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The initial sequencing and survey of sequence variation in 17 inbred strains was completed in 2011 and included comprehensive catalogue of single nucleotide polymorphisms, short insertion\u002Fdeletions, larger structural variants including their fine scale architecture and landscape of transposable element variation, and genomic sites subject to post-transcriptional alteration of RNA. From this beginning, the resource has expanded significantly to include 36 fully sequenced inbred laboratory mouse strains, a refined and updated data processing pipeline, and new variation querying and data visualisation tools which are available on the project’s website (\n                  http:\u002F\u002Fwww.sanger.ac.uk\u002Fresources\u002Fmouse\u002Fgenomes\u002F\n                  \n                ). The focus of the project is now the completion of de novo assembled chromosome sequences and strain-specific gene structures for the core strains. We discuss how the assembled chromosomes will power comparative analysis, data access tools and future directions of mouse genetics.",{"EN":214,"VI":215},"The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes","Dự án Mouse Genomes: Kho lưu trữ bộ gen các dòng chuột nhắt thí nghiệm cận huyết",{"VOID":217},"Bahn JH, Lee J-H, Li G, Greer C, Peng G, Xiao X (2012) Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Res 22:142–150\nBass BL, Nishikura K, Keller W, Seeburg PH, Emeson RB, O’Connell MA, Samuel CE, Herbert A (1997) A standardized nomenclature for adenosine deaminases that act on RNA. RNA 3:947–949\nBlanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A et al (2014) Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biol 15:R79\nBoyden ED, Dietrich WF (2006) Nalp1b controls mouse macrophage susceptibility to anthrax lethal toxin. Nat Genet 38:240–244\nChinwalla AT, Cook LL, Delehaunty KD, Fewell GA, Fulton LA, Fulton RS, Graves TA, Hillier LW, Mardis ER, McPherson JD et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562\nChurch DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M et al (2009) Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 7:e1000112\nChurch DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen H-C, Agarwala R, McLaren WM, Ritchie GRS et al (2011) Modernizing reference genome assemblies. PLoS Biol 9:e1001091\nDanecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S, Ponting CP, Flint J, Durbin R, Keane TM, Adams DJ (2012) High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol 13:r26\nDown TA, Piipari M, Hubbard TJP (2011) Dalliance: interactive genome viewing on the web. Bioinformatics 27:889–890\nEilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M (2005) The sequence ontology: a tool for the unification of genome annotations. Genome Biol 6:R44\nFrazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB et al (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448:1050–1053\nGu T, Buaas FW, Simons AK, Ackert-Bicknell CL, Braun RE, Hibbs MA (2012) Canonical A-to-I and C-to-U RNA editing is enriched at 3’UTRs and microRNA target sites in multiple mouse tissues. PLoS One 7:e33720\nHaldane JBS, Sprunt AD, Haldane NM (1915) Reduplication in mice (preliminary communication). J. Genet. 5:133–135\nHarrow J, Denoeud F, Frankish A, Reymond A, Chen C-K, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al (2006) GENCODE: producing a reference annotation for ENCODE. Genome Biol 7:S4\nKeane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M et al (2011) Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477:289–294\nKirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA et al (2010) Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics 185:1081–1095\nKlein J, Figueroa F (1981) Polymorphism of the mouse H-2 loci. Immunol Rev 60:23–57\nLagarrigue S, Hormozdiari F, Martin LJ, Lecerf F, Hasin Y, Rau C, Hagopian R, Xiao Y, Yan J, Drake TA et al (2013) Limited RNA editing in exons of mouse liver and adipose. Genetics 193:1107–1115\nLangmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25\nLi H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv13033997 Q-Bio\nLi H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760\nLi H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858\nLi H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment\u002Fmap format and SAMtools. Bioinformatics 25:2078–2079\nLiao P, Yong TF, Liang MC, Yue DT, Soong TW (2005) Splicing for alternative structures of Cav1.2 Ca2+ channels in cardiac and smooth muscles. Cardiovasc Res 68:197–203\nLilue J, Müller UB, Steinfeldt T, Howard JC (2013) Reciprocal virulence and resistance polymorphism in the relationship between Toxoplasma gondii and the house mouse. Elife 2:e01298\nLindner R, Friedel CC (2012) A comprehensive evaluation of alignment algorithms in the context of RNA-seq. PLoS One 7:e52403\nMcLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26:2069–2070\nMendelowitz L, Pop M (2014) Computational methods for optical mapping. GigaScience 3:33\nMudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL (2008) Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol 9:R91\nNeeman Y, Levanon EY, Jantsch MF, Eisenberg E (2006) RNA editing level in the mouse is determined by the genomic repeat repertoire. RNA 12:1802–1809\nPaigen K (2003) One hundred years of mouse genetics: an intellectual history. I. The classical period (1902-1980). Genetics 163:1–7\nPaul MS, Bass BL (1998) Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J 17:1120–1127\nPeng Z, Cheng Y, Tan BC-M, Kang L, Tian Z, Zhu Y, Zhang W, Liang Y, Hu X, Tan X et al (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol 30:253–260\nPowell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J (1987) A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50:831–840\nRamaswami