Tnfrsf11a (TNF receptor superfamily member 11A) - Rat Genome Database

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Gene: Tnfrsf11a (TNF receptor superfamily member 11A) Rattus norvegicus
Analyze
Symbol: Tnfrsf11a
Name: TNF receptor superfamily member 11A
RGD ID: 1563614
Description: Predicted to enable cytokine binding activity and tumor necrosis factor-activated receptor activity. Involved in response to radiation. Predicted to be located in cell surface; cytosol; and plasma membrane. Predicted to be active in external side of plasma membrane. Biomarker of myocarditis. Human ortholog(s) of this gene implicated in Paget's disease of bone; autosomal recessive osteopetrosis 7; bone development disease; familial expansile osteolysis; and osteoporosis. Orthologous to human TNFRSF11A (TNF receptor superfamily member 11a); PARTICIPATES IN cytokine mediated signaling pathway; rheumatoid arthritis pathway; INTERACTS WITH 2,6-dinitrotoluene; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC498206; RANK; RGD1563614; similar to Tumor necrosis factor receptor superfamily, member 11a; tumor necrosis factor receptor superfamily member 11a; Tumor necrosis factor receptor superfamily, member 11a; tumor necrosis factor receptor superfamily, member 11a, NFKB activator
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
mRatBN7.21321,928,370 - 21,986,719 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1325,778,317 - 25,835,957 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01325,778,306 - 25,835,802 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01330,966,261 - 30,997,692 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41311,958,002 - 12,014,371 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1321,798,588 - 21,856,355 (+)NCBICelera
Cytogenetic Map13p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
azadirachtin A  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
desferrioxamine B  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dorsomorphin  (ISO)
ellagic acid  (ISO)
endosulfan  (EXP)
folic acid  (ISO)
furosemide  (EXP)
gentamycin  (EXP)
glycidol  (EXP)
indole-3-methanol  (EXP)
isoflurane  (EXP)
kaempferol  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lipopolysaccharide  (ISO)
mangiferin  (ISO)
modafinil  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (EXP)
naringin  (ISO)
nitrates  (EXP)
o-anisidine  (ISO)
O-methyleugenol  (ISO)
ozone  (EXP)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
pentobarbital  (EXP)
pirinixic acid  (ISO)
progesterone  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium fluoride  (ISO)
thymol  (ISO)
thymol sulfate(1-)  (ISO)
titanium atom  (ISO)
titanium dioxide  (EXP,ISO)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9367155   PMID:10500098   PMID:11051546   PMID:11805147   PMID:12296995   PMID:18606301   PMID:19325147   PMID:19940926   PMID:20074454   PMID:20818503   PMID:21327437   PMID:21844205  
PMID:21893222   PMID:22848465   PMID:23443487   PMID:25406873   PMID:29211121   PMID:29297549   PMID:29529595  


