Alc25 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: Alc25 (Alcohol consumption QTL 25) Rattus norvegicus

Symbol: Alc25
Name: Alcohol consumption QTL 25
RGD ID: 8693618
Trait: drinking behavior trait   (VT:0001422)    
Measurement Type: calculated ethanol drink intake rate   (CMO:0001615)    
LOD Score: 3.0
P Value: 0.28
Variance: Not Available
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21207,987,464 - 228,627,600RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.01227,509,470 - 249,252,048RGD_MAPPER_PIPELINERnor6.0
Rnor_5.01234,574,271 - 256,490,738RGD_MAPPER_PIPELINERnor5.0
RGSC_v3.41213,847,769 - 234,642,714RGD_MAPPER_PIPELINERGSC3.4
Cross Type: Not Available
Strains Crossed: BXH/Ipcv HXB/Ipcv 




  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25Ratalcohol use disorder  IAGP 8663441 RGD 

Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25Ratincreased alcohol consumption  IDA 8663441 RGD 

Clinical Measurement
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25Ratcalculated ethanol drink intake rate  IDA 8663441 RGD 

Experimental Condition
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25Ratcontrolled ethanol content drinking water with water as an optional drink source  IDA 8663441 RGD 

Measurement Method
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25Ratscale  IDA 8663441 RGD 

Rat Strain
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25RatBXH/Ipcv  IEA 8663441 RGD 
Alc25RatHXB/Ipcv  IEA 8663441 RGD 

Vertebrate Trait
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Alc25Ratdrinking behavior trait  IDA 8663441 RGD 


#
Reference Title
Reference Citation
1. Is the Alcohol Deprivation Effect Genetically Mediated? Studies with HXB/BXH Recombinant Inbred Rat Strains. Vanderlinden LA, etal., Alcohol Clin Exp Res. 2014 Jun 24. doi: 10.1111/acer.12471.


1 to 20 of 306 rows
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD ID
Symbol
Name
Chr
Start
Stop
Species
1307006Ms4a4amembrane spanning 4-domains A4A1208060507208085121Rat
41006787LOC120099990uncharacterized LOC1200999901208070936208079981Rat
2323335Hmgn1-ps2high mobility group nucleosome binding domain 1, pseudogene 21208088793208089355Rat
1583863Ms4a4cmembrane-spanning 4-domains, subfamily A, member 4C1208125063208146338Rat
1589849Ms4a6cmembrane-spanning 4-domains, subfamily A, member 6C1208153504208174721Rat
1590964Eif5-ps11eukaryotic translation initiation factor 5, pseudogene 111208169194208170649Rat
1590971Ms4a4cl1membrane-spanning 4-domains, subfamily A, member 4C like 11208217979208236368Rat
1359381Ms4a6bl1membrane-spanning 4-domains, subfamily A, member 6B-like 11208243561208255400Rat
1311761Ms4a6bmembrane-spanning 4-domains, subfamily A, member 6B1208281016208301771Rat
7598744LOC102551452uncharacterized LOC1025514521208318075208328601Rat
1590996Ms4a4c-ps1membrane-spanning 4-domains, subfamily A, member 4C, pseudogene 11208368380208387638Rat
2323952Ms4a6bl2membrane-spanning 4-domains, subfamily A, member 6B-like 21208398337208405671Rat
1305800Ms4a6amembrane spanning 4-domains A6A1208401465208414831Rat
41134996LOC120100458small nucleolar RNA SNORA171208417326208417423Rat
2598Ms4a2membrane spanning 4-domains A21208440179208448716Rat
1310598Ms4a3membrane spanning 4-domains A31208462300208480129Rat
1590948Oosp2oocyte secreted protein 21208480265208496843Rat
1590944Oosp1oocyte secreted protein 11208515497208547077Rat
40933068Oosp4aoocyte secreted protein family member 4A1208547232208561558Rat
62084Cblifcobalamin binding intrinsic factor1208605983208620231Rat

1 to 20 of 306 rows
1 to 20 of 305 rows
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Expected Size
Chr
Start
Stop
Species
Match
33945D1Mit181271218753689218753816Ratregion
34009D1Mit341051225126575225126682Ratregion
36021D1Rat1151601209979959209980119Ratregion
36219D1Rat3841481223390805223390953Ratregion
35525D1Rat1161661212458494212458660Ratregion
35525D1Rat1161661212458494212458660Ratregion
35551D1Rat1171331213533809213533942Ratregion
36866D1Rat731701218748008218748178Ratregion
36960D1Rat761441224569538224569684Ratregion
37162D1Rat721571219008538219008695Ratregion
37754D1Rat1231971218108584218108781Ratregion
37902D1Rat1691271224054293224054420Ratregion
37982D1Rat2232001222987545222987745Ratregion
36757D1Rat711461210702053210702199Ratregion
35909D1Rat741811221264111221264292Ratregion
40422D1Rat3712921228617884228618176Ratregion
40028D1Rat3011761228581588228581766Ratregion
39560D1Rat3242021223506828223507030Ratregion
42280D1Rat4721191208962849208962968Ratregion
41168D1Rat2992261218972999218973225Ratregion
1 to 20 of 305 rows

Flank 1: (rs107452597)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21207,987,464 - 207,987,464RGD
Rnor_6.01227,509,470 - 227,509,470RGD
Celera1205,462,252 - 205,462,252RGD
Peak: (rs64042903)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21221,112,979 - 221,112,979RGD
Rnor_6.01241,320,305 - 241,320,305RGD
Celera1218,326,594 - 218,326,594RGD
Flank 2: (rs64209861)
Rat AssemblyChrPosition (strand)Source
mRatBN7.21228,627,600 - 228,627,600RGD
Rnor_6.01249,252,048 - 249,252,048RGD
Celera1225,759,203 - 225,759,203RGD


1 to 10 of 120 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
8693637Alc29Alcohol consumption QTL 292.70.258drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1207987464234238494Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1150700247252085048Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1197814409242814409Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)181591954219808434Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1214537555238757011Rat
1302787Stl25Serum triglyceride level QTL 252.70.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1180359209210702199Rat
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
70163Bw20Body weight QTL 205.1body mass (VT:0001259)body weight (CMO:0000012)1174133260219133260Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat

1 to 10 of 120 rows


Note Type Note Reference
qtl_general spans 234.9-256.4 Mb 8663441
qtl_general measurement method: rats were given 10% EtOH for 1 week, then for 7 weeks they were given 2-bottle choice of water and EtOH followed by 2 week period of only water (alcohol deprivation); then 2 weeks of 2-bottle choice of water and EtOH followed by second 2 weeks of alcohol deprivation then 2 weeks of 2-bottle choice of water and EtOH followed by third 2 weeks of alcohol deprivation and 1 week of 2-bottle choice of water and EtOH 8663441
qtl_general water and alcohol consumption were measured by weight 8663441
qtl_general alcohol deprivation effect (ADE) was calculated as the amount of alcohol consumed (g/kg) during 24 hrs after deprivation minus average daily amount consumed in the week before deprivation period 8663441
qtl_general this QTL correlates to week 2 pre-ADE alcohol consumption 8663441
qtl_general software used: ANOVA 8663441
qtl_general number of animals used: 70-100 days old males from HXB/BXH RI strains and the parental BN-Lx/CubPrin, SHR/OlaIpcvPrin 8663441