G, Lin W, Piskol R, Tan MH, Davis C, Li JB (2012) Accurate identification of human Alu and non-Alu RNA editing sites. Nat Methods 9:579–581\nSchadt EE, Turner S, Kasarskis A (2010) A window into third-generation sequencing. Hum Mol Genet 19:R227–R240\nSherry ST, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311\nSkarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T et al (2011) A conditional knockout resource for the genome-wide study of mouse gene function. Nature 474:337–342\nSteward CA, Gonzalez JM, Trevanion S, Sheppard D, Kerry G, Gilbert JGR, Wicker LS, Rogers J, Harrow JL (2013) The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes. Database 2013:bat032\nSudbery I, Stalker J, Simpson JT, Keane T, Rust AG, Hurles ME, Walter K, Lynch D, Teboul L, Brown SD et al (2009) Deep short-read sequencing of chromosome 17 from the mouse strains A\u002FJ and CAST\u002FEi identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol 10:R112\nVan der Weyden L, Adams DJ, Bradley A (2002) Tools for targeted manipulation of the mouse genome. Physiol Genomics 11:133–164\nWong K, Bumpstead S, Weyden LVD, Reinholdt LG, Wilming LG, Adams DJ, Keane TM (2012) Sequencing and characterization of the FVB\u002FNJ mouse genome. Genome Biol 13:R72\nYalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellaker C, Goodstadt L, Nicod J, Bhomra A et al (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477:326–329\nYalcin B, Wong K, Bhomra A, Goodson M, Keane TM, Adams DJ, Flint J (2012) The fine-scale architecture of structural variants in 17 mouse genomes. Genome Biol 13:R18\nZhang X, Firestein S (2002) The olfactory receptor gene superfamily of the mouse. Nat Neurosci 5:124–133",{"VOID":219},"10.1007\u002Fs00335-015-9579-6","PUBLICATION","VERIFIED","2025-02-17T22:09:31.732+00:00","Auto Verify",[225],"VI","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs00335-015-9579-6",[228,244,258,272],{"id":229,"sortIndex":21,"researcher":20,"roles":230,"affiliations":232,"properties":241,"displayName":243,"givenName":20,"familyName":20},"8b48a6cb-c97b-47e2-8a6d-50b289934f4b",[231],"AUTHOR",[233],{"id":234,"sortIndex":21,"affiliation":235,"properties":20},"422a8694-81f8-4bf7-8066-b96fe3fc8b99",{"id":234,"createTime":20,"updateTime":20,"relativeEntities":236,"slug":20,"properties":237,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":240,"statistic":20},[],{"title":238},{"VI":239},"Wellcome Trust Sanger Institute, Cambridge, UK",[],{"title":242},{"VI":243},"David J. Adams",{"id":245,"sortIndex":246,"researcher":20,"roles":247,"affiliations":248,"properties":255,"displayName":257,"givenName":20,"familyName":20},"d93022cd-2d19-4dcc-8936-d96316463099",1,[231],[249],{"id":234,"sortIndex":21,"affiliation":250,"properties":20},{"id":234,"createTime":20,"updateTime":20,"relativeEntities":251,"slug":20,"properties":252,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":254,"statistic":20},[],{"title":253},{"VI":239},[],{"title":256},{"VI":257},"Anthony G. 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Our gene unification method employs an algorithm (fjoin—feature join) for efficient detection of genome coordinate overlaps among features represented in two annotation data sets. Following the analysis with fjoin, genome features are binned into six possible categories (1:1, 1:0, 0:1, 1:n, n:1, n:m) based on coordinate overlaps. These categories are subsequently prioritized for assessment of annotation equivalencies and differences. The version of the unified catalog reported here contains more than 59,000 entries, including 22,599 protein-coding coding genes, 12,455 pseudogenes, and 24,007 other feature types (e.g., microRNAs, lincRNAs, etc.). More than 23,000 of the entries in the MGI gene catalog have equivalent gene models in the annotation files obtained from NCBI, Vega, and Ensembl. 12,719 of the features are unique to NCBI relative to Ensembl\u002FVega; 11,957 are unique to Ensembl\u002FVega relative to NCBI, and 3095 are unique to MGI. More than 4000 genome features fall into categories that require manual inspection to resolve structural differences in the gene models from different annotation sources. Using the MGI unified gene catalog, researchers can easily generate a comprehensive report of mouse genome features from a single source and compare the details of gene and transcript structure using MGI’s mouse genome browser.",{"EN":349,"VI":350},"A unified gene catalog for the laboratory mouse reference genome","Danh mục gen thống nhất cho hệ gen tham chiếu của chuột nhắt phòng thí nghiệm",{"VOID":352},"Bradley A, Anastassiadis K, Ayadi A, Battey JF, Bell C, Birling MC, Bottomley J, Brown SD, Burger A, Bult CJ, Bushell W, Collins FS, Desaintes C, Doe B, Economides A, Eppig JT, Finnell RH, Fletcher C, Fray M, Frendewey D, Friedel RH, Grosveld FG, Hansen J, Herault Y, Hicks G, Horlein A, Houghton R, Hrabe de Angelis M, Huylebroeck D, Iyer V, de Jong PJ, Kadin JA, Kaloff C, Kennedy K, Koutsourakis M, Lloyd KC, Marschall S, Mason J, McKerlie C, McLeod MP, von Melchner H, Moore M, Mujica AO, Nagy A, Nefedov M, Nutter LM, Pavlovic G, Peterson JL, Pollock J, Ramirez-Solis R, Rancourt DE, Raspa M, Remacle JE, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Schick JZ, Schnutgen F, Schofield P, Seisenberger C, Selloum M, Simpson EM, Skarnes WC, Smedley D, Stanford WL, Stewart AF, Stone K, Swan K, Tadepally H, Teboul L, Tocchini-Valentini GP, Valenzuela D, West AP, Yamamura K, Yoshinaga Y, Wurst W (2012) The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome 23:580–586\nBrown GR, Hem V, Katz KS, Ovetsky M, Wallin C, Ermolaeva O, Tolstoy I, Tatusova T, Pruitt KD, Maglott DR, Murphy TD (2015) Gene: a gene-centered information resource at NCBI. Nucleic Acids Res 