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
Previously 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

References - curated
# Reference Title Reference Citation
1. Quantitative trait loci disposing for both experimental arthritis and encephalomyelitis in the DA rat; impact on severity of myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis and antibody isotype pattern. Dahlman I, etal., Eur J Immunol 1998 Jul;28(7):2188-96
2. Identification of a new quantitative trait locus on chromosome 7 controlling disease severity of collagen-induced arthritis in rats. Dracheva SV, etal., Immunogenetics 1999 Aug;49(9):787-91
3. Genetic dissection of a rat model for rheumatoid arthritis: significant gender influences on autosomal modifier loci Furuya T, etal., Hum Mol Genet 2000 Sep 22;9(15):2241-50
4. Quest for arthritis-causative genetic factors in the rat. Joe B Physiol Genomics. 2006 Oct 3;27(1):1-11. Epub 2006 Jun 27.
5. The Arthritis Severity Quantitative Trait Loci Cia4 and Cia6 Regulate Neutrophil Migration into Inflammatory Sites and Levels of TNF-{alpha} and Nitric Oxide. Laragione T, etal., J Immunol. 2007 Feb 15;178(4):2344-51.
6. A genome scan localizes five non-MHC loci controlling collagen-induced arthritis in rats. Remmers EF, etal., Nat Genet 1996 Sep;14(1):82-5
7. The complexity in hunting for candidate genes within QTL that determine susceptibility to arthritis in rats. Xiong Q, etal., Crit Rev Immunol. 2008;28(2):127-57.
8. Genetic and molecular basis of quantitative trait loci of arthritis in rat: genes and polymorphisms. Xiong Q, etal., J Immunol. 2008 Jul 15;181(2):859-64.
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
2185Avpr1aarginine vasopressin receptor 1A75811430658118230Rat
3691Slc16a7solute carrier family 16 member 776104366761211547Rat
628795Usp15ubiquitin specific peptidase 1575875671458848778Rat
1308808Mon2MON2 homolog, regulator of endosome-to-Golgi trafficking75864937858728102Rat
1309528Ppm1hprotein phosphatase, Mg2+/Mn2+ dependent, 1H75833866158599547Rat
1561255Lrig3leucine-rich repeats and immunoglobulin-like domains 376181631361866275Rat
1589429Tafa2TAFA chemokine like family member 275894259859418640Rat
2325604Mirlet7imicroRNA let-7i75864248558642569Rat
7654942LOC102552637uncharacterized LOC10255263776144449561496656Rat
7628604LOC102552423uncharacterized LOC10255242376149810261533554Rat
7695057LOC102552186uncharacterized LOC10255218676097594361088913Rat
9685075Snora19small nucleolar RNA, H/ACA box 1975878050358780571Rat
11463103LOC108351469uncharacterized LOC10835146975847271758482369Rat
11466148Snurfl1SNRPN upstream open reading frame like 175871471358716587Rat
41286787Crb1-ps3crumbs cell polarity complex component 1, pseudogene 375958331659598561Rat
41098039LOC120093624uncharacterized LOC12009362475952784359540971Rat
41375035LOC120093987small nucleolar RNA SNORA1775967884959678980Rat
41130914LOC120093622translation initiation factor IF-2-like75864181658646386Rat
40952871LOC120093870basic proline-rich protein-like75944207559443292Rat
40939206Ftl1-ps8ferritin light chain 1, pseudogene 876082544560837640Rat
40991943LOC120093626uncharacterized LOC12009362676193670861940112Rat
41075487Snrpn-ps2small nuclear ribonucleoprotein polypeptide N, pseudogene 275871471358725898Rat
41222853LOC120093625uncharacterized LOC12009362576107541061098225Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
10221D7Arb1775811322458113450Ratregion
34634D4Mgh538375811434658114729Ratregion
36317D7Rat16617475922594759226115Ratregion
35180D7Rat4317076173665261736830Ratregion
34999D7Rat4416276200445262004598Ratregion
38198D7Rat6923076046045260460686Ratregion
38754D7Rat5721775920106959201286Ratregion
39094D7Rat5824575826487858265113Ratregion
42339D7Rat22024775853205558532298Ratregion
40862D7Rat14511876129036361290481Ratregion
44262D7Got4426075852809758528354Ratregion
44267D7Got4814275814366558143807Ratregion
66379D7Uia539176137158761371978Ratregion
67753D7Uwm2033375863234358632680Ratregion
1632357D7Got22918376161027161610449Ratregion
1628011D7Got20910776081152960811636Ratregion
1641372D7Got2089776015611560156212Ratregion
1640598D7Got25225676090697860907234Ratregion
1637384D7Wox3675811321258113629Ratregion
5036609AU04858517676172405261724228Ratregion
5026230RH131414075875832358758425Ratregion
5029488AI50193721575941814159418356Ratregion
5029687BF41951525075860198058602230Ratregion
5030707BI30184419775852908558529282Ratregion
5033489RH13901915476104380961043963Ratregion
5028253D4Mit3536875900140359001471Ratregion
5054401RH14320313575864959458649729Ratregion
5047046RH13210320375860236458602567Ratregion
5048416RH13289120075859930458599504Ratregion
5079682RH14114221375865255858652771Ratregion
5078168RH14018319175811796158118152Ratregion
5071024RH13484218775875011958750306Ratregion
5066922AU04807021175823791258238123Ratregion
5068668AU04700520176014162860141829Ratregion
5069806AU04793122776187412561874352Ratregion
5069806AU04793122776187412561874370Ratregion
5062542BF40339810375844504458445147Ratregion
5066024BE11657916776184172961841896Ratregion
5084878AA80018417575875681158756986Ratregion
5083109BI28174821375865120358651416Ratregion
5505514DXS1232076070644760707416Ratregion
5501436Snrpn35875871475758715094Ratregion
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)759238038104238038Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)761074194106074194Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)74725178365728867Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)753612714103945643Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
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)762004452101773158Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)762004452101773158Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
61435Cia4Collagen induced arthritis QTL 45.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)75811322462004598Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
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)73429328279293282Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat


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