Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blocker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowski J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.
Article
CAS
PubMed
Google Scholar
Goodier JL, Ostertag EM, Du K, Kazazian HH: A novel active L1 retrotransposon subfamily in the mouse. Genome Res. 2001, 11: 1677-1685. 10.1101/gr.198301.
Article
CAS
PubMed Central
PubMed
Google Scholar
Penzkofer T, Dandekar T, Zemojtel T: L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res. 2005, 33: D498-500. 10.1093/nar/gki044.
Article
CAS
PubMed Central
PubMed
Google Scholar
Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH: Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A. 2003, 100: 5280-5285. 10.1073/pnas.0831042100.
Article
CAS
PubMed Central
PubMed
Google Scholar
DeBerardinis RJ, Goodier JL, Ostertag EM, Kazazian HH: Rapid amplification of a retrotransposon subfamily is evolving the mouse genome. Nat Genet. 1998, 20: 288-290. 10.1038/3104.
Article
CAS
PubMed
Google Scholar
Han JS, Szak ST, Boeke JD: Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature. 2004, 429: 268-274. 10.1038/nature02536.
Article
CAS
PubMed
Google Scholar
Han JS, Boeke JD: LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?. Bioessays. 2005, 27: 775-784. 10.1002/bies.20257.
Article
CAS
PubMed
Google Scholar
Matlik K, Redik K, Speek M: L1 antisense promoter drives tissue-specific transcription of human genes. J Biomed Biotechnol. 2006, 2006: 71753-
Article
PubMed Central
PubMed
Google Scholar
Speek M: Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol Cell Biol. 2001, 21: 1973-1985. 10.1128/MCB.21.6.1973-1985.2001.
Article
CAS
PubMed Central
PubMed
Google Scholar
Nigumann P, Redik K, Matlik K, Speek M: Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics. 2002, 79: 628-634. 10.1006/geno.2002.6758.
Article
CAS
PubMed
Google Scholar
Perepelitsa-Belancio V, Deininger P: RNA truncation by premature polyadenylation attenuates human mobile element activity. Nat Genet. 2003, 35: 363-366. 10.1038/ng1269.
Article
CAS
PubMed
Google Scholar
Narita N, Nishio H, Kitoh Y, Ishikawa Y, Minami R, Nakamura H, Matsuo M: Insertion of a 5' truncated L1 element into the 3' end of exon 44 of the dystrophin gene resulted in skipping of the exon during splicing in a case of Duchenne muscular dystrophy. J Clin Invest. 1993, 91: 1862-1867.
Article
CAS
PubMed Central
PubMed
Google Scholar
Nekrutenko A, Li WH: Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001, 17: 619-621. 10.1016/S0168-9525(01)02445-3.
Article
CAS
PubMed
Google Scholar
Li WH, Gu Z, Wang H, Nekrutenko A: Evolutionary analyses of the human genome. Nature. 2001, 409: 847-849. 10.1038/35057039.
Article
CAS
PubMed
Google Scholar
Belancio VP, Hedges DJ, Deininger P: LINE-1 RNA splicing and influences on mammalian gene expression. Nucleic Acids Res. 2006, 34: 1512-1521. 10.1093/nar/gkl027.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kim DS, Kim TH, Huh JW, Kim IC, Kim SW, Park HS, Kim HS: LINE FUSION GENES: a database of LINE expression in human genes. BMC Genomics. 2006, 7: 139-10.1186/1471-2164-7-139.
Article
PubMed Central
PubMed
Google Scholar
Perou CM, Pryor RJ, Naas TP, Kaplan J: The bg allele mutation is due to a LINE1 element retrotransposition. Genomics. 1997, 42: 366-368. 10.1006/geno.1997.4740.
Article
CAS
PubMed
Google Scholar
L1Base. [http://l1base.molgen.mpg.de]
DeBerardinis RJ, Kazazian HH: Analysis of the promoter from an expanding mouse retrotransposon subfamily. Genomics. 1999, 56: 317-323. 10.1006/geno.1998.5729.
Article
CAS
PubMed
Google Scholar
Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene. 1999, 238: 115-134. 10.1016/S0378-1119(99)00227-9.
Article
CAS
PubMed
Google Scholar
Breathnach R, Chambon P: Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem. 1981, 50: 349-383. 10.1146/annurev.bi.50.070181.002025.