43:D36–D42\nBurge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41:D226–D232\nChan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37:D93–D97\nChurch DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P (2015) Extending reference assembly models. Genome Biol 16:13\nEppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE, Mouse Genome Database G (2015) The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res 43:D726–D736\nFarrell CM, O’Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD (2014) Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res 42:D865–D872\nFlicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Garcia-Giron C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kahari AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SM (2013) Ensembl 2013. Nucleic Acids Res 41:D48–D55\nGumucio DL, Wiebauer K, Dranginis A, Samuelson LC, Treisman LO, Caldwell RM, Antonucci TK, Meisler MH (1985) Evolution of the amylase multigene family. YBR\u002FKi mice express a pancreatic amylase gene which is silent in other strains. J Biol Chem 260:13483–13489\nInternational Mouse Knockout C, Collins FS, Rossant J, Wurst W (2007) A mouse for all reasons. Cell 128:9–13\nKapustin Y, Souvorov A, Tatusova T, Lipman D (2008) Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct 3:20\nKozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42:D68–D73\nMungall CJ, Batchelor C, Eilbeck K (2011) Evolution of the Sequence Ontology terms and relationships. J Biomed Inform 44:87–93\nOkazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schonbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, LE Corbani, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y, Consortium F, I RGERGP, Team II (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420:563–573\nPruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O’Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 42:D756–D763\nRichardson JE (2006) fjoin: simple and efficient computation of feature overlaps. J Comput Biol 13:1457–1464\nSayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 40:D13–D25\nShumway M, Cochrane G, Sugawara H (2010) Archiving next generation sequencing data. Nucleic Acids Res 38:D870–D871\nStrahler JR, Meisler M (1982) Two distinct pancreatic amylase genes are active in YBR mice. Genetics 101:91–102\nWilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL (2008) The vertebrate genome annotation (Vega) database. Nucleic Acids Res 36:D753–D760\nYue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse EC (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature 515:355–364",{"VOID":354},"10.1007\u002Fs00335-015-9571-1",[225],"https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs00335-015-9571-1",[358,375,390,405,418,434,450,464,486],{"id":359,"sortIndex":21,"researcher":20,"roles":360,"affiliations":361,"properties":372,"displayName":374,"givenName":20,"familyName":20},"d56bf603-374e-4606-9c3a-51053c7189d8",[231],[362],{"id":363,"sortIndex":21,"affiliation":364,"properties":370},"41ccba3c-8771-45b0-b3c6-5241810e5ddc",{"id":363,"createTime":20,"updateTime":20,"relativeEntities":365,"slug":20,"properties":366,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":369,"statistic":20},[],{"title":367},{"VI":368},"The Jackson Laboratory, Bar Harbor, USA",[],{"title":371},{"VI":368},{"title":373},{"VI":374},"Y. 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Richardson",{"id":391,"sortIndex":260,"researcher":20,"roles":392,"affiliations":393,"properties":402,"displayName":404,"givenName":20,"familyName":20},"8fad56d8-0a0d-46e6-aa4e-5d36ffe000f9",[231],[394],{"id":363,"sortIndex":21,"affiliation":395,"properties":400},{"id":363,"createTime":20,"updateTime":20,"relativeEntities":396,"slug":20,"properties":397,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":399,"statistic":20},[],{"title":398},{"VI":368},[],{"title":401},{"VI":368},{"title":403},{"VI":404},"P. 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Baldarelli",{"id":419,"sortIndex":420,"researcher":20,"roles":421,"affiliations":422,"properties":431,"displayName":433,"givenName":20,"familyName":20},"190d3acd-9e3f-400d-a617-6a57bd46f0f2",4,[231],[423],{"id":363,"sortIndex":21,"affiliation":424,"properties":429},{"id":363,"createTime":20,"updateTime":20,"relativeEntities":425,"slug":20,"properties":426,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":428,"statistic":20},[],{"title":427},{"VI":368},[],{"title":430},{"VI":368},{"title":432},{"VI":433},"D. J. Reed",{"id":435,"sortIndex":436,"researcher":20,"roles":437,"affiliations":438,"properties":447,"displayName":449,"givenName":20,"familyName":20},"430b2716-fe32-42c7-841d-2a25b5f64206",5,[231],[439],{"id":363,"sortIndex":21,"affiliation":440,"properties":445},{"id":363,"createTime":20,"updateTime":20,"relativeEntities":441,"slug":20,"properties":442,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":444,"statistic":20},[],{"title":443},{"VI":368},[],{"title":446},{"VI":368},{"title":448},{"VI":449},"J. M. Recla",{"id":451,"sortIndex":452,"researcher":20,"roles":453,"affiliations":454,"properties":461,"displayName":463,"givenName":20,"familyName":20},"a9990170-a856-4f15-8481-0bbbfebeeb08",6,[231],[455],{"id":363,"sortIndex":21,"affiliation":456,"properties":20},{"id":363,"createTime":20,"updateTime":20,"relativeEntities":457,"slug":20,"properties":458,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":460,"statistic":20},[],{"title":459},{"VI":368},[],{"title":462},{"VI":463},"R. 