Tcs1 QTL Report (Rattus norvegicus) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
QTL Registration

QTL: Tcs1 (T cell selection QTL 1) Rattus norvegicus

Symbol: Tcs1
Name: T cell selection QTL 1
RGD ID: 7175096
Trait: T cell selection
Measurement Type: expression
LOD Score: Not Available
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,727,078 - 5,024,580RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0203,910,555 - 5,533,640RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0207,323,184 - 7,592,657RGD_MAPPER_PIPELINERnor5.0
RGSC_v3.4204,864,606 - 5,176,689RGDRGSC3.4
Cross Type: Not Available
Strains Crossed: DA/ZtmRhd DA.LEW.RT1f-(D20Wox15-D20Wox13)/Rhd DA.E3-(RT1-DMa-Ggnbp1) 
JBrowse: View Region in Genome Browser (JBrowse)
Model



References

References - curated
# Reference Title Reference Citation
1. Data registered by Dr. Rikard Holmdahl's group Personal communication between Dr. Rikard Holmdahl's group and the RGD curators.
2. Class II major histocompatibility complex-associated response to type XI collagen regulates the development of chronic arthritis in rats. Tuncel J, etal., Arthritis Rheum. 2012 Aug;64(8):2537-47. doi: 10.1002/art.34461.

Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
2209Wdr46WD repeat domain 462049378454945796Rat
3618Vps52VPS52 subunit of GARP complex2049207154931685Rat
2373Col11a2collagen type XI alpha 2 chain2047869324816598Rat
3595Rps18ribosomal protein S182049314274935538Rat
3611Rxrbretinoid X receptor beta2048168134823267Rat
621227Daxxdeath-domain associated protein2049700904976145Rat
3819TapbpTAP binding protein2049569374966191Rat
1303205Phf1PHD finger protein 12050177655022872Rat
1303158Hsd17b8hydroxysteroid (17-beta) dehydrogenase 82048267254828742Rat
620328B3galt4Beta-1,3-galactosyltransferase 42049360894937664Rat
1303006Pfdn6prefoldin subunit 62049459594947433Rat
1303306CutacutA divalent cation tolerance homolog2050229565024580Rat
3576Ring1ring finger protein 12048301204833623Rat
3477RT1-DOaRT1 class II, locus DOa2047535874756590Rat
1302985Ralgdsl2ral guanine nucleotide dissociation stimulator like 22049484954956774Rat
1303072AA926063AA926063gene2049764624988984Rat
1359627Zbtb22zinc finger and BTB domain containing 222049663314969853Rat
1359118Kifc1kinesin family member C12049988325017107Rat
1359610RT1-A3RT1 class I, locus A32048475184851344Rat
1303324Brd2bromodomain containing 22047270784735389Rat
1595921RT1-HaRT1 class II, locus Ha2047606314770662Rat
1595923RT1-A2RT1 class Ia, locus A22048709394910183Rat
1595924RT1-A1RT1 class Ia, locus A12049053094914593Rat
1594398Sacm2l-ps2Sacm2l-ps2 pseudogene2048602074861343Rat
1594399Sacm2l-ps1Sacm2l-ps1 pseudogene2048614394861499Rat
1594400LOC224733l-2LOC224733l-2 pseudogene2048669864867269Rat
1594401LOC224733l-1LOC224733l-1 pseudogene2048937044901482Rat
1593280Slc39a7solute carrier family 39 member 72048231664826538Rat
1591984Cdk2ap1-ps1Cdk2ap1-pseudogene 12048778724878222Rat
1591985Sec61-psSec61 pseudogene2049909544991292Rat
1591986Rps25-ps1ribosomal protein S25, pseudogene 12049971124997779Rat
1595866RT1-Hb-ps1RT1 class II, locus Hb, pseudogene 12047755984779590Rat
2325545Mir219a1microRNA 219a-12048296874829796Rat
11496771Smim40small integral membrane protein 402049786584989050Rat
41363335Trnaa-agc96transfer RNA alanine (anticodon AGC) 962049960874996159Rat
41106045LOC120099050U6 spliceosomal RNA2049281454928241Rat
41315246LOC120098897uncharacterized LOC1200988972048430814847572Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
38324D20Rat321602048391514839323Ratregion
2303227D20Yum781522047678524768004Ratregion
2303227D20Yum781522047678524768004Ratregion
2303243D20Yum821512049295044929655Ratregion
2303291D20Yum791582047956504795808Ratregion
7206734MARC_5897-5898:997299407:12592048180114818559Ratregion
5036051Zfp2974542049672254967679Ratregion
5036334H2-D11562049085014908657Ratregion
7205922UniSTS:4634054202047875704788444Ratregion
5032973RH1371622322049207674921002Ratregion
5033661RH1396421882049372464937434Ratregion
5057247AA9260632152049764974976712Ratregion
5058954BF3938581402048307114830851Ratregion
5058200BI2777091972049824174982614Ratregion
7193040Rxrb02048206574821131Ratregion
5051671Rxrb2882048188814820582Ratregion
5044600RH1306972172049665244966741Ratregion
5041594RH1289472052050226445022847Ratregion
5041598RH1289491802049786694978849Ratregion
5049182RH1333331942048284584828652Ratregion
5042260RH1293321872048263274826514Ratregion
5042402RH1294132052049569494957154Ratregion
5043582RH13010802049207224920922Ratregion
5072084RH1366422152048941464894361Ratregion
5074022RH1377741552049786924978847Ratregion
5075694RH1387421372049575204957657Ratregion
5079980RH1413132062049219834922189Ratregion
5078896RH1406141912049485254948716Ratregion
5078716RH1405092222049372124937434Ratregion
5070211RH94536892047539554754044Ratregion
5060654BE1041851042049381004938204Ratregion
5062480BE1067281572049584824958639Ratregion
5087914H2-Q63612049057184906260Ratregion
5082835BF3902031652049645194964684Ratregion
5084500AI2352232242048521044852328Ratregion
5080934RH1418682082049225914922798Ratregion
5086553BM3858171882048243484824536Ratregion
5084022AI2324781342049214324921566Ratregion
5503258UniSTS:2376241832049663694966552Ratregion
5503262UniSTS:2376262382048168724817110Ratregion
5503354CGCb741762047316994731873Ratregion
5503354CGCb741762047316994731873Ratregion
5503520H2-Ke610272048273294828356Ratregion
5503522UniSTS:46341511942050098835011077Ratregion
5503524Slc39a712342048251084826342Ratregion
5503528UniSTS:46343714872049247334926220Ratregion
5500011UniSTS:2361251432050112135011477Ratregion
5502150MARC_6301-6302:997299518:102048177794818347Ratregion
Position Markers