Article
CAS
PubMed
Google Scholar
L1Exon. [http://l1base.molgen.mpg.de/l1exon]
Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G: Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol. 2007, 8: R127-10.1186/gb-2007-8-6-r127.
Article
PubMed Central
PubMed
Google Scholar
Wheelan SJ, Aizawa Y, Han JS, Boeke JD: Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution. Genome Res. 2005, 15: 1073-1078. 10.1101/gr.3688905.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, Kannouche P, Wider G, Peter M, Lehmann AR, Hofmann K, Dikic I: Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science. 2005, 310: 1821-1824. 10.1126/science.1120615.
Article
CAS
PubMed
Google Scholar
Krull M, Brosius J, Schmitz J: Alu-SINE exonization: en route to protein-coding function. Mol Biol Evol. 2005, 22: 1702-1711. 10.1093/molbev/msi164.
Article
CAS
PubMed
Google Scholar
Krull M, Petrusma M, Makalowski W, Brosius J, Schmitz J: Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). Genome Res. 2007
Google Scholar
Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T: Can an arbitrary sequence evolve towards acquiring a biological function?. J Mol Evol. 2003, 56: 162-168. 10.1007/s00239-002-2389-y.
Article
CAS
PubMed
Google Scholar
Fellenberg F, Hartmann TB, Dummer R, Usener D, Schadendorf D, Eichmuller S: GBP-5 splicing variants: New guanylate-binding proteins with tumor-associated expression and antigenicity. J Invest Dermatol. 2004, 122: 1510-1517. 10.1111/j.0022-202X.2004.22613.x.
Article
CAS
PubMed
Google Scholar
Nguyen TT, Hu Y, Widney DP, Mar RA, Smith JB: Murine GBP-5, a new member of the murine guanylate-binding protein family, is coordinately regulated with other GBPs in vivo and in vitro. J Interferon Cytokine Res. 2002, 22: 899-909. 10.1089/107999002760274926.
Article
CAS
PubMed
Google Scholar
Yeo G, Hoon S, Venkatesh B, Burge CB: Variation in sequence and organization of splicing regulatory elements in vertebrate genes. Proc Natl Acad Sci U S A. 2004, 101: 15700-15705. 10.1073/pnas.0404901101.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chen J, Rattner A, Nathans J: Effects of L1 retrotransposon insertion on transcript processing, localization and accumulation: lessons from the retinal degeneration 7 mouse and implications for the genomic ecology of L1 elements. Hum Mol Genet. 2006, 15: 2146-2156. 10.1093/hmg/ddl138.
Article
CAS
PubMed
Google Scholar
Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV: Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol. 2001, 21: 1429-1439. 10.1128/MCB.21.4.1429-1439.2001.
Article
CAS
PubMed Central
PubMed
Google Scholar
Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y: Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet. 2006, 2: e62-10.1371/journal.pgen.0020062.
Article
PubMed Central
PubMed
Google Scholar
Kent WJ: BLAT--the BLAST-like alignment tool. Genome Res. 2002, 12: 656-664. 10.1101/gr.229202. Article published online before March 2002.
Article
CAS
PubMed Central
PubMed
Google Scholar
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Graf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ: Ensembl 2006. Nucleic Acids Res. 2006, 34: D556-61. 10.1093/nar/gkj133.
Article
CAS
PubMed Central
PubMed
Google Scholar
NCBI Nucleotide Database. [http://www.ncbi.nlm.nih.gov]
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Ostell J, Miller V, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E: Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2007, 35: D5-12. 10.1093/nar/gkl1031.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16: 276-277. 10.1016/S0168-9525(00)02024-2.
Article
CAS
PubMed
Google Scholar
Schichman SA, Adey NB, Edgell MH, Hutchison CA: L1 A-monomer tandem arrays have expanded during the course of mouse L1 evolution. Mol Biol Evol. 1993, 10: 552-570.
CAS
PubMed
Google Scholar
PHP. [http://www.php.net]
MySQL. [http://www.mysql.com]
Eddy SR: Multiple alignment using hidden Markov models. Proc Int Conf Intell Syst Mol Biol. 1995, 3: 114-120.
CAS
PubMed
Google Scholar