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B. K. Reddy",{"id":487,"sortIndex":488,"researcher":20,"roles":489,"affiliations":490,"properties":499,"displayName":501,"givenName":20,"familyName":20},"ceb584a2-3369-4741-b659-e2db95a2b1d8",8,[231],[491],{"id":363,"sortIndex":21,"affiliation":492,"properties":497},{"id":363,"createTime":20,"updateTime":20,"relativeEntities":493,"slug":20,"properties":494,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":496,"statistic":20},[],{"title":495},{"VI":368},[],{"title":498},{"VI":368},{"title":500},{"VI":501},"C. J. Bult",{"url":356,"publisher":503,"properties":545},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":504,"slug":10,"properties":505,"entityType":18,"verifyStatus":19,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":21,"subjectFields":509,"manageAffiliations":514,"indexDatabases":525,"url":20,"thumbnailPath":20,"statistic":540,"gsStatistic":20,"type":20,"analyzePriority":20},[],{"issn":506,"title":507,"eissn":508},{"VOID":13},{"EN":15},{"VOID":17},[510],{"id":24,"createTime":20,"updateTime":20,"relativeEntities":511,"label":512,"description":513,"parentId":20,"standard":20,"scholarHubFieldId":20},[],{"EN":27},{},[515,520],{"id":31,"createTime":20,"updateTime":20,"relativeEntities":516,"slug":20,"properties":517,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":519,"statistic":20},[],{"title":518},{"EN":35},[],{"id":38,"createTime":20,"updateTime":20,"relativeEntities":521,"slug":20,"properties":522,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":524,"statistic":20},[],{"title":523},{"EN":42},[44],[526,533],{"id":47,"indexDatabase":527,"url":60,"indexYears":20,"academicFieldIds":532,"indexDatabaseRanking":20},{"id":49,"createTime":20,"updateTime":20,"relativeEntities":528,"label":529,"description":530,"key":56,"publicationTags":531,"standard":20},[],{"EN":52,"VI":52},{"EN":54,"VI":55},[58,59],[62,63,64],{"id":66,"indexDatabase":534,"url":77,"indexYears":78,"academicFieldIds":539,"indexDatabaseRanking":81},{"id":68,"createTime":20,"updateTime":20,"relativeEntities":535,"label":536,"description":537,"key":74,"publicationTags":538,"standard":20},[],{"EN":71,"VI":71},{"EN":71,"VI":73},[76],[80],{"impactFactor":21,"impactFactorByYear":541,"i10Index":96,"i10IndexLast5Year":97,"totalPublication":98,"totalPublicationByYear":542,"totalCitation":132,"totalCitationByYear":543,"totalCitationPerPublication":166,"totalCitationPerPublicationByYear":544,"hindexLast5Year":164,"hindex":164},{"2012":84,"2013":85,"2014":86,"2015":87,"2016":88,"2017":89,"2018":90,"2019":91,"2020":92,"2021":93,"2022":94,"2023":95},{"1991":100,"1992":101,"1993":102,"1994":103,"1995":104,"1996":105,"1997":106,"1998":107,"1999":108,"2000":109,"2001":110,"2002":111,"2003":112,"2004":113,"2005":114,"2006":115,"2007":116,"2008":117,"2009":118,"2010":119,"2011":120,"2012":121,"2013":122,"2014":123,"2015":124,"2016":125,"2017":126,"2018":121,"2019":127,"2020":128,"2021":129,"2022":126,"2023":130,"2024":131},{"1991":134,"1992":135,"1993":136,"1994":137,"1995":138,"1996":139,"1997":140,"1998":141,"1999":142,"2000":143,"2001":144,"2002":145,"2003":146,"2004":147,"2005":148,"2006":149,"2007":150,"2008":151,"2009":152,"2010":153,"2011":154,"2012":155,"2013":156,"2014":157,"2015":158,"2016":159,"2017":160,"2018":161,"2019":102,"2020":162,"2021":163,"2022":164,"2023":165},{"1991":168,"1992":169,"1993":170,"1994":171,"1995":172,"1996":173,"1997":174,"1998":175,"1999":176,"2000":177,"2001":178,"2002":179,"2003":180,"2004":181,"2005":182,"2006":183,"2007":184,"2008":185,"2009":186,"2010":187,"2011":188,"2012":189,"2013":190,"2014":86,"2015":191,"2016":192,"2017":193,"2018":194,"2019":195,"2020":196,"2021":197,"2022":198,"2023":199},{"pages":546,"volume":548},{"VOID":547},"295-304",{"VOID":334},"2015-06-18",[81,58],{"id":552,"createTime":553,"updateTime":554,"relativeEntities":555,"slug":556,"properties":557,"entityType":220,"verifyStatus":221,"verifyTime":568,"verifyNote":223,"languages":20,"translateLanguages":20,"viewCount":21,"primaryUrl":569,"fullTextUrl":20,"authors":570,"publicationType":286,"publisherRelationship":755,"citationCount":20,"citationInfo":20,"publishDate":803,"publishYear":804,"citationAnalyzeStatus":805,"lastCitationAnalyze":554,"indexDatabases":806,"openAccess":20,"references":20,"isForceReanalyzing":338},"c53247a6-c467-49b8-8170-b0a45e598428","2024-01-19T05:30:39.792+00:00","2026-08-24T23:41:06.381+00:00",[],"Structural-and-functional-analysis-of-the-ovine-laminin-receptor-gene-RPSA-Possible-involvement-of-the-LRP-LR-protein-in-scrapie-response",{"abstract":558,"title":560,"gsPaper":562,"references":564,"doi":566},{"EN":559},"Scrapie is a prion disease affecting sheep and goats. Susceptibility to this neurodegenerative disease shows polygenic variance. The involvement of the laminin receptor (LRP\u002FLR) in the metabolism and propagation of prions has previously been demonstrated. In the present work, the ovine laminin receptor gene (RPSA) was isolated, characterized, and mapped to ovine chromosome OAR19q13. Real-time RT-PCR revealed a significant decrease in RPSA mRNA in cerebellum after scrapie infection. Conversely, no differences were detected in other brain regions such as diencephalon and medulla oblongata. Association analysis showed that a polymorphism reflecting the presence of a RPSA pseudogene was overrepresented in a group of sheep resistant to scrapie infection. No amino acid change in the LRP\u002FLR protein was found in the 126 sheep analyzed. However, interesting amino acid positions (241, 272, and 290), which could participate in the species barrier to scrapie and maybe to other transmissible spongiform encephalopathies, were identified by comparing LRP\u002FLR sequences from various mammals with variable levels of resistance to scrapie.",{"EN":561},"Structural and functional analysis of the ovine laminin receptor gene (RPSA): Possible involvement of the LRP\u002FLR protein in scrapie response",{"VOID":563},"[]",{"VOID":565},"Adjou KT, Simoneau S, Sales N, Lamoury F, Dormont D et al. (2003) A novel generation of heparan sulfate mimetics for the treatment of prion diseases. J Gen Virol 84:2595–2603\nAsano Y, Takashima S, Asakura M, Shintani Y, Liao Y et al. (2004) Lamr1 functional retroposon causes right ventricular dysplasia in mice. Nat Genet 36:123–130\nAuth D, Brawerman G (1992) A 33-kDa polypeptide with homology to the laminin receptor: component of translation machinery. 