Cia25 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Cia25 (Collagen induced arthritis QTL 25) Rattus norvegicus

Symbol: Cia25
Name: Collagen induced arthritis QTL 25
RGD ID: 1298081
Trait: joint integrity trait   (VT:0010548)    
Measurement Type: joint inflammation composite score   (CMO:0000919)    
LOD Score: 4.7
P Value: Not Available
Variance: Not Available
Inheritance Type: recessive
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8122,747,694 - 47,747,694RGD_MAPPER_PIPELINE
mRatBN7.21219,610,889 - 35,682,913RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01222,650,721 - 41,291,738RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01224,663,002 - 43,150,909RGDRnor5.0
RGSC_v3.41220,932,555 - 36,894,750RGDRGSC3.4
RGSC_v3.11220,922,167 - 36,758,138RGD
Cross Type: intercross
Strains Crossed: DA/BklArbN ACI/SegHsd 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Ncf1 is a candidate Gene for Cia25


  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25RatExperimental Arthritis  IDA 1285224 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25Ratjoint swelling  QTM 1285224 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25Ratjoint inflammation composite score  IDA 1285224 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25RatFreund's incomplete adjuvant  IDA 1285224 RGD 
Cia25Rattype II collagen  IDA 1285224 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25Ratin vivo visual assessment  IDA 1285224 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25RatACI/SegHsd  IEA 1285224 RGD 
Cia25RatDA/BklArbN  IEA 1285224 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia25Ratjoint integrity trait  IDA 1285224 RGD 


#
Reference Title
Reference Citation
1. Cia25 On rat chromosome 12 regulates severity of autoimmune arthritis induced with pristane and collagen. Brenner M, etal., Ann Rheum Dis. 2007 Feb 28;.
2. Quest for arthritis-causative genetic factors in the rat. Joe B Physiol Genomics. 2006 Oct 3;27(1):1-11. Epub 2006 Jun 27.
3. Identification of Two Novel Female-Specific Non-MHC Loci Regulating Collagen-Induced Arthritis Severity and Chronicity, and Evidence for Epistasis. Meng HC,etal., Arthritis Rheum. 2004 Aug;50(8):2695-705.
4. 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.
5. 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 QTL Description Reference
Cia12 maps to same region RGD:1285224



1 to 20 of 318 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
3249Serpine1serpin family E member 1121960127219611657Rat
1305911Ap1s1adaptor related protein complex 1 subunit sigma 1121962526719635792Rat
69399VgfVGF nerve growth factor inducible121963731319645123Rat
1592588Mogat3monoacylglycerol O-acyltransferase 3121966870319669420Rat
631339Plod3procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3121967638419686945Rat
4888576Mir702microRNA 702121968180919681915Rat
2322870Znhit1zinc finger, HIT-type containing 1121968660619692880Rat
1310678Cldn15claudin 15121969816719708419Rat
1306668Fis1fission, mitochondrial 1121970856019723392Rat
6496734LOC100910802uncharacterized LOC100910802121974235519757486Rat
1305370Ift22intraflagellar transport 22121975907219768859Rat
1591401Col26a1collagen type XXVI alpha 1 chain121979269319938556Rat
1561258Myl10myosin light chain 10121996917419982627Rat
41397405LOC120095912uncharacterized LOC120095912122004641720053457Rat
620618Cux1cut-like homeobox 1122010706220425868Rat
69284Sh2b2SH2B adaptor protein 2122042705720456845Rat
1595708Prkrip1PRKR interacting protein 1122047080220491789Rat
1310213Orai2ORAI calcium release-activated calcium modulator 2122050030820520428Rat
1308608Alkbh4alkB homolog 4, lysine demethylase122052403020529947Rat
1359442Lrwd1leucine-rich repeats and WD repeat domain containing 1122053003520543078Rat