Genomics

Comparative Map Data
Tnfrsf11a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21321,928,370 - 21,986,719 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1325,778,317 - 25,835,957 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01325,778,306 - 25,835,802 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01330,966,261 - 30,997,692 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41311,958,002 - 12,014,371 (+)NCBIRGSC3.4rn4RGSC3.4
Celera1321,798,588 - 21,856,355 (+)NCBICelera
Cytogenetic Map13p11NCBI
TNFRSF11A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1862,325,287 - 62,391,288 (+)EnsemblGRCh38hg38GRCh38
GRCh381862,325,310 - 62,391,288 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371859,992,543 - 60,058,521 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361858,143,528 - 58,204,484 (+)NCBINCBI36hg18NCBI36
Build 341858,143,527 - 58,204,482NCBI
Celera1856,711,789 - 56,772,745 (+)NCBI
Cytogenetic Map18q21.33NCBI
HuRef1856,726,294 - 56,766,005 (+)NCBIHuRef
CHM1_11859,988,087 - 60,050,490 (+)NCBICHM1_1
Tnfrsf11a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391105,708,448 - 105,777,172 (+)NCBIGRCm39mm39
GRCm39 Ensembl1105,708,443 - 105,775,709 (+)Ensembl
GRCm381105,780,673 - 105,849,444 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1105,780,718 - 105,847,981 (+)EnsemblGRCm38mm10GRCm38
MGSCv371107,677,300 - 107,744,558 (+)NCBIGRCm37mm9NCBIm37
MGSCv361107,608,270 - 107,672,989 (+)NCBImm8
Celera1108,658,349 - 108,696,865 (+)NCBICelera
Cytogenetic Map1E2.1NCBI
Tnfrsf11a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540246,264,164 - 46,296,368 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540246,242,329 - 46,298,157 (+)NCBIChiLan1.0ChiLan1.0
TNFRSF11A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11859,032,727 - 59,075,044 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1859,034,770 - 59,075,044 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01855,695,394 - 55,761,307 (+)NCBIMhudiblu_PPA_v0panPan3
TNFRSF11A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1114,504,595 - 14,555,956 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl114,503,033 - 14,556,041 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha115,469,086 - 15,523,233 (-)NCBI
ROS_Cfam_1.0114,362,189 - 14,416,396 (-)NCBI
UMICH_Zoey_3.1114,398,162 - 14,452,574 (-)NCBI
UNSW_CanFamBas_1.0114,331,546 - 14,385,610 (-)NCBI
UU_Cfam_GSD_1.0114,578,257 - 14,632,411 (-)NCBI
Tnfrsf11a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494427,705,806 - 27,756,172 (-)NCBI
SpeTri2.0NW_0049364972,944,841 - 2,986,113 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNFRSF11A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1159,128,038 - 159,187,481 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11159,128,039 - 159,187,476 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21176,590,571 - 176,650,002 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TNFRSF11A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11817,385,251 - 17,446,442 (-)NCBI
Vero_WHO_p1.0NW_0236660608,239,048 - 8,304,073 (+)NCBI
Tnfrsf11a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247928,029,383 - 8,087,824 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317027Aia22Adjuvant induced arthritis QTL 222.29joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)13136779181Rat
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13147622148Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)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)systolic blood pressure (CMO:0000004)131107975663Rat
631672Iddm12Insulin dependent diabetes mellitus QTL 122.20.0032blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)13901674239373058Rat
61339Bp24Blood pressure QTL 240.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)13901674250513953Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13901690682995569Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)131409633059096330Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)131409633059096330Rat
2303031Bp326Blood pressure QTL 326arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131427908126919398Rat
2317034Aia9Adjuvant induced arthritis QTL 94.62joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131427908137124697Rat
2317044Aia23Adjuvant induced arthritis QTL 232.3joint integrity trait (VT:0010548)ankle joint diameter (CMO:0002148)131427908137124697Rat
1300163Cardf1Cardiac cell morphology QTL 14.18aorta morphology trait (VT:0000272)artery lesion measurement (CMO:0000975)131444158250799665Rat
2302275Gluco37Glucose level QTL 373.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)131444158251577031Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)131462463159624631Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131981081464810814Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)132005247765052477Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)132148248158537177Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:97
Interacting mature miRNAs:104
Transcripts:ENSRNOT00000021129
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 5
Low 33 51 35 19 35 8 11 59 35 32 11 8
Below cutoff 10 6 6 6 10 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021129   ⟹   ENSRNOP00000021129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1325,778,317 - 25,835,957 (+)Ensembl
RefSeq Acc Id: NM_001271235   ⟹   NP_001258164
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,928,408 - 21,986,695 (+)NCBI
Rnor_6.01325,778,306 - 25,835,802 (+)NCBI
Rnor_5.01330,966,261 - 30,997,692 (+)NCBI
Celera1321,798,588 - 21,856,355 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008769487   ⟹   XP_008767709
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21321,928,370 - 21,986,719 (+)NCBI
Rnor_6.01325,778,329 - 25,835,802 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001258164 (Get FASTA)   NCBI Sequence Viewer  
  XP_008767709 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL91736 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001258164   ⟸   NM_001271235
- Peptide Label: precursor
- UniProtKB: F1M8Z6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767709   ⟸   XM_008769487
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000021129   ⟸   ENSRNOT00000021129
Protein Domains
TNFR-Cys

Transcriptome

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

Promoters
RGD ID:13698746
Promoter ID:EPDNEW_R9271
Type:initiation region
Name:Tnfrsf11a_1
Description:TNF receptor superfamily member 11A
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_6.01325,778,305 - 25,778,365EPDNEW

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)
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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:1563614 AgrOrtholog
Ensembl Genes ENSRNOG00000015615 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021129 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021129 ENTREZGENE, UniProtKB/TrEMBL
InterPro RANK_CRD_2 UniProtKB/TrEMBL
  TNFR_11 UniProtKB/TrEMBL
  TNFR_11A UniProtKB/TrEMBL
  TNFR_Cys_rich_reg UniProtKB/TrEMBL
  TNFRSF11A_N UniProtKB/TrEMBL
KEGG Report rno:498206 UniProtKB/TrEMBL
NCBI Gene 498206 ENTREZGENE
Pfam RANK_CRD_2 UniProtKB/TrEMBL
  TNFR_c6 UniProtKB/TrEMBL
PhenoGen Tnfrsf11a PhenoGen
PRINTS TNFACTORR11 UniProtKB/TrEMBL
  TNFACTORR11A UniProtKB/TrEMBL
PROSITE TNFR_NGFR_1 UniProtKB/TrEMBL
  TNFR_NGFR_2 UniProtKB/TrEMBL
SMART TNFR UniProtKB/TrEMBL
UniProt F1M8Z6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-05 Tnfrsf11a  TNF receptor superfamily member 11A  Tnfrsf11a  tumor necrosis factor receptor superfamily member 11a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-25 Tnfrsf11a  tumor necrosis factor receptor superfamily member 11a  Tnfrsf11a  tumor necrosis factor receptor superfamily, member 11a, NFKB activator  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-02-02 Tnfrsf11a  tumor necrosis factor receptor superfamily, member 11a, NFKB activator  Tnfrsf11a  Tumor necrosis factor receptor superfamily, member 11a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tnfrsf11a  Tumor necrosis factor receptor superfamily, member 11a   Tnfrsf11a_predicted  Tumor necrosis factor receptor superfamily, member 11a (predicted)  'predicted' is removed 2292626 APPROVED
2007-02-05 Tnfrsf11a_predicted  Tumor necrosis factor receptor superfamily, member 11a (predicted)  RGD1563614_predicted  similar to Tumor necrosis factor receptor superfamily, member 11a (predicted)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563614_predicted  similar to Tumor necrosis factor receptor superfamily, member 11a (predicted)  LOC498206  similar to Tumor necrosis factor receptor superfamily, member 11a  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498206  similar to Tumor necrosis factor receptor superfamily, member 11a      Symbol and Name status set to provisional 70820 PROVISIONAL