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J Virol Meth 36:137–146\nVorberg I, Groschup MH, Pfaff E, Priola SA (2003) Multiple amino acid residues within the rabbit prion protein inhibit formation of its abnormal isoform. J Virol 77:2003–2009\nYenofsky R, Bergmann I, Brawerman G (1982) Messenger RNA species partially in a repressed state in mouse sarcoma ascites cells. Proc Natl Acad Sci USA 79:5876–5880\nYenofsky R, Cereghini S, Krowczynska A, Brawerman G (1983) Regulation of mRNA utilization in mouse erythroleukemia cells induced to differentiate by exposure to dimethyl sulfoxide. Mol Cell Biol 3:1197–1203\nYow H, Wong JM, Chen HS, Lee C, Steele GD et al. (1988) Increased mRNA expression of a laminin-binding protein in human colon carcinoma: complete sequence of a full-length cDNA encoding the protein. 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In Free Radicals in Biology, Vol. 5, New York: Academic Press, pp. 115–160.",{"doi":1010},"10.1016\u002FB978-0-12-566505-6.50012-0",{"id":20,"text":1012,"url":20,"identifiers":1013},"Hodgson, E.K., Fridovich, I. (1975). Biochemistry 14, 5294–5299.",{"doi":1014},"10.1021\u002Fbi00695a010",{"id":20,"text":1016,"url":20,"identifiers":1017},"Imai, K., Kingsley, D.M. (1994). Mamm. Genome 5(Suppl.): 139–153.",{},{"id":20,"text":1019,"url":20,"identifiers":1020},"Meier, H., McPike, A.D. (1970). Exp. Med. Surg. 28, 256–269.",{},{"id":20,"text":1022,"url":20,"identifiers":1023},"Rosen, D.R., Siddique, T., Patterson, D., Figlewicz, D.A., Sapp, P., Hentati, A., Donaldson, D., Goto, J., O’Regan, J.P., Deng, H.-X., Rahmani, Z., Krizus, A., McKenna-Yasek, D., Cayabyab, A., Gaston, S.M., Berger, R., Tanzi, R.E., Halperin, J.J., Herzfeldt, B., Van den Bergh, R., Hung, W.-Y., Bird, T., Deng, G., Mulder, D.W., Smyth, C, Laing, N.G., Soriano, E., Pericak-Vance, M.A., Haines, J., Rouleau, G.A., Gusella, J.S., Horvitz, H.R., Brown, Jr., R.H. (1993). Nature 362, 59–62.",{"doi":1024},"10.1038\u002F362059a0",{"id":1026,"createTime":1027,"updateTime":1028,"relativeEntities":1029,"slug":1030,"properties":1031,"entityType":220,"verifyStatus":221,"verifyTime":1042,"verifyNote":223,"languages":20,"translateLanguages":20,"viewCount":21,"primaryUrl":1043,"fullTextUrl":20,"authors":1044,"publicationType":286,"publisherRelationship":1157,"citationCount":21,"citationInfo":1205,"publishDate":1208,"publishYear":1206,"citationAnalyzeStatus":989,"lastCitationAnalyze":1028,"indexDatabases":1209,"openAccess":20,"references":20,"isForceReanalyzing":338},"cc5c3db5-af2d-48cd-8138-009faa3cc7e0","2024-02-05T22:23:38.844+00:00","2026-08-15T09:11:02.390+00:00",[],"Lack-of-Pwcr1-MBII-85-snoRNA-is-critical-for-neonatal-lethality-in-Prader-Willi-syndrome-mouse-models",{"abstract":1032,"title":1034,"gsPaper":1036,"references":1038,"doi":1040},{"EN":1033},"Prader–Willi syndrome (PWS) is a neurobehavioral disorder caused by the lack of paternal expression of imprinted genes in the human chromosome region 15q11–13. Recent studies of rare human translocation patients narrowed the PWS critical genes to a 121-kb region containing PWCR1\u002FHBII-85 and HBII-438 snoRNA genes. The existing mouse models of PWS that lack the expression of multiple genes, including Snrpn, Ube3a, and many intronic snoRNA genes, are characterized by 80%–100% neonatal lethality. To define the candidate region for PWS-like phenotypes in mice, we analyzed the expression of several genetic elements in mice carrying the large radiation-induced p\n                  30PUb\n                 deletion that includes the p locus. Mice having inherited this deletion from either parent develop normally into adulthood. By Northern blot and RT-PCR assays of brain tissue, we found that Pwcr1\u002FMBII-85 snoRNAs are expressed normally, while MBII-52 snoRNAs are not expressed when the deletion is paternally inherited. Mapping of the distal deletion breakpoint indicated that the p\n                  30PUb\n                 deletion includes the entire MBII-52 snoRNA gene cluster and three previously unmapped EST sequences. The lack of expression of these elements in mice with a paternal p\n                  30PUb\n                 deletion indicates that they are not critical for the neonatal lethality observed in PWS mouse models. In addition, we identified MBII-436, the mouse homolog of the HBII-436 snoRNA, confirmed its imprinting status, and mapped it outside of the p\n                  30PUb\n                 deletion. Taking together all available data, we conclude that the lack of Pwcr1\u002FMBII-85 snoRNA expression is the most likely cause for the neonatal lethality in PWS model mice.",{"EN":1035},"Lack of Pwcr1\u002FMBII-85 snoRNA is critical for neonatal lethality in Prader–Willi syndrome mouse models",{"VOID":1037},"[\"4279392040535180248\"]",{"VOID":1039},"Bachellerie JP, Cavaille J, Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84: 775–790\nCavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, et al. (2000) Identification of brain-specific and imprinted small nucleloar RNA gnes exhibiting an unusual genomic organization. Proc Natl Acad Sci USA 97: 14311–14316\nde los Santos T, Schweizer J, Rees CA, Francke U (2000) small evolutionarily conserved RNA, resembling C\u002FD box small nuceolar RNA, is transcribed from PWCRI, a novel imprinted gene in the Prader–Willi deletion region, which highly expressed in brain, Am J Hum Genet 67: 1067–1082\nDhar MS, Johnson DK (1997) A microsatellite map of the pink-eyed dilution (p) deletion complex in mouse chromosome 7. Mamm Genome 8: 143–145\nDhar M, Webb LS, Smith L, Hauser L