Cia16 QTL Report (Rattus norvegicus) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
QTL Registration

QTL: Cia16 (Collagen induced arthritis QTL 16) Rattus norvegicus

Symbol: Cia16
Name: Collagen induced arthritis QTL 16
RGD ID: 61427
Previously known as: Type II Collagen induced arthritis QTL 16
Trait: joint integrity trait   (VT:0010548)    
Measurement Type: joint inflammation composite score   (CMO:0000919)    
LOD Score: 3.2
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8106,864,618 - 96,620,484RGD_MAPPER_PIPELINE
mRatBN7.2106,357,896 - 96,121,100RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.0106,429,075 - 99,492,409RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0105,243,736 - 99,184,250RGDRnor5.0
RGSC_v3.4106,380,753 - 100,633,982RGDRGSC3.4
RGSC_v3.1106,380,796 - 100,648,218RGD
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)
Cia16RatExperimental Arthritis  IDA 61067 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia16Ratjoint swelling  QTM 61067 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia16Ratjoint inflammation composite score  IDA 61067 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia16RatFreund's incomplete adjuvant  IDA 61067 RGD 
Cia16Rattype II collagen  IDA 61067 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia16Ratin vivo visual assessment  IDA 61067 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia16RatBBDR/Rhw  IEA 61067 RGD 
Cia16RatBN  IEA 61067 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Cia16Ratjoint 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 2238 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
7607054LOC102554563uncharacterized LOC1025545631063773766389405Rat
11378146LOC10835205560S ribosomal protein L7 pseudogene1065647066565810Rat
11458070LOC108352212uncharacterized LOC1083522121067134056714467Rat
9117786LOC103693272uncharacterized LOC1036932721067204026726491Rat
1309748Hapstr1HUWE1 associated protein modifying stress responses1067460376774992Rat
7653599LOC102546403uncharacterized LOC1025464031067935136798116Rat
11467871LOC108352056cytochrome c oxidase subunit 6B1 pseudogene1068761746876517Rat
1306915Usp7ubiquitin specific peptidase 71068806846925355Rat
1564086LitafdLITAF domain containing1069317196935869Rat
708415Carhsp1calcium regulated heat stable protein 11069460366960556Rat
1309366Pmm2phosphomannomutase 21069615216982913Rat
1561167Tmem186transmembrane protein 1861069829386986256Rat
620948Abat4-aminobutyrate aminotransferase1069966887092835Rat
41168947LOC120095023uncharacterized LOC1200950231071027787108907Rat
1311433Mettl22methyltransferase 22, Kin17 lysine1071136027130715Rat
40952738LOC120095024uncharacterized LOC1200950241071529107159730Rat
11427363Rpl35al9ribosomal protein L35A like 91071616277162832Rat
1560593Tmem114transmembrane protein 1141071689987185251Rat
41202743LOC120095443small nucleolar RNA SNORA171071905427190673Rat
7609447LOC102546970uncharacterized LOC1025469701071919417198779Rat

1 to 20 of 2238 rows
1 to 20 of 2907 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
10062D10Wox19230108541268585412915Ratregion
10141D10Wox15254106322103763221291Ratregion
10142D10Arb9129106322109463221223Ratregion
10195D10Wox14158105477580754775965Ratregion
10196D10Mgh22270105477574554776015Ratregion
10662D10Wox23258108097644580976703Ratregion
10664D10Uwm1158105467188954672047Ratregion
10792D10Wox10850103840624038407090Ratregion
10794D10Mgh9130103777589037776020Ratregion
10795D10Wox9188103777583737776025Ratregion
10874D10Rat83173104539382945394002Ratregion
10926D10Wox21130108913584589135975Ratregion
10949D10Wox11150105178628251786432Ratregion
10980D10Wox16125108051612580516250Ratregion
10981D10Arb21199108051614780516346Ratregion
10982D10Mit13165108051613480516299Ratregion
10995D10Wox24138106381361463813752Ratregion
11137D10Wox17153108705512187055282Ratregion
11169D10Mgh21140108853913988539279Ratregion
33846D10Mit2188106364253963642727Ratregion
1 to 20 of 2907 rows

Flank 1: (D10Rat95)
Rat AssemblyChrPosition (strand)Source
GRCr8106,864,618 - 6,864,840 (+)Marker Load Pipeline
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_v3.4106,380,753 - 6,381,051RGD
RGSC_v3.4106,380,796 - 6,381,017UniSTS
RGSC_v3.1106,380,796 - 6,381,017RGD
Celera105,357,468 - 5,357,689UniSTS
RH 3.4 Map1076.2UniSTS
RH 3.4 Map1076.2RGD
RH 2.0 Map102.9RGD
SHRSP x BN Map100.04RGD
FHH x ACI Map104.54RGD
Cytogenetic Map10q11-q12UniSTS
Peak: (D10Rat49)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21010,274,131 - 10,274,293 (+)MAPPER
Rnor_6.01010,464,401 - 10,464,562NCBI
Rnor_5.0109,238,813 - 9,238,974UniSTS
RGSC_v3.41010,385,187 - 10,385,349RGD
RGSC_v3.41010,385,188 - 10,385,349UniSTS
RGSC_v3.11010,385,188 - 10,385,349RGD
Celera109,240,933 - 9,241,094UniSTS
RH 3.4 Map10104.0UniSTS
RH 3.4 Map10104.0RGD
RH 2.0 Map1035.6RGD
SHRSP x BN Map105.71RGD
Cytogenetic Map10 RGD
Flank 2: (D10Rat11)
Rat AssemblyChrPosition (strand)Source
GRCr81096,620,293 - 96,620,484 (+)Marker Load Pipeline
mRatBN7.21096,120,911 - 96,121,100 (+)MAPPER
Rnor_6.01099,492,217 - 99,492,409NCBI
Rnor_5.01099,184,058 - 99,184,250UniSTS
RGSC_v3.410100,633,654 - 100,633,848UniSTS
RGSC_v3.410100,633,512 - 100,633,982RGD
RGSC_v3.110100,648,024 - 100,648,218RGD
Celera1094,766,403 - 94,766,596UniSTS
RH 3.4 Map101084.8RGD
RH 3.4 Map101084.8UniSTS
RH 2.0 Map101218.2RGD
SHRSP x BN Map1077.15RGD
FHH x ACI Map1082.4RGD


1 to 10 of 207 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
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
12902615Bw185Body weight QTL 1850.01body mass (VT:0001259)body weight (CMO:0000012)107111521772606468Rat
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101724551319388279Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat

1 to 10 of 207 rows


Database
Acc Id
Source(s)
NCBI Gene Cia16


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-14 Cia16  Collagen induced arthritis QTL 16    Type II Collagen induced arthritis QTL 16  Name updated 1299863 APPROVED

Note Type Note Reference
qtl_gene whole genome analysis using PGMapper revealed Map3k14, Tnfsf13, Ace, Mefv, Ccl2, Stat3, Il4, Ccl3, Ccl5, Cxcl16, Il13, Tp53, I13 and Tbs21 as RA associated genes and Ace, I14 and I13 as RA associated polymorphism either in coding or regulatory region 2300074
qtl_gene 1451 known and 239 novel genes were found in an analysis based on PubMed and OMIM data 2307198