Alc4 QTL Report (Rattus norvegicus) - Rat Genome Database

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QTL: Alc4 (Alcohol consumption QTL 4) Rattus norvegicus

Symbol: Alc4
Name: Alcohol consumption QTL 4
RGD ID: 631827
Previously known as: Alcohol preference QTL 4
Trait: consumption behavior trait   (VT:0002069)    
Measurement Type: ethanol drink intake rate   (CMO:0001407)    
LOD Score: 3.5
P Value: Not Available
Variance: 3.0
Inheritance Type: additive
Position
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.258,187,501 - 18,616,199RGD_MAPPER_PIPELINEmRatBN7.2
Rnor_6.057,875,611 - 18,592,319RGD_MAPPER_PIPELINERnor6.0
Rnor_5.0512,694,705 - 23,381,659RGDRnor5.0
RGSC_v3.4510,517,466 - 18,944,220RGDRGSC3.4
RGSC_v3.1510,517,466 - 18,944,220RGD
Cross Type: Intercross
Strains Crossed: HAD1 LAD1 
JBrowse: View Region in Genome Browser (JBrowse)
Model



Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
Experimental Data Annotations     Click to see Annotation Detail View

Clinical Measurement

Experimental Condition

Measurement Method

Vertebrate Trait

Rat Strain
HAD1  (IEA)
LAD1  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Analyses of quantitative trait loci contributing to alcohol preference in HAD1/LAD1 and HAD2/LAD2 rats. Carr LG, etal., Alcohol Clin Exp Res 2003 Nov;27(11):1710-7.
2. Identification of quantitative trait loci influencing alcohol consumption in the high alcohol drinking and low alcohol drinking rat lines. Foroud T, etal., Behav Genet 2000 Mar;30(2):131-40.
3. Confirmation of alcohol preference quantitative trait loci in the replicate high alcohol drinking and low alcohol drinking rat lines. Foroud T, etal., Psychiatr Genet 2003 Sep;13(3):155-61.
Related QTLs

Related QTL Description Reference
Alc12 interacts with RGD:731212
Alc10 interacts with RGD:731212
Alc9 interacts with RGD:731212
Alc11 interacts with RGD:731212
Alc13 interacts with RGD:731212