Johnson D, West DB (2000) A novel ATPase on mouse chromosome 7 is a candidate gene for increased body fat. Physiol Genomics 4: 93–100\nDhar MS, Sommardahl CS, Kirkland T, Nelson S, Donnell R, et al. (2004) Mice heterozygous for Atp10c, a putative amphipath, represent a novel model of obesity and type 2 diabetes. J Nutr 134 799–805\nGabriel JM, Merchant M Ohta T, Ji Y, Caldwell RTG, et al. (1999) A transgene insertion creating a heritable chromosome deletion mouse model of Prader–Willi and Angelman syndromes. Proc Natl Acad Sci U S A 96: 9258–9263\nGallagher RC, Pils B, Albalwi M, Francke U (2002) Evidence for the role of PWCR1\u002FHBII-85 C\u002FD box small nucleolar RNAs in Prader–Willi syndrome. Am J Hum Genet 71: 669–678\nJohnson DK, Stubbs LJ, Culiat CT, Montgomery CS Russell LB, et al. M (1995) Molecular analysis of 36 mutations at the mouse pink-eyed dilution (p) locus. Genetics 141: 1563–1571\nLevings PP, Bungert J (2002) The human beta-globin locus control region. Eur J Biochem 269: 1589–1599\nNicholls RD, Knepper JL (2001) Genome organization, function, and imprinting in Prader–Willi and Angelman syndromes. Annu Rev Genomics Hum Genet 2: 153–175\nRunte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B. et al. (2001) The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 10: 2687–2700\nRunte M, Varon R, Horn D, Horstherake B, Buiting K (2005) Exclusion of the C\u002FD box snoRNA gene cluster HBII-52 from a major role in Prader–Willi syndrome. Hum Genet 116: 228–300\nRussell LB, Montgomery CS, Cacherio NL, Johnson DK (1995) Complementation analyses for 45 mutations encompassing the pink-eyed dilution (p) locus of the mouse. Genetics 141: 1547–1562\nSchüle B, Albalwi M, Northrop E, Francis DI, Rowell M, et al. Molecular breakpoint cloning and gene expression studies of a novel translocation t(4;15) (q27;q11.2) associated with Prader-Willi Syndrome. BMC Medical Genetics6, 18\nTsai TF, Jiang YH, Bressler J, Armstrong D, Beaudety AL (1999) Paternal deletion from Snrpn to Ube3a in the mouse causes hypotonia, growth retardation and partial lethality and provides evidence for a gene contributing to Prader–Willi syndrome. Hum Mol Genet 8: 1357–1364\nYang T, Adamson TE, Resnick JL, Leff S, Wevrick R, et al. (1998) A mouse model for Prader–Willi syndrome imprinting-centre mutations. 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We have used a combination of PCR-based restriction site (PBR) analysis and DNA sequencing to perform a high-resolution analysis of a 2-million base pair (Mbp) segment in the middle of In17(4). We examined 21 restriction sites that are polymorphic between t haplotypes and their wild-type homologs, over nine distinct loci. In addition, we examined several other polymorphic sites through DNA sequence analysis of two of these nine loci. We analyzed several haplotypes in this way, including the “complete” t haplotypes t\n                        \n                  w2\n                , t\n                        \n                  0\n                , t\n                        \n                  w32\n                , t\n                        \n                  w71\n                , and t\n                        \n                  w75\n                . We show that only t\n                        \n                  w32\n                 is a true “complete” t haplotype; the remaining four t haplotypes have segments of wild-type DNA ranging from less than 100 bp to 2 Mbp. The sizes of these wild-type DNA segments are consistent with their being generated by gene-conversion events. The 2-Mbp segment is located in a region that may contain the t-complex distorter gene Tcd2. One of the nine loci examined in this study is Fgd2, a gene that has been proposed to encode Tcd2. Sequencing and PBR data show that at least a portion of the Fgd2 gene has been converted to the wild-type within t\n                        \n                  w71\n                 and t\n                        \n                  w75\n                mice.",{"EN":1378},"Recombination within mouse t haplotypes has replaced significant segments of t-specific DNA",{"VOID":1380},"[\"15899597168843898276\"]",{"VOID":1382},"Artzt K, Barlow D, Dove WF, Fischer-Lindahl K, Klein J et al (1991) Mouse chromosome 17. Mamm Genome 1 Spec No:S280–S300\nBauer H, Veron N, Willert J, Koschorz B, Herrmann BG (2007) The t-complex-encoded guanine nucleotide exchange factor Fgd2 reveals that two opposing signaling pathways promote transmission ratio distortion in the mouse. Genes Dev 21(2):143–147\nBennett D (1975) The T-locus of the mouse. Cell 6:441–454\nBenson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27(2):573–580. Available at http:\u002F\u002Fc3.biomath.mssm.edu\u002Ftrf.submit.options.html\nBucan M, Herrmann BG, Frischauf AM, Bautch VL, Bode V et al (1987) Deletion and duplication of DNA sequences is associated with the embryonic lethal phenotype of the t9 complementation group of the mouse t complex. Genes Dev 1:376–385\nChovnick A (1973) Gene conversion and transfer of genetic information within the inverted region of inversion heterozygotes. Genetics 75:123–131\nCurtis D, Clark SH, Chovnick A, Bender W (1989) Molecular analysis of recombination events in Drosophila. Genetics 122:653–661\nDembic Z, Singer PA, Klein J (1984) E0: a history of a mutation. EMBO J 3:1647–1654\nEbersole T, Lai F, Artzt K (1992) New molecular markers for the distal end of the t-complex and their relationships to mutations affecting mouse development. Genetics 131:175–182\nEppig JT, Bult CJ, Kadin JA, Richardson JE, Blake JA, members of the Mouse Genome Database Group (2005) The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology. Nucleic Acids Res 33:D471–D475. Available at http:\u002F\u002Fwww.infomatics.jax.org\u002F\nErhart MA, Phillips