Neuinf3 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Neuinf3 (Neuroinflammation QTL 3) Rattus norvegicus

Symbol: Neuinf3
Name: Neuroinflammation QTL 3
RGD ID: 1549898
Trait: nervous system integrity trait   (VT:0010566)    
Measurement Type: MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio   (CMO:0001980)    
LOD Score: 26.4
P Value: Not Available
Variance: Not Available
Inheritance Type: additive
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2103,406,320 - 5,387,112RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0102,847,625 - 5,460,218RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0101,728,277 - 4,281,241RGDRnor5.0
RGSC_v3.4103,219,701 - 5,339,859RGDRGSC3.4
RGSC_v3.1103,219,701 - 5,339,859RGD
Cross Type: Not Available
Strains Crossed: PVG.1AV1 DA/Ztm 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Candidate Gene Status
Ciita is a candidate Gene for Neuinf3

Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
Experimental Data Annotations     Click to see Annotation Detail View

Experimental Condition

Vertebrate Trait

Rat Strain
DA/Ztm  (IEA)
PVG.1AV1  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Discrete gene loci regulate neurodegeneration, lymphocyte infiltration, and major histocompatibility complex class II expression in the CNS. Lidman O, etal., J Neurosci 2003 Oct 29;23(30):9817-23.
2. MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction. Swanberg M, etal., Nat Genet 2005 May;37(5):486-94. Epub 2005 Apr 10.
Related QTLs

Related QTL Description Reference
Neuinf2 sub_region RGD:1358146


Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
2320726Shisa9shisa family member 91033356163629334Rat
41086909LOC120095014uncharacterized LOC1200950141036004053607994Rat
1306568Cpped1calcineurin-like phosphoesterase domain containing 11037015223821050Rat
41293248LOC120095441small nucleolar RNA SNORA481037322853732427Rat
1596162Snx29sorting nexin 291038848804298699Rat
40955000LOC120095243uncharacterized LOC1200952431038885883895956Rat
1304703Tnfrsf17TNF receptor superfamily member 171043010234306889Rat
41139965LOC120095016uncharacterized LOC1200950161043604994362535Rat
2751Gspt1G1 to S phase transition 11043625284397215Rat
6491522LOC100911627uncharacterized LOC1009116271044139214424815Rat
1359295Rsl1d1ribosomal L1 domain containing 11044248684436753Rat
1311225Zc3h7azinc finger CCCH type containing 7 A1044731774512668Rat
1307538Txndc11thioredoxin domain containing 111045154574572999Rat
3730Snnstannin1045729334581606Rat
41394605Bcl2l12-ps2BCL2 like 12, pseudogene 21045942844599505Rat
41352403Mrto4-ps1mRNA turnover 4, ribosome maturation factor, pseudogene 11046077154608332Rat
41077137LOC120095017uncharacterized LOC1200950171046254384644624Rat
69294Litaflipopolysaccharide-induced TNF factor1046563084692981Rat
41139147Tmsb10-ps2thymosin, beta 10, pseudogene 21046703064670687Rat
7618014LOC102552269uncharacterized LOC1025522691047096804810582Rat
1563163Rmi2RecQ mediated genome instability 21048293334837264Rat
1583873Prm1protamine 11048718174872312Rat
3409Prm2protamine 21048762854877026Rat
1587265Prm3protamine 31048774714877985Rat
40961788LOC120095020uncharacterized LOC1200950201048788464879969Rat
3885Tnp2transition protein 21048798124880540Rat
69272Socs1suppressor of cytokine signaling 11048826514884342Rat
1305773Clec16aC-type lectin domain containing 16A1049277995123749Rat
40971359LOC120095021uncharacterized LOC1200950211050099215026599Rat
1564938DexiDexi homolog1051260215138746Rat
619813Ciitaclass II, major histocompatibility complex, transactivator1051399475187493Rat
41005309Ywhaz-ps1tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta, pseudogene 11051985565206803Rat
2320268Cnbp-ps2CCHC-type zinc finger, nucleic acid binding protein, pseudogene 21052150065216182Rat
1566405Tvp23atrans-golgi network vesicle protein 23 homolog A1052271985263185Rat
1310514Nubp1NUBP iron-sulfur cluster assembly factor 11052593285270848Rat
7663456LOC102553451uncharacterized LOC1025534511052722505277055Rat
1307081Tekt5tektin 51052798565316619Rat
1359629Emp2epithelial membrane protein 21053600735394734Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
34361D10Mgh251411051440275144168Ratregion
33591D10Mit14921053870145387112Ratregion
33600D10Mit151851048263974826582Ratregion
36468D10Rat672021045217884521990Ratregion
39664D10Rat2002461053590115359247Ratregion
41937D10Arb262321048789024879130Ratregion
44670D10Got11071047655274765634Ratregion
44671D10Got111341053047965304932Ratregion
44679D10Got21571047686584768815Ratregion
44681D10Got72341051821515182387Ratregion
59978D10Got31821038839253884109Ratregion
59980D10Got42821043123144312596Ratregion
59981D10Got51681046420934642261Ratregion
59985D10Got62741034063203406594Ratregion
59989D10Got81151044949894495104Ratregion
66423D10Mco461601047175514717711Ratregion
1634319D10Cebr11741037747803774954Ratregion
5035735WI-191802331043967804397013Ratregion
5028577U883251011048840504884151Ratregion
5028823RH1424671531037821473782300Ratregion
5026752RH1333952181038208113821029Ratregion
5026862RH1338142071043621264362333Ratregion
5027783RH947251061048768734876979Ratregion
5033583RH139357711038850643885135Ratregion
5056755RH1445611561038205773820733Ratregion
5051905RH947261011048760954876196Ratregion
5055917RH1440771171052629775263093Ratregion
5057342D10Bda41741045730694573243Ratregion
5052719RH1422311021048802184880322Ratregion
5054455RH1432342851048838724884157Ratregion
5044680RH1307421921045122594512450Ratregion
5044842RH1308351851051400405140225Ratregion
5044128RH1304261501044139514414101Ratregion
5047322RH1322612011043060764306277Ratregion
5040006RH1280352021043969364397138Ratregion
5043522RH1300731901044007644400954Ratregion
5043090RH1298261871049280834928270Ratregion
5072518RH1368951911045730354573226Ratregion
5076212RH1390441831043011224301305Ratregion
5076938RH1394661821039711403971322Ratregion
5071554RH1351492161043986174398833Ratregion
5062114BE1062201541034914923491646Ratregion
5063558BE1077961611037282023728363Ratregion
5080792RH1417841811038199853820166Ratregion
5505796UniSTS:4941892731038602143860487Ratregion
5506195UniSTS:498766751048768854876960Ratregion
Position Markers