Region

Genes in Region
The following Genes overlap with this region.    Full Report CSV TAB Printer Analysis Tools
RGD IDSymbolNameChrStartStopSpecies
69426Oprk1opioid receptor, kappa 151386001613877823Rat
621017LynLYN proto-oncogene, Src family tyrosine kinase51663951216755501Rat
620242Sgk3serum/glucocorticoid regulated kinase family, member 3593457619472243Rat
708520Vcpip1valosin containing protein interacting protein 1595342479560889Rat
3025Lypla1lysophospholipase 151467960514708774Rat
1307055Cspp1centrosome and spindle pole associated protein 1590771619192402Rat
621037Rps20ribosomal protein S2051681931316820475Rat
1305917Npbwr1neuropeptides B and W receptor 151349542613496415Rat
1304796Mrpl15mitochondrial ribosomal protein L1551472996614741276Rat
3103MosMOS proto-oncogene, serine/threonine kinase51685995716861264Rat
1306455Bpnt23'(2'), 5'-bisphosphate nucleotidase 251777568417802570Rat
1305371Sox17SRY-box transcription factor 1751501666015022228Rat
708566St18ST18 C2H2C-type zinc finger transcription factor51258249312914221Rat
1309880Tcea1transcription elongation factor A151463145414668769Rat
1309006Tmem68transmembrane protein 6851649405416524842Rat
1549780Xkr4XK related 451589618816297733Rat
1310301Cops5COP9 signalosome subunit 5591922339210498Rat
1309346Rb1cc1RB1-inducible coiled-coil 151316164813225560Rat
1306940Mybl1MYB proto-oncogene like 1595829059618179Rat
1311403Rrs1ribosome biogenesis regulator 1 homolog597334869735119Rat
1308863Adhfe1alcohol dehydrogenase, iron containing, 1597059669732580Rat
1311764Cpa6carboxypeptidase A6585597458888492Rat
1305286Plag1PLAG1 zinc finger51690205716956727Rat
1309953Tgs1trimethylguanosine synthase 151652486416558399Rat
1307865Prex2phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2579376928253112Rat
1561068Mcmdc2minichromosome maintenance domain containing 2592919679337526Rat
1562060Sdr16c6short chain dehydrogenase/reductase family 16C, member 651709520817118713Rat
1560290Sntg1syntrophin, gamma 15998055010794666Rat
68946Penkproenkephalin51718379917189160Rat
1562450Atp6v1hATPase H+ transporting V1 subunit H51437902914484703Rat
1560793Arfgef1ADP ribosylation factor guanine nucleotide exchange factor 1589820619076326Rat
1564095RGD1564095similar to 60S acidic ribosomal protein P251255128712552204Rat
1585792Kif1c-ps1kinesin family member 1C, pseudogene 151090616110908936Rat
1585836Tra2a-ps3transformer 2 alpha, pseudogene 351010664210108431Rat
1585679Ppp1r42protein phosphatase 1, regulatory subunit 42592271099274461Rat
1586095Psmd12-ps1proteasome 26S subunit, non-ATPase 12, pseudogene 151362624113708195Rat
1586096Pcmtd1protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 151228471112355680Rat
1586146Rgs20regulator of G-protein signaling 2051448432014614321Rat
1586147Eef1g-ps4eukaryotic translation elongation factor 1 gamma, pseudogene 4594987619503171Rat
1565999Sdr16c5short chain dehydrogenase/reductase family 16C, member 551701881317043974Rat
1564981Scp2-ps1sterol carrier protein 2, pseudogene 151660859516609025Rat
1561849Vxnvexin596592139684684Rat
1583530Alkal1ALK and LTK ligand 151301972913049913Rat
1563405RGD1563405similar to protein tyrosine phosphatase 4a251753051517532157Rat
1565647Cyld-ps1CYLD lysine 63 deubiquitinase, pseudogene 151520207415205290Rat
1584848Hnrnpa1-ps5heterogeneous nuclear ribonucleoprotein A1, pseudogene 551085591210856695Rat
1592689Chchd7coiled-coil-helix-coiled-coil-helix domain containing 751695708116969388Rat
1598345Got2-ps2glutamic-oxaloacetic transaminase 2, pseudogene 251221532912216562Rat
1595256Sumo4small ubiquitin-like modifier 451509932215099913Rat
1589398Tcf24transcription factor 24592746599282876Rat
1597763Dnajb6-ps2DnaJ heat shock protein family (Hsp40) member B6, pseudogene 251687884816879742Rat
1596713Rp1RP1, axonemal microtubule associated51512110415582363Rat
1596418Zfp652-ps1zinc finger protein 652, pseudogene 151787251017899024Rat
2318103Nhp2-ps2NHP2 ribonucleoprotein, pseudogene 251392485214056332Rat
2318732Ago2-ps1argonaute RISC catalytic component 2, pseudogene 151102054911023395Rat
2318359Tiprl-ps2TOR signaling pathway regulator, pseudogene 251245487912455761Rat
2321393LOC100364265ribosomal protein L19-like51688089916898782Rat
6486737LOC100912510uncharacterized LOC10091251051719041417192458Rat
6494602Rps15-ps4ribosomal protein S15, pseudogene 451245778012458197Rat
6502160Ppid-ps3peptidylprolyl isomerase D, pseudogene 351852878218540240Rat
7637993LOC102552817uncharacterized LOC10255281751497160815016234Rat
7618446LOC102549737uncharacterized LOC10254973751325044113272830Rat
7711861LOC102549805uncharacterized LOC10254980551328171613326776Rat
7721328LOC102556004uncharacterized LOC102556004592960849316974Rat
9196141Son-ps1SON DNA and RNA binding protein, pseudogene 151846947618473456Rat
9323738LOC103695237uncharacterized LOC10369523751619288716195997Rat
9452275LOC103692281BET1 homolog pseudogene51167072111671079Rat
11366818Rpl30-ps4ribosomal protein L30, pseudogene 4584204618420804Rat
11453663LOC108350924uncharacterized LOC10835092451804101118060823Rat
11385100LOC108350923uncharacterized LOC10835092351430730214312194Rat
11502483LOC108350922uncharacterized LOC108350922583808758383459Rat
11517012LOC108351080endogenous retrovirus group K member 9 Pol protein-like51373648313737690Rat
41091925Hnrnpa1-ps48heterogeneous nuclear ribonucleoprotein A1, pseudogene 4851143347611439810Rat
41390808LOC120103319small nucleolar RNA SNORA1751684576216845890Rat
41120437LOC120102815uncharacterized LOC12010281551673192316761548Rat
41121936LOC120102814uncharacterized LOC12010281451497213414983916Rat
41098563Pramel7-ps2preferentially expressed antigen in melanoma-like 7, pseudogene 251183103711832415Rat
41395404LOC120103059uncharacterized LOC12010305951628400116429252Rat
41182145Snord87small nucleolar RNA, C/D box 87592974899297573Rat
41186497LOC120102811uncharacterized LOC12010281151224979812254124Rat
41108305Hspd1-ps36heat shock protein family D (Hsp60) member 1, pseudogene 3651449799614499931Rat
41164745Snord54small nucleolar RNA, C/D box 5451681994516820012Rat
40974341LOC120103228U6 spliceosomal RNA51026308710263191Rat
40976711LOC120102817uncharacterized LOC12010281751808972818103756Rat
41001063LOC120103384U6 spliceosomal RNA51537542215375528Rat
41008049LOC120102812uncharacterized LOC12010281251332942413361574Rat
40943670Rnu6-1297RNA, U6 small nuclear 1297592263019226401Rat
41025792LOC120102816uncharacterized LOC12010281651769069117736386Rat
41052978LOC120103297small nucleolar RNA SNORA1751773591417736044Rat
41035118LOC120103058uncharacterized LOC12010305851601108516015518Rat
41038477LOC120103270small nucleolar RNA SNORA851321464613214785Rat