1 to 20 of 318 rows
1 to 20 of 557 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
10125DXMgh7230123381916733819400Ratregion
10888D12Wox1089122089438020894469Ratregion
11051D12Mit2217121961087019611091Ratregion
11052D12Wox11200121961088619611090Ratregion
11053D12Wox12202121961088919611095Ratregion
33955D1Mit22124123140994231410080Ratregion
34017D12Mit9142122184936621849508Ratregion
34246D12Mgh3118122423477724234895Ratregion
34417D12Mgh2163121983578919835952Ratregion
34729D12Mgh5124122806443328064557Ratregion
11449D12Wox14158122200342822003586Ratregion
11450D12Mgh12140122199658621996726Ratregion
11451D12Mgh13139122200341122003550Ratregion
36025D12Rat23145122413905724139202Ratregion
36101D12Rat15167122830212328302290Ratregion
36119D12Rat94267122905763229057901Ratregion
36125D12Rat14163122862266528622828Ratregion
36344D12Mit10121122363264523632770Ratregion
37250D12Rat26179122269248122692658Ratregion
37334D12Rat46158123039512130395279Ratregion
1 to 20 of 557 rows

Flank 1: (D12Wox12)
Rat AssemblyChrPosition (strand)Source
GRCr81225,247,593 - 25,247,795 (+)Marker Load Pipeline
mRatBN7.21219,610,889 - 19,611,095 (+)MAPPER
Rnor_6.01222,650,721 - 22,650,922NCBI
Rnor_5.01224,663,002 - 24,663,203UniSTS
RGSC_v3.41220,932,555 - 20,932,757RGD
RGSC_v3.41220,932,556 - 20,932,757UniSTS
RGSC_v3.11220,922,167 - 20,922,369RGD
Celera1221,386,649 - 21,386,850UniSTS
RH 3.4 Map12277.5RGD
RH 3.4 Map12277.5UniSTS
RH 2.0 Map12197.1RGD
Cytogenetic Map12q11-q12UniSTS
Peak: (D12Wox12)
Rat AssemblyChrPosition (strand)Source
GRCr81225,247,593 - 25,247,795 (+)Marker Load Pipeline
mRatBN7.21219,610,889 - 19,611,095 (+)MAPPER
Rnor_6.01222,650,721 - 22,650,922NCBI
Rnor_5.01224,663,002 - 24,663,203UniSTS
RGSC_v3.41220,932,555 - 20,932,757RGD
RGSC_v3.41220,932,556 - 20,932,757UniSTS
RGSC_v3.11220,922,167 - 20,922,369RGD
Celera1221,386,649 - 21,386,850UniSTS
RH 3.4 Map12277.5RGD
RH 3.4 Map12277.5UniSTS
RH 2.0 Map12197.1RGD
Cytogenetic Map12q11-q12UniSTS
Flank 2: (D12Arb6)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21235,682,559 - 35,682,913 (+)MAPPER
mRatBN7.21235,682,559 - 35,682,913 (-)MAPPER
Rnor_6.01241,291,378 - 41,291,738NCBI
Rnor_6.01241,213,448 - 41,213,801NCBI
Rnor_5.01243,150,549 - 43,150,909UniSTS
RGSC_v3.41236,818,780 - 36,819,134RGD
RGSC_v3.41236,894,446 - 36,894,750RGD
RGSC_v3.41236,818,781 - 36,819,134UniSTS
RGSC_v3.41236,894,447 - 36,894,750UniSTS
RGSC_v3.11236,757,835 - 36,758,138RGD
Celera1237,422,909 - 37,423,212UniSTS
Celera1237,346,026 - 37,346,376UniSTS
RH 3.4 Map12618.9UniSTS
RH 3.4 Map12618.9RGD
RH 2.0 Map12466.8RGD
SHRSP x BN Map1244.35RGD
Cytogenetic Map12 RGD


1 to 10 of 67 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)121914436246669029Rat
61443Btemp2Thermal response to stress QTL 23.30.000094body temperature trait (VT:0005535)core body temperature (CMO:0001036)121502518320794014Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12556449546669029Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122308134044726024Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)121961087046669029Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)12142110980Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)12960327746669029Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)12852542328064601Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)121961087040218516Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121587265332974238Rat

1 to 10 of 67 rows


Database
Acc Id
Source(s)
NCBI Gene Cia25

Note Type Note Reference
qtl_cross_type intercross  
qtl_disease involved in regulating mean arthritis scores and severity during mid-to-late disease course 1285224
qtl_gene whole genome analysis using PGMapper revealed Ncf1 as RA associated gene and Ncf1 as RA associated polymorphism either in coding or regulatory region 2300074
qtl_gene 471 known and 117 novel genes were found in an analysis based on PubMed and OMIM data 2307198
qtl_general female-specific arthritis-severity recessive locus in which maximum LOD was observed on day 28 1285224