SJ, Bonhomme F, Boursout P, Wakeland EK et al (1989) Haplotypes that are mosaic for wild-type and t complex-specific alleles in wild mice. Genetics 12:405–415\nErhart MA, Lekgothoane S, Grenier J, Nadeau JH (2002) Pattern of segmental recombination in the distal inversion of mouse t haplotypes. Mamm Genome 13:438–444\nHall T (1997) BioEdit version 7.0.0. Available at http:\u002F\u002Fwww.mbio.ncsu.edu\u002FBioEdit\u002Fbioedit.html. Accessed 15 Aug 2007\nHammer MF, Silver LM (1993) Phylogenetic analysis of the alpha-globin pseudogene-4 (Hba-ps4) locus in the house mouse species complex reveals a stepwise evolution of t haplotypes. Mol Biol Evol 10:971–1001\nHammer MF, Bliss S, Silver LM (1991) Genetic exchange across a paracentric inversion of the mouse t complex. Genetics 128:799–812\nHeiman M (1997) Webcutter version 2.0. Available at http:\u002F\u002Fwww.rna.lundberg.gu.se\u002Fcutter2\u002F\nHuang SW, Ardlie KG, Yu HT (2001) Frequency and distribution of t-haplotypes in the southeast asian house mouse (Mus musculus castaneus) in Taiwan. Mol Ecol 10:2349–2354\nHubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M et al (2007) Ensembl 2007. Nucleic Acids Res 35(database issue):D610–D617. Available at http:\u002F\u002Fwww.ensembl.org\u002FMus_musculus\u002F\nJensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM et al (2004) Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 14(4):528–538\nKumar S, Subramanian S (2002) Mutation rates in mammalian genomes. Proc Natl Acad Sci USA 99:803–808\nLyon MF (1984) Transmission ratio distortion in mouse t-haplotypes is due to multiple distorter genes acting on a responder locus. Cell 37:621–628\nLyon MF (2003) Transmission ratio distortion in mice. Ann Rev Genet 37:393–408\nMorita T, Kubota H, Murata K, Nozaki M, Delarbre C et al (1992) Evolution of the mouse t haplotype: recent and worldwide introgression to Mus musculus. Proc Natl Acad Sci USA 89:6851–6855\nNadeau JH, Phillips SJ (1987) The putative oncogene Pim-1 in the mouse: its linkage and variation among t haplotypes. Genetics 117:533–541\nNavarro A, Betran E, Barbadilla A, Ruiz A (1997) Recombination and gene flux caused by gene conversion and crossing over in inversion heterokaryotypes. Genetics 146:695–709\nNeufeld E, Vincek V, Figueroa F, Klein J (1991) Limits of the distal inversion in the t complex of the house mouse: evidence from linkage disequilibria. Mamm Genome 1:242–248\nNovitski E, Braver G (1954) An analysis of crossing over within a heterozygous inversion in Drosophila melanogaster. Genetics 39:197–209\nPerkins DD (1962) Crossing-over and interference in a multiply marked chromosome arm of Neurospora. Genetics 47:1253–1274\nPhillips SJ, Nadeau JH (1984) Personal communication. Mouse Newslett 70:83\nRozas J, Aguade M (1994) Gene conversion is involved in the transfer of genetic information between naturally occurring inversions of Drosophila. Proc Natl Acad Sci USA 91:11517–11521\nRozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmer. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386. Available at http:\u002F\u002Ffrodo.wi.mit.edu\u002Fcgi-bin\u002Fprimer3\u002Fprimer3_www.cgi\nSchaeffer SW, Anderson WW (2005) Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics 171:1729–1739\nSilver LM (1990) Gene dosage effects on transmission ratio distortion and fertility in mice that carry t haplotypes. Genet Res 54:221–225\nSilver L (1993) The peculiar journey of a selfish chromosome: mouse t haplotypes and meiotic drive. Trends Genet 9:250–254\nSilver LM, Remis D (1987) Five of the nine genetically defined regions of mouse t haplotypes are involved in transmission ratio distortion. Genet Res 49:51–56\nSkow LC, Nadeau JN, Ahn JC, Shin HS, Artzt K et al (1987) Polymorphism and linkage of the A-crystallin gene in t-haplotypes of the mouse. 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However, little is known about the genetic architecture of baseline erythroid traits in pigs. In this study, hematocrit (Hct), hemoglobin (Hgb), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell (RBC), and red cell distribution width (RDW) were measured in 1420 (day 18), 1410 (day 46), and 1033 (day 240) F2 pigs from a White Duroc × Erhualian intercross resource population. The entire resource population was genotyped for 183 microsatellite loci across the pig genome, and the quantitative trait loci (QTL) analysis was performed for all erythroid-related traits measured with QTL Express based on a least-squares method. A total of 101 QTL, including 46 genome-wide significant QTL and 55 chromosome-wide significant QTL, regulating erythroid traits were found on all pig chromosomes (SSC) except for SSC15 and SSC18. The genome-wide significant QTL were mainly localized on SSC1, 7, 8, 10, and X. These results confirmed most of QTL previously identified in the swine. More importantly, this study detected age-specific QTL for baseline erythroid traits in pigs for the first time. Notably, the QTL for MCV and MCH on day 18 on SSC8 with small intervals of 3 and 4 cM, respectively, provided a good starting point for identifying causal genes underlying MCV and MCH in the future.",{"EN":1619},"Quantitative trait loci for porcine baseline erythroid traits at three growth ages in a White Duroc × Erhualian F2 resource population",{"VOID":1621},"[\"13425737888484362822\"]",{"VOID":1623},"Andersson L, Haley CS, Ellegren H, Knott SA, Johansson M et al (1994) Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263:1771–1774\nBidanel JP, Rothschild MF (2002) Current status of quantitative trait loci mapping in pigs. Pig News Inf 23:N39–N54\nChurchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971\nEdfors-Lilja I, Wattrang E, Marklund L, Moller M, Andersson-Eklund L et al (1998) Mapping quantitative trait loci for immune capacity in the