Markers in Region
The following Markers overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolExpected SizeChrStartStopSpeciesMatch
34387D5Mgh1719951452922514529436Ratregion
34599D5Mit1823651718969817189930Ratregion
39756D5Rat12320751861599218616199Ratregion
40562D5Rat187172589482288948404Ratregion
40718D5Rat120140581875018187645Ratregion
40250D5Rat12523451739773617397969Ratregion
42312D5Rat248239589591978959394Ratregion
42731D5Rat215124593596939359791Ratregion
41076D5Rat121200598232669823460Ratregion
41728D5Rat18820451817359018173792Ratregion
44552D9Wox21136598842169884268Ratregion
43871D16Got27149594531439453292Ratregion
43872D5Rat18612751237395512374084Ratregion
60752D5Rat24724351402600914026245Ratregion
69542D5Uwm821851278975112789935Ratregion
69543D5Uwm913951635002416350163Ratregion
69544D5Uwm1012151499583414995947Ratregion
69572D5Uwm5814951479387814794021Ratregion
66706D5Mco3620051037271110372890Ratregion
1630208D5Got20726551381391613814181Ratregion
1631652D5Got26299582084788208579Ratregion
1628062D5Got26125051453776414538012Ratregion
1629035D5Got20321451453226914532484Ratregion
1629653D5Wox2619451386131313861507Ratregion
1641068D5Got20515351454121014541363Ratregion
1641273D5Got32211251219114212191254Ratregion
1641312D5Got32115151654023616540387Ratregion
1633225D5Got20612551396962113969746Ratregion
1640560D5Got31718351674906616749249Ratregion
1635180D5Got28020151187609311876294Ratregion
1635380D5Got20412151364416513644286Ratregion
1638319D5Got20814451602944716029591Ratregion
1633881D5Got202117589027568902873Ratregion
7193066D5Mit1823651718969817189929Ratregion
5038908RH127402207597060739706280Ratregion
5038982RH12744521951718380617184025Ratregion
5039222RH12758219251316288213163074Ratregion
5036673AU048828256595295209529776Ratregion
5035566SON9851846946018469551Ratregion
5033849RH140347136597282889728424Ratregion
5033893RH14051814851463158214631725Ratregion
5033903RH14055421151675462516754836Ratregion
5027225AI1964529351604613116046224Ratregion
5030231BE11111315151719048217190633Ratregion
5025146RH12709222251846952118469743Ratregion
5025146RH12709222251846952118469743Ratregion
5033233RH13807413751655823716558374Ratregion
5028037MHAa74a4.seq195589621528962347Ratregion
5028208D1Mit296158595326129532770Ratregion
5030849BE120681209591300579130266Ratregion
5052095RH9483714051675436216754500Ratregion
5055167RH14364419751235485212355049Ratregion
5051679RH9459519951386057213860771Ratregion
5052097RH9483817351675482716755000Ratregion
5054341RH143168202597156829715884Ratregion
5056821RH14460016051281734012817500Ratregion
5053179RH142499109595407549540863Ratregion
5050656RH13418219451778053117780725Ratregion
5043950RH130324207596592639659470Ratregion
5044696RH130751181596178119617992Ratregion
5044484RH13062920351502188215022085Ratregion
5044558RH130672201593459819346182Ratregion
5045180RH13103020751681381616814023Ratregion
5046716RH13191419551473885014739045Ratregion
5046734RH13192418851606835016068538Ratregion
5048028RH13266720951470498414705193Ratregion
5039544RH127766217588880258888242Ratregion
5040866RH12852921651467966514679881Ratregion
5043498RH13005919951228486512285064Ratregion
5072506RH13688918151675666016756841Ratregion
5075998RH13891817351327157713272664Ratregion
5077450RH13976321451780341917803633Ratregion
5078432RH14034016151079096110791122Ratregion
5079854RH14124118051642937116429453Ratregion
5079854RH14124118051807330918073391Ratregion
5078046RH14011120351464862114648824Ratregion
5070780RH13470121151517583815176049Ratregion
5080252RH14147315051463226414632414Ratregion
5080252RH14147315051463226414632414Ratregion
5080464RH14159419451228139912281593Ratregion
5078658RH1404739251473806114738153Ratregion
5072110RH13665618251520593215206114Ratregion
5072110RH13665618251520593215206114Ratregion
5071506RH13512118751681917716819364Ratregion
5065108BF40587822651826690918267135Ratregion
5066720AU04819015751109859511098756Ratregion
5066986AU04803329151605032816050619Ratregion
5067124AU047949263598356469835906Ratregion
5067494AU04771020851503440915034617Ratregion
5067942AU04744423151721760817218054Ratregion
5068412AU04716128251677797716778256Ratregion
5068550AU04707811251374764613747758Ratregion
5069991RH9440617851511031815110494Ratregion
5062158BE10628222051050382310504043Ratregion
5063596BE10780820251629596216296164Ratregion
5062424BF40325520651386018913860395Ratregion
5064416BI30215016551288925012889415Ratregion
5064350BI30206516851426690914267077Ratregion
5063288BI30167219351548902215489215Ratregion
5066446AU04835221251719810617198318Ratregion
5087424STS-D294955551457139014571445Ratregion
5089781AU049360167597725989772767Ratregion
5088030Oprk112751386726113867388Ratregion
5087153BQ20910718351639144716391630Ratregion
5085611BM39205421651709276017092976Ratregion
5082981BF39055615851317448513174643Ratregion
5083515BF39159212251629085516290977Ratregion
5086801BE114642152590453679045519Ratregion
5081963BE11892616751473999914740166Ratregion
5507559RH68043103851342313513424173Ratregion
5506735G4487015651789659617896752Ratregion
5502431RH1248149651846945818469554Ratregion
Position Markers