Flank 1: (D10Got6)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2103,406,320 - 3,406,594 (+)MAPPER
Rnor_6.0102,847,625 - 2,847,898NCBI
Rnor_5.0101,728,277 - 1,728,550UniSTS
RGSC_v3.4103,219,701 - 3,219,975RGD
RGSC_v3.4103,219,702 - 3,219,975UniSTS
RGSC_v3.1103,219,701 - 3,219,975RGD
Celera102,440,770 - 2,441,043UniSTS
Peak: (D10Mgh25)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,144,027 - 5,144,168 (+)MAPPER
Rnor_6.0105,217,199 - 5,217,339NCBI
Rnor_5.0104,040,517 - 4,040,657UniSTS
RGSC_v3.4105,090,008 - 5,090,149RGD
RGSC_v3.4105,090,009 - 5,090,149UniSTS
RGSC_v3.1105,090,008 - 5,090,149RGD
Celera104,162,284 - 4,162,424UniSTS
Cytogenetic Map10q11UniSTS
Flank 2: (D10Mit14)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2105,387,014 - 5,387,112 (+)MAPPER
Rnor_6.0105,460,119 - 5,460,218NCBI
Rnor_5.0104,281,142 - 4,281,241UniSTS
RGSC_v3.4105,339,759 - 5,339,859RGD
RGSC_v3.4105,339,760 - 5,339,859UniSTS
RGSC_v3.1105,339,760 - 5,339,859RGD
Celera104,402,915 - 4,403,014UniSTS
RH 3.4 Map1068.5UniSTS
RH 3.4 Map1068.5RGD
RH 2.0 Map100.0RGD
Cytogenetic Map10q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1034063205387112Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat


Additional Information

RGD Curation Notes
Note Type Note Reference
qtl_cand_genes MHC2TA 1358146
qtl_general number of animals used: 24 parental rats and 126 male rats from F8 generation 1358146
qtl_general measurement method: all animals were anesthetized by isoflurane at 6-8 weeks of age and subjected to unilateral avulsion of the left L3-L5 ventral roots, they were killed and spinal cord examined; serial transverse sections of L4 were cut and examined, T cell infiltration was measured by the assessment of the number of CD3 positive cells 1358146
qtl_statistics_details linkage analysis was performed using MAPMAKER/QTL 1358146