Cia4 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL: Cia4 (Collagen induced arthritis QTL 4) Rattus norvegicus

Symbol: Cia4
Name: Collagen induced arthritis QTL 4
RGD ID: 61435
Also known as: Type II Collagen induced arthritis QTL 4
Trait: joint integrity trait   (VT:0010548)    
Measurement Type: joint inflammation composite score   (CMO:0000919)    
LOD Score: 5.3
P Value: Not Available
Variance: Not Available
Inheritance Type: recessive
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2758,113,224 - 62,004,598RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0767,346,146 - 69,399,731RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0767,533,138 - 69,590,450RGDRnor5.0
RGSC_v3.4762,224,456 - 66,202,126RGDRGSC3.4
RGSC_v3.1721,222,856 - 66,222,856RGD
Cross Type: F2
Strains Crossed: F344/NHsd DA/Bkl 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Candidate Gene Status
Il2rb is a candidate Gene for Cia4
Pdgfrb is a candidate Gene for Cia4

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

Clinical Measurement

Experimental Condition

Measurement Method

Vertebrate Trait

Rat Strain
DA/Bkl  (IEA)
F344/NHsd  (IEA)

References

Related QTLs

Related QTL Description Reference
Cia8 interacts with RGD:61069


Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
9443040LOC103692868uncharacterized LOC10369286876817832568214512Rat
7551992LOC102552064uncharacterized LOC10255206476823186568264490Rat
7594610LOC102552291uncharacterized LOC10255229176834276868370985Rat
7695057LOC102552186uncharacterized LOC10255218676837094568384877Rat
3691Slc16a7solute carrier family 16 member 776843834168606312Rat
9447793LOC103692869uncharacterized LOC10369286976862260668624262Rat
7654942LOC102552637uncharacterized LOC10255263776887946368890194Rat
7628604LOC102552423uncharacterized LOC10255242376889187668929032Rat
7599899LOC102552702uncharacterized LOC10255270276903401169059540Rat
1560867LOC500846hypothetical protein LOC50084676907047169104950Rat
9152489LOC103692872uncharacterized LOC10369287276915067569198552Rat
9104967LOC103692871uncharacterized LOC10369287176915765369161517Rat
1561255Lrig3leucine-rich repeats and immunoglobulin-like domains 376921309869263251Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
10221D7Arb1776734614667346371Ratregion
35180D7Rat4317076912885269129028Ratregion
34999D7Rat4416276939958669399731Ratregion
38198D7Rat6923076780145767801690Ratregion
40862D7Rat14511876868516468685281Ratregion
66379D7Uia539176876639568766785Ratregion
1632357D7Got22918376900434969004526Ratregion
1628011D7Got20910776814951368149619Ratregion
1641372D7Got2089776750572267505818Ratregion
1640598D7Got25225676830161968301874Ratregion
1637384D7Wox3676734596767346383Ratregion
5033489RH13901915476843846968438622Ratregion
5068668AU04700520176749123467491434Ratregion
5069806AU04793122776927089269271274Ratregion
5069806AU04793122776927089269271118Ratregion
5066024BE11657916776923851469238680Ratregion
5505514DXS1232076804434968045317Ratregion
Position Markers

Flank 1: (D7Arb17)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2758,113,224 - 58,113,450 (-)MAPPER
Rnor_6.0767,346,146 - 67,346,371NCBI
Rnor_5.0767,533,138 - 67,533,363UniSTS
RGSC_v3.4762,224,456 - 62,224,681UniSTS
Celera755,285,893 - 55,286,110UniSTS
Cytogenetic Map7q21UniSTS
Flank 2: (D7Rat44)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2762,004,452 - 62,004,598 (+)MAPPER
Rnor_6.0769,399,586 - 69,399,731NCBI
Rnor_5.0769,590,305 - 69,590,450UniSTS
RGSC_v3.4766,201,980 - 66,202,126RGD
RGSC_v3.4766,201,981 - 66,202,126UniSTS
RGSC_v3.1766,222,710 - 66,222,856RGD
Celera759,158,360 - 59,158,505UniSTS
FHH x ACI Map733.38UniSTS
FHH x ACI Map733.38RGD
Cytogenetic Map7 RGD


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72820465373204653Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)73304444971352127Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)75453499673293934Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)75507286269399731Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)761047589113228378Rat
61435Cia4Collagen induced arthritis QTL 45.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)76734614669399731Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)768518460113518460Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)769399586111043530Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)769399586111043530Rat


Additional Information

Database Acc Id Source(s)
NCBI Gene Cia4


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-14 Cia4  Collagen induced arthritis QTL 4    Type II Collagen induced arthritis QTL 4  Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
qtl_gene 264 known and 79 novel genes were found in an analysis based on PubMed and OMIM data 2307198
qtl_gene whole genome analysis using PGMapper revealed Ifng, Myc as RA associated genes and Ifng as RA associated polymorphism either in coding or regulatory region 2300074
qtl_general recessive and additive genetic models give the highest LOD scores 61069
qtl_map 2 LOD support interval (99% confidence interval) = 33 cM 61069