Arrd1 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: Arrd1 (Age-related retinal degeneration QTL 1) Rattus norvegicus

Symbol: Arrd1
Name: Age-related retinal degeneration QTL 1
RGD ID: 8655649
Trait: retinal layer morphology trait   (VT:0003727)    
Measurement Type: percentage of study population developing retinopathy during a period of time   (CMO:0002453)    
LOD Score: 4.89
P Value: Not Available
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81109,493,780 - 193,400,781RGD_MAPPER_PIPELINE
mRatBN7.21100,357,752 - 183,970,443RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01106,002,252 - 202,571,904RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01107,049,754 - 209,588,735RGD_MAPPER_PIPELINERnor5.0
RGSC_v3.41100,539,980 - 188,654,926RGD_MAPPER_PIPELINERGSC3.4
Cross Type: intercross
Strains Crossed: OXYS/Nov WAG/Nov 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Rlbp1 is a candidate Gene for Arrd1


  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1Ratmacular degeneration  IAGP 7794750 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1Ratabnormal retina layer morphology  IDA 7794750 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1Ratpercentage of study population developing retinopathy during a period of time  IDA 7794750 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1Ratcontrol condition  IDA 7794750 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1Ratslit-lamp direct ophthalmoscopy  IDA 7794750 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1RatOXYS/Nov  IEA 7794750 RGD 
Arrd1RatWAG/Nov  IEA 7794750 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Arrd1Ratretinal layer morphology trait  IDA 7794750 RGD 


#
Reference Title
Reference Citation
1. Quantitative trait loci on chromosome 1 for cataract and AMD-like retinopathy in senescence-accelerated OXYS rats. Korbolina EE, etal., Aging (Albany NY). 2012 Jan;4(1):49-59.
2. Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats. Korbolina EE, etal., BMC Genomics. 2014 Dec 19;15 Suppl 12:S3. doi: 10.1186/1471-2164-15-S12-S3. Epub 2014 Dec 19.

Related QTL Description Reference
Arrd2 interacts with RGD:7794750



1 to 20 of 1444 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
620998Nell1neural EGFL like 1199709305100573872Rat
41395739Nsa2-ps7NSA2 ribosome biogenesis factor, pseudogene 71100469200100469968Rat
41271806Trnaa-agc61transfer RNA alanine (anticodon AGC) 611100836137100836210Rat
6500416Ftl1-ps1ferritin light chain 1, pseudogene 11100923579100924459Rat
41060898LOC120099814uncharacterized LOC1200998141101052794101087616Rat
1564265Ano5anoctamin 51101086490101187547Rat
7709992Csde1-ps1cold shock domain containing E1, pseudogene 11101128263101131688Rat
620531Slc17a6solute carrier family 17 member 61101212489101252543Rat
1583792Rpl18a-ps4ribosomal protein L18A, pseudogene 41101322809101323617Rat
40935431LOC120099815uncharacterized LOC1200998151101354768101380898Rat
1561456FancfFA complementation group F1101449120101451936Rat
1563167Gas2growth arrest-specific 21101452361101582619Rat
1565432Svipsmall VCP interacting protein1101587128101592818Rat
1559980Ccdc179coiled-coil domain containing 1791101600369101604288Rat
1585077Stip1-ps1stress-induced phosphoprotein 1, pseudogene 11101898734101900378Rat
6498966Ybx1-ps5Y box binding protein 1, pseudogene 51102225708102227243Rat
1585067Trim25-ps1tripartite motif-containing 25, pseudogene 11102350230102400041Rat
41070218LOC120099817uncharacterized LOC1200998171102476477102497194Rat
2321314Atxn1-ps1ataxin 1, pseudogene 11102516795102517889Rat
41236487Dnajb6-ps3DnaJ heat shock protein family (Hsp40) member B6, pseudogene 31102565949102567063Rat