Flank 1: (D5Rat120)
Rat AssemblyChrPosition (strand)Source
mRatBN7.258,187,501 - 8,187,645 (+)MAPPER
Rnor_6.057,875,611 - 7,875,754NCBI
Rnor_5.0512,694,705 - 12,694,848UniSTS
Celera57,724,876 - 7,725,019UniSTS
SHRSP x BN Map52.3599RGD
SHRSP x BN Map52.3599UniSTS
Cytogenetic Map5q11UniSTS
Peak: (D5Mgh17)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2514,529,225 - 14,529,436 (+)MAPPER
Rnor_6.0514,408,903 - 14,409,113NCBI
Rnor_5.0519,190,627 - 19,190,837UniSTS
RGSC_v3.4514,730,738 - 14,730,949RGD
RGSC_v3.4514,730,739 - 14,730,949UniSTS
RGSC_v3.1514,730,738 - 14,730,949RGD
Celera513,900,026 - 13,900,236UniSTS
RH 2.0 Map573.0RGD
SHRSP x BN Map55.82RGD
FHH x ACI Map52.2099RGD
Cytogenetic Map5 RGD
Flank 2: (D5Rat123)
Rat AssemblyChrPosition (strand)Source
mRatBN7.2518,615,992 - 18,616,199 (+)MAPPER
Rnor_6.0518,592,113 - 18,592,319NCBI
Rnor_5.0523,381,453 - 23,381,659UniSTS
RGSC_v3.4518,944,014 - 18,944,220UniSTS
RGSC_v3.4518,944,014 - 18,944,220RGD
RGSC_v3.1518,944,014 - 18,944,220RGD
Celera517,927,471 - 17,927,677UniSTS
SHRSP x BN Map510.3199UniSTS
SHRSP x BN Map510.3199RGD
Cytogenetic Map5q12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5511215947171491Rat
631827Alc4Alcohol consumption QTL 43.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)5818750118616199Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5894822853948228Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51268928557689285Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat


Additional Information

Database Acc Id Source(s)
NCBI Gene Alc4


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-04-14 Alc4  Alcohol consumption QTL 4    Alcohol preference QTL 4  Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
qtl_cross_pair HDA1 x LDA1, HAD2 x LAD2 631230
qtl_cross_type Intercross  
qtl_general crossing of replicate lines of HAD2 x LAD2 supported the existence of QTL phenotypes in this region 724636