Cia17 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL Registration

QTL: Cia17 (Collagen induced arthritis QTL 17) Rattus norvegicus

Symbol: Cia17
Name: Collagen induced arthritis QTL 17
RGD ID: 61429
Previously known as: Type II Collagen induced arthritis QTL 17
Trait: joint integrity trait   (VT:0010548)    
Measurement Type: joint inflammation composite score   (CMO:0000919)    
LOD Score: 4.6
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81831,610,505 - 72,538,878RGD_MAPPER_PIPELINE
mRatBN7.21831,359,408 - 70,263,868RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01832,670,352 - 73,016,546RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01832,348,154 - 72,695,235RGDRnor5.0
RGSC_v3.41832,458,819 - 73,666,623RGDRGSC3.4
RGSC_v3.11832,494,084 - 73,739,829RGD
Cross Type: F2
Strains Crossed: BBDR/Rhw BN 
JBrowse: View Region in Genome Browser (JBrowse)
Model




  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17RatExperimental Arthritis  IDA 61067 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17Ratjoint swelling  QTM 61067 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17Ratjoint inflammation composite score  IDA 61067 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17RatFreund's incomplete adjuvant  IDA 61067 RGD 
Cia17Rattype II collagen  IDA 61067 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17Ratin vivo visual assessment  IDA 61067 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17RatBBDR/Rhw  IEA 61067 RGD 
Cia17RatBN  IEA 61067 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia17Ratjoint integrity trait  IDA 61067 RGD 


#
Reference Title
Reference Citation
1. 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
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. 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.
4. 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.


1 to 20 of 467 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
2741Nr3c1nuclear receptor subfamily 3, group C, member 1183127168131393320Rat
1310759Pabpc2poly(A) binding protein, cytoplasmic 2183165421831656486Rat
11361905LOC108348849glyceraldehyde-3-phosphate dehydrogenase pseudogene183189817631899193Rat
1359165Yipf5Yip1 domain family, member 5183212381432136947Rat
1559856Kctd16potassium channel tetramerization domain containing 16183216623632473067Rat
41244098Ube2c-ps3ubiquitin-conjugating enzyme E2C, pseudogene 3183232131632321725Rat
40943372Trnap-agg42transfer RNA proline (anticodon AGG) 42183263524732635327Rat
41231671LOC120098435U6 spliceosomal RNA183274616632746268Rat
1590896Kpna1-ps4karyopherin subunit alpha 1, pseudogene 4183276966932776779Rat
41196987LOC120093049small nucleolar RNA SNORA19183304590833046048Rat
1585817Rpl36-ps14ribosomal protein L36, pseudogene183328138633281699Rat
2323363Rplp0-ps6ribosomal protein lateral stalk subunit P0, pseudogene 6183366415833665636Rat
41130071Ppp2r2d-ps1protein phosphatase 2, regulatory subunit B, delta, pseudogene 1183376815333771743Rat
2323168Selenok-ps5selenoprotein K, pseudogene 5183377230033772969Rat
6502918Atp5mg-ps5ATP synthase membrane subunit g, pseudogene 5183382700033827309Rat
41168943LOC120098429U6 spliceosomal RNA183383705933837165Rat
1588514Tkt-ps1transketolase, pseudogene 1183384251033844384Rat
11502477LOC10834885040S ribosomal protein S28 pseudogene183385617433856387Rat
1584707Prelid2PRELI domain containing 2183386993433961320Rat
9179805LOC103694262cyclin-dependent kinase 1 pseudogene183390562033906471Rat

1 to 20 of 467 rows
1 to 20 of 630 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
10108D18Mgh11341185564260755642948Ratregion
10647D18Wox12140186037761560377755Ratregion
10648D18Wox13163186037759060377753Ratregion
10667D18Mit17117186076313260763249Ratregion
10689D18Mit5122183135940831359530Ratregion
33856D18Mit10225186040871960408944Ratregion
33884D18Mit8147185979647859796643Ratregion
34043D18Mit16148186169831761698465Ratregion
34156D18Mgh1114184698893946989053Ratregion
34182D18Mgh3145186584495065845095Ratregion
34218D18Mgh2183185971223459712417Ratregion
34256D4Mgh18124186205711662057171Ratregion
34270D18Mgh6132186702536067025492Ratregion
11337D18Wox9242183586942035869662Ratregion
37412D18Rat40154185933040959330563Ratregion
37514D18Rat43227186357104063571267Ratregion
37548D18Rat52195185853611658536311Ratregion
37568D18Rat55100185253976352539863Ratregion
35463D18Rat34147184770914747709294Ratregion
36816D18Rat12234186938409269384326Ratregion
1 to 20 of 630 rows