1 to 20 of 1444 rows
1 to 20 of 1596 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
10138D1Arb191891181406902181407091Ratregion
10165D1Wox341341164747424164747558Ratregion
10273D1Smu111931168879333168879526Ratregion
10613D1Arb103931108698333108698726Ratregion
10818D1Smu101271182657959182658086Ratregion
10923D1Wox191551181133855181134010Ratregion
10951D1Mit133431181829673181830018Ratregion
10952D1Wox211041181829824181829932Ratregion
10953D1Arb183801181829744181830126Ratregion
10954D1Wox321901181829796181829988Ratregion
11033D1Mgh191971152441635152441834Ratregion
11142D1Smu91711177061421177061592Ratregion
11185D1Wox351541167512327167512481Ratregion
11270D1Smu81291176447349176447478Ratregion
33806D1Mit241091163747690163747797Ratregion
33806D1Mit241091163747690163748014Ratregion
33870D1Mit171891126242834126243023Ratregion
33959D1Mit31371144267353144267490Ratregion
33959D1Mit31371144267353144267916Ratregion
34074D1Mgh81171153136852153136969Ratregion
1 to 20 of 1596 rows

Flank 1: (D1Rat30)
Rat AssemblyChrPosition (strand)Source
GRCr81109,493,780 - 109,494,029 (+)Marker Load Pipeline
mRatBN7.21100,357,752 - 100,358,001 (+)MAPPER
Rnor_6.01106,002,252 - 106,002,500NCBI
Rnor_5.01107,049,754 - 107,050,002UniSTS
RGSC_v3.41100,539,980 - 100,540,384RGD
RGSC_v3.41100,540,030 - 100,540,278UniSTS
RGSC_v3.11100,618,141 - 100,618,389RGD
Celera194,544,373 - 94,544,621UniSTS
RH 3.4 Map1929.2UniSTS
RH 3.4 Map1929.2RGD
RH 2.0 Map1605.1RGD
SHRSP x BN Map151.4199RGD
Cytogenetic Map1q22UniSTS
Flank 2: (D1Rat219)
Rat AssemblyChrPosition (strand)Source
GRCr81193,400,541 - 193,400,781 (+)Marker Load Pipeline
mRatBN7.21183,970,203 - 183,970,443 (+)MAPPER
Rnor_6.01202,571,665 - 202,571,904NCBI
Rnor_5.01209,588,496 - 209,588,735UniSTS
RGSC_v3.41188,654,686 - 188,654,926RGD
RGSC_v3.41188,654,687 - 188,654,926UniSTS
RGSC_v3.11188,804,568 - 188,804,807RGD
Celera1181,604,272 - 181,604,511UniSTS
RH 2.0 Map1972.1RGD
SHRSP x BN Map194.8399RGD


1 to 10 of 165 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
4889419Cstrr2Cold stress response QTL 20.05urine catecholamine amount (VT:0010502)absolute change in urine norepinephrine level (CMO:0001634)1155866514158592016Rat
61442Strs1Sensitivity to stroke QTL 17.4cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)1121767634166767634Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1123350408182418476Rat
1302787Stl25Serum triglyceride level QTL 252.70.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1180359209210702199Rat
70160Bw18Body weight QTL 185.7body mass (VT:0001259)body weight (CMO:0000012)1144267353196383668Rat
1549830Bss1Bone structure and strength QTL 14.8femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1172609619217609619Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1115540693238914717Rat

1 to 10 of 165 rows



Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-06-25 Arrd1  Age-related retinal degeneration QTL 1  Lecl3  Lens clarity QTL 3  Symbol updated 68687 APPROVED
2014-06-25 Arrd1  Age-related retinal degeneration QTL 1  Lecl3  Lens clarity QTL 3  Name updated 68913 APPROVED
2014-05-21 Lecl3  Lens clarity QTL 3  lecl3  Lens clarity QTL 3  Symbol updated 68687 APPROVED
2014-05-21 Lecl3  Lens clarity QTL 3  lecl3  Lens clarity QTL 3  Name updated 68913 APPROVED

Note Type Note Reference
qtl_general incidence of retinopathy increase significantly in male F2 as compared to male F1 7794750
qtl_general measurement method: beta direct ophthalmoscope was used to examine the eyes after dilation with 1% tropicamide at ages 1.5-2 and 3-4 months 7794750
qtl_general number of animals used: F1 and F2 hybrids from reciprocal crosses 7794750
qtl_general retinopathy was determined based on pathological changes of the retina 7794750
qtl_general software used: ANOVA 7794750