pig. J Immunol 161:829–835\nEvans DM, Frazer IH, Martin NG (1999) Genetic and environmental causes of variation in basal levels of blood cells. Twin Res 2:250–257\nGagnon DR, Zhang TJ, Brand FN, Kannel WB (1994) Hematocrit and the risk of cardiovascular disease—the Framingham study: a 34-year follow-up. Am Heart J 127:674–682\nGuo YM, Mao HR, Ren J, Yan XM, Duan YY et al (2008) A comprehensive linkage map of the porcine genome from a large scale White Duroc × Erhualian resource population and evaluation of factors affecting recombination rates. Anim Genet 39 (Accepted)\nHaley CS, Knott SA, Elsen JM (1994) Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136:1195–1207\nHaltmayer M, Mueller T, Luft C, Poelz W, Haidinger D (2002) Erythrocyte mean corpuscular volume associated with severity of peripheral arterial disease: an angiographic evaluation. Ann Vasc Surg 16:474–479\nHoll JW, Cassady JP, Pomp D, Johnson RK (2004) A genome scan for quantitative trait loci and imprinted regions affecting reproduction in pigs. J Anim Sci 82:3421–3429\nJackson IJ, Budd P, Horn JM, Johnson R, Raymond S et al (1994) Genetics and molecular biology of mouse pigmentation. Pigment Cell Res 7:73–80\nJohannes F, Blizard DA, Lionikas A, Lang DH, Vandenbergh DJ et al (2006) QTL influencing baseline hematocrit in the C57BL\u002F6J and DBA\u002F2J lineage: age-related effects. Mamm Genome 17:689–699\nJohansson A, Pielberg G, Andersson L, Edfors-Lilja I (2005) Polymorphism at the porcine Dominant white\u002FKIT locus influence coat colour and peripheral blood cell measures. Anim Genet 36:288–296\nLander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363–2367\nLippi G, Manzato F, Franchini M, Guidi G (2002) Relationship between hematocrit, primary hemostasis, and cardiovascular disease in athletes. Am Heart J 144:14\nMueller T, Haidinger D, Luft C, Horvath W, Poelz W et al (2001) Association between erythrocyte mean corpuscular volume and peripheral arterial disease in male subjects: a case control study. Angiology 52:605–613\nMueller T, Luft C, Haidinger D, Poelz W, Haltmayer M (2002) Erythrocyte mean corpuscular volume associated with the anatomical distribution in peripheral arterial disease. Vasa 31:81–85\nOhene-Frempong K, Weiner SJ, Sleeper LA, Miller ST, Embury S et al (1998) Cerebrovascular accidents in sickle cell disease: rates and risk factors. Blood 91:288–294\nPeters LL, Zhang W, Lambert AJ, Brugnara C, Churchill GA et al (2005) Quantitative trait loci for baseline white blood cell count, platelet count, and mean platelet volume. Mamm Genome 16:749–763\nPeters LL, Lambert AJ, Zhang W, Churchill GA, Brugnara C et al (2006) Quantitative trait loci for baseline erythroid traits. Mamm Genome 17:298–309\nPeterson LF, Boyapati A, Ranganathan V, Iwama A, Tenen DG et al (2005) The hematopoietic transcription factor AML1 (RUNX1) is negatively regulated by the cell cycle protein cyclin D3. Mol Cell Biol 25:10205–10219\nPuddu PE, Lanti M, Menotti A, Mancini M, Zanchetti A et al (2002) Red blood cell count in short-term prediction of cardiovascular disease incidence in the Gubbio population study. Acta Cardiol 57:177–185\nReiner G, Fischer R, Hepp S, Berge T, Kohler F et al (2007) Quantitative trait loci for red blood cell traits in swine. Anim Genet 38:447–452\nReiner G, Fischer R, Hepp S, Berge T, Kohler F et al (2008) Quantitative trait loci for white blood cell numbers in swine. Anim Genet 39:163–168\nRen DR, Ren J, Xing YY, Guo YM, Wu YB et al (2008) A genome scan for quantitative trait loci affecting male reproductive traits in a White Duroc × Chinese Erhualian resource population. J Anim Sci 39 [Epub ahead of print]. Available online on July 3, 2008. doi:10.2527\u002Fjas.2008-0923\nRussell ES (1979) Hereditary anemias of the mouse: a review for geneticists. Adv Genet 20:357–459\nSeaton G, Haley CS, Knott SA, Kearsey M, Visscher PM (2002) QTL Express: mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics 18:339–340\nVisscher PM, Thompson R, Haley CS (1996) Confidence intervals in QTL mapping by bootstrapping. Genetics 143:1013–1020\nWattrang E, Almqvist M, Johansson A, Fossum C, Wallgren P et al (2005) Confirmation of QTL on porcine chromosomes 1 and 8 influencing leukocyte numbers, haematological parameters and leukocyte function. 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GPSM2\u002FLGN, a mitotic spindle-orienting protein associated with deafness in humans, is a PCP effector involved in kinocilium migration. Here, we link human and mouse truncating mutations in the GPSM2\u002FLGN gene, both leading to hearing loss. The human variant, p.(Trp326*), was identified by targeted genomic enrichment of genes associated with deafness, followed by massively parallel sequencing. Lgn\n                        ΔC\n                         mice, with a targeted deletion truncating the C-terminal GoLoco motifs, are profoundly deaf and show misorientation of the hair bundle and severe malformations in stereocilia shape that deteriorates over time. Full-length protein levels are greatly reduced in mutant mice, with upregulated mRNA levels. The truncated Lgn\n                        ΔC\n                         allele is translated in vitro, suggesting that mutant mice may have partially functioning Lgn. Gαi and aPKC, known to function in the same pathway as Lgn, are dependent on Lgn for proper localization. The polarization of core PCP proteins is not affected in Lgn mutants; however, Lgn and Gαi are misoriented in a PCP mutant, supporting the role of Lgn as a PCP effector. The kinocilium, previously shown to be dependent on Lgn for robust localization, is essential for proper localization of Lgn, as well as Gαi and aPKC, suggesting that cilium function plays a role in positioning of apical proteins. 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