Neuinf2 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL: Neuinf2 (Neuroinflammation QTL 2) Rattus norvegicus

Symbol: Neuinf2
Name: Neuroinflammation QTL 2
RGD ID: 1549907
Previously known as: Vra4
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: 27.0
P Value: 0.0
Variance: Not Available
Inheritance Type: additive
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2106,154,377 - 6,357,896RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0106,229,289 - 6,429,075RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0105,044,836 - 5,243,736RGDRnor5.0
RGSC_v3.4106,172,805 - 6,380,753RGDRGSC3.4
RGSC_v3.1106,172,805 - 6,380,796RGD
Cross Type: Not Available
Strains Crossed: PVG/OlaHsd DA/Ztm 
JBrowse: View Region in Genome Browser (JBrowse)

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/OlaHsd  (IEA)


References - curated
# Reference Title Reference Citation
1. Vra4 congenic rats with allelic differences in the class II transactivator gene display altered susceptibility to experimental autoimmune encephalomyelitis. Harnesk K, etal., J Immunol. 2008 Mar 1;180(5):3289-96.
2. 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.
3. Genetic dissection of neurodegeneration and CNS inflammation. Olsson T, etal., J Neurol Sci 2005 Jun 15;233(1-2):99-108.
4. 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
Neuinf3 sub_region RGD:1358146


Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
1583743LOC497861similar to 60S ribosomal protein L23a1062439726249916Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
Position Markers

Flank 1: (D10Rat95)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2106,357,896 - 6,358,120 (+)MAPPER
Rnor_6.0106,429,075 - 6,429,296NCBI
Rnor_5.0105,243,736 - 5,243,957UniSTS
RGSC_v3.4106,380,796 - 6,381,017UniSTS
RGSC_v3.4106,380,753 - 6,381,051RGD
RGSC_v3.1106,380,796 - 6,381,017RGD
Celera105,357,468 - 5,357,689UniSTS
RH 3.4 Map1076.2RGD
RH 3.4 Map1076.2UniSTS
RH 2.0 Map102.9RGD
SHRSP x BN Map100.04RGD
FHH x ACI Map104.54RGD
Cytogenetic Map10q11-q12UniSTS
Flank 2: (D10Rat96)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2106,154,182 - 6,154,377 (+)MAPPER
Rnor_6.0106,229,095 - 6,229,289NCBI
Rnor_5.0105,044,642 - 5,044,836UniSTS
RGSC_v3.4106,172,611 - 6,172,805UniSTS
RGSC_v3.4106,172,610 - 6,172,805RGD
RGSC_v3.1106,172,611 - 6,172,805RGD
Celera105,158,089 - 5,158,283UniSTS
RH 3.4 Map1070.5UniSTS
RH 3.4 Map1070.5RGD
RH 2.0 Map100.0RGD
SHRSP x BN Map100.08RGD
FHH x ACI Map100.0RGD
Cytogenetic Map12q15UniSTS

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
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
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
1549907Neuinf2Neuroinflammation QTL 2270nervous 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)1061543776357896Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat

Additional Information

RGD Curation Notes
Note Type Note Reference
qtl_general number of animals used: 18 DA/Ztm, 18 PVG/OlaHsd, 24 F1 and 186 F2 1358788
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, degree of MHC class II expression and infiltration of CD3 positive cells was determined 1358788
qtl_general Maps to F8 advanced intercross lines with a sharp peak at LOD 26.4 at marker D10Mgh25 1358146
qtl_statistics_details linkage analysis performed using MAPMAKER/QTL and R/qtl computer software 1358788