383,504,334 - 83,527,924 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446248 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF61729 (Get FASTA)   NCBI Sequence Viewer  
  AAF78250 (Get FASTA)   NCBI Sequence Viewer  
  AAH65309 (Get FASTA)   NCBI Sequence Viewer  
  EDL94656 (Get FASTA)   NCBI Sequence Viewer  
  Q9JHY1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446248   ⟸   NM_053796
- Peptide Label: precursor
- UniProtKB: Q9JHY1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006141   ⟸   ENSRNOT00000006141
Protein Domains
Ig-like V-type

Transcriptome

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

Promoters
RGD ID:13699008
Promoter ID:EPDNEW_R9533
Type:multiple initiation site
Name:F11r_1
Description:F11 receptor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01389,826,279 - 89,826,339EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621842 AgrOrtholog
Ensembl Genes ENSRNOG00000004414 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000006141 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006141 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5599898 IMAGE-MGC_LOAD
InterPro F11R UniProtKB/Swiss-Prot
  Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  Ig_sub2 UniProtKB/Swiss-Prot
  Ig_V-set UniProtKB/Swiss-Prot
KEGG Report rno:116479 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72346 IMAGE-MGC_LOAD
NCBI Gene 116479 ENTREZGENE
PANTHER PTHR45113 UniProtKB/Swiss-Prot
Pfam V-set UniProtKB/Swiss-Prot
PhenoGen F11r PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
SMART IGc2 UniProtKB/Swiss-Prot
  IGv UniProtKB/Swiss-Prot
  SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt JAM1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 F11r  F11 receptor    junctional adhesion molecule 1  Name updated 1299863 APPROVED
2004-09-10 F11r  junctional adhesion molecule 1  Jam1    Symbol and Name updated 1299863 APPROVED
2002-08-07 Jam1  junctional adhesion molecule 1      Symbol and Name status set to provisional 70820 PROVISIONAL