Flank 1: (Brd2)
Rat AssemblyChrPosition (strand)Source
GRCr8204,728,282 - 4,737,286 (+)NCBI
mRatBN7.2204,727,078 - 4,735,389 (+)NCBI
mRatBN7.2 Ensembl204,728,151 - 4,735,388 (+)Ensembl
UTH_Rnor_SHR_Utx205,480,415 - 5,487,612 (+)NCBI
UTH_Rnor_SHRSP_BbbUtx_1.0204,842,158 - 4,849,355 (+)NCBI
UTH_Rnor_WKY_Bbb_1.0205,323,436 - 5,330,635 (+)NCBI
Rnor_6.0203,910,555 - 3,921,074 (-)NCBI
Rnor_6.0 Ensembl205,262,120 - 5,269,337 (+)Ensembl
Rnor_6.0 Ensembl203,910,555 - 3,917,426 (-)Ensembl
Rnor_5.0207,323,184 - 7,330,398 (+)NCBI
RGSC_v3.4204,864,606 - 4,871,813 (+)NCBI
RGSC_v3.1204,864,832 - 4,872,040 (+)NCBI
Celera206,328,831 - 6,336,038 (+)NCBI
Cytogenetic Map20p12NCBI
Flank 2: (Cuta)
Rat AssemblyChrPosition (strand)Source
GRCr8205,024,816 - 5,026,446 (-)NCBI
mRatBN7.2205,022,956 - 5,024,580 (-)NCBI
mRatBN7.2 Ensembl205,022,956 - 5,024,552 (-)Ensembl
UTH_Rnor_SHR_Utx205,748,342 - 5,750,042 (-)NCBI
UTH_Rnor_SHRSP_BbbUtx_1.0205,110,079 - 5,111,779 (-)NCBI
UTH_Rnor_WKY_Bbb_1.0205,588,515 - 5,590,087 (-)NCBI
Rnor_6.0205,532,024 - 5,533,640 (-)NCBI
Rnor_6.0 Ensembl205,532,024 - 5,533,620 (-)Ensembl
Rnor_5.0207,591,037 - 7,592,657 (-)NCBI
RGSC_v3.4205,175,113 - 5,176,689 (-)NCBI
RGSC_v3.1205,175,343 - 5,176,834 (-)NCBI
Celera206,605,378 - 6,606,954 (-)NCBI
Cytogenetic Map20p12NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
7175096Tcs1T cell selection QTL 1T cell selectionexpression2047270785024580Rat


Additional Information

RGD Curation Notes
Note Type Note Reference