Flank 1: (D18Mit5)
Rat AssemblyChrPosition (strand)Source
GRCr81831,610,505 - 31,610,627 (+)Marker Load Pipeline
mRatBN7.21831,359,408 - 31,359,530 (+)MAPPER
Rnor_6.01832,670,352 - 32,670,473NCBI
Rnor_5.01832,348,154 - 32,348,275UniSTS
RGSC_v3.41832,458,819 - 32,458,940UniSTS
RGSC_v3.11832,494,084 - 32,494,206RGD
Celera1830,993,196 - 30,993,317UniSTS
SHRSP x BN Map1817.1599UniSTS
SHRSP x BN Map1817.1599RGD
Cytogenetic Map18p12UniSTS
Peak: (D18Rat82)
Rat AssemblyChrPosition (strand)Source
GRCr81872,538,710 - 72,538,878 (+)Marker Load Pipeline
mRatBN7.21870,263,698 - 70,263,868 (+)MAPPER
Rnor_6.01873,016,379 - 73,016,546NCBI
Rnor_5.01872,695,068 - 72,695,235UniSTS
RGSC_v3.41873,666,205 - 73,666,623RGD
RGSC_v3.41873,666,389 - 73,666,556UniSTS
RGSC_v3.11873,739,662 - 73,739,829RGD
Celera1868,791,744 - 68,791,911UniSTS
RH 3.4 Map18718.1UniSTS
RH 3.4 Map18718.1RGD
RH 2.0 Map18155.5RGD
SHRSP x BN Map1844.4299RGD
Cytogenetic Map18 RGD
Flank 2: (D18Rat82)
Rat AssemblyChrPosition (strand)Source
GRCr81872,538,710 - 72,538,878 (+)Marker Load Pipeline
mRatBN7.21870,263,698 - 70,263,868 (+)MAPPER
Rnor_6.01873,016,379 - 73,016,546NCBI
Rnor_5.01872,695,068 - 72,695,235UniSTS
RGSC_v3.41873,666,205 - 73,666,623RGD
RGSC_v3.41873,666,389 - 73,666,556UniSTS
RGSC_v3.11873,739,662 - 73,739,829RGD
Celera1868,791,744 - 68,791,911UniSTS
RH 3.4 Map18718.1UniSTS
RH 3.4 Map18718.1RGD
RH 2.0 Map18155.5RGD
SHRSP x BN Map1844.4299RGD
Cytogenetic Map18 RGD


1 to 10 of 93 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
1331733Bp233Blood pressure QTL 2333.97196arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)182479697779788953Rat
1358358Sradr6Stress Responsive Adrenal Weight QTL 62.49adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)181194429959330563Rat
1331735Rf44Renal function QTL 442.981urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)181823456431359530Rat
1331730Scl27Serum cholesterol level QTL 273.826blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)185229287559796643Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
1331742Bp228Blood pressure QTL 2283.88752arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183135940859796643Rat
1298072Cia26Collagen induced arthritis QTL 263.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)185470976983828827Rat
1331736Bp227Blood pressure QTL 2272.791arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)184671876359796643Rat
1300125Rf26Renal function QTL 263.2urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)185253986365844950Rat
631834Sach3Saccharin preference QTL 33.90.01consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)185880568763636873Rat

1 to 10 of 93 rows


Database
Acc Id
Source(s)
NCBI Gene Cia17


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-14 Cia17  Collagen induced arthritis QTL 17    Type II Collagen induced arthritis QTL 17  Name updated 1299863 APPROVED

Note Type Note Reference
qtl_gene whole genome analysis using PGMapper revealed Dcc, Adrb2 and Slc26a2 as RA associated genes, Adrb2 and Slc26a2 as RA associated polymorphism either in coding or regulatory region 2300074
qtl_gene 246 known and 79 novel genes were found in an analysis based on PubMed and OMIM data 2307198