Examination of sequence homology between human chromosome 20 and the mouse genome: Intense conservation of many genomic elements

Human Genetics

Volumn 113, Issue 1, 2003, Pages 60-70

  Zhu, Lingxiang ^a   Swergold, Gary D ^b   Seldin, Michael F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CHROMOSOME 2; CHROMOSOME 20; CHROMOSOME ARM; CODING; COMPARATIVE STUDY; CONSERVATION GENETICS; CONTROLLED STUDY; EVOLUTIONARY HOMOLOGY; EXON; GENOME ANALYSIS; HUMAN; HUMAN CELL; INTRON; MAMMAL; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES COMPARISON; STRUCTURE ANALYSIS; TELOMERE; ANIMAL; BIOLOGICAL MODEL; EVOLUTION; GENETICS; GENOME; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; UNTRANSLATED REGION;

MAMMALIA;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, HUMAN, PAIR 20; CONSERVED SEQUENCE; EVOLUTION; EXONS; GENOME; HUMANS; INTRONS; MICE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; UNTRANSLATED REGIONS;

EID: 0038609020     PISSN: 03406717     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00439-003-0920-x     Document Type: Article

References (25)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. Boissinot S, Entezam A, Furano AV (2001) Selection against deleterious LINE-1-containing loci in the human lineage. Mol Biol Evol 18:926-35
3. Burge C, Karlin S (1977) Prediction of complete gene structures in human genomic. DNA J Mol Biol 268:78-94
4. DeBry RW, Seldin MF (1996) Human/mouse homology relationships. Genomics 33:337-351
5. Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S, Land M, Terry A, Zhou CLE, Rash S, Zhang Q, Gordon L, Kim J, Elkin C, Pollard MJ, Richardson P, Rokhsar D, Uberbacher E, Hawkins T, Branscomb E, Stubbs L (2001) Human chromosome 19 and related regions in mouse: Conservative and LINEage-specific evolution. Science 293:104-111
6. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome Nature 409: 860-921
7. Lundin, LG (1993) Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16:1-19
8. Makalowski W, Boguski, MS (1998) Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci USA 95:9407-9412
9. Makalowski W, Zhang J, Boguski MS (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Res 6:846-57
10. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562
11. Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, Deng Z, Evangelista CC, Gan W, Heiman TJ, Li J, Li Z, Merkulov GV, Milshina NV, Naik AK, Qi R, Shue BC, Wang A, Wang J, Wang X, Yan X, Ye J, Yooseph S, Zhao Q, Zheng L, Zhu SC, Biddick K, Bolanos R, Delcher AL, Dew IM, Fasulo D, Flanigan MJ, Huson DH, Kravitz SA, Miller JR, Mobarry CM, Reinert K, Remington KA, Zhang Q, Zheng XH, Nusskern DR, Lai Z, Lei Y, Zhong W, Yao A, Guan P, Ji RR, Gu Z, Wang ZY, Zhong F, Xiao C, Chiang CC, Yandell M, Wortman JR, Amanatides PG, Hladun SL, Pratts EC, Johnson JE, Dodson KL, Woodford KJ, Evans CA, Gropman B, Rusch DB, Venter E, Wang M, Smith TJ, Houck JT, Tompkins DE, Haynes C, Jacob D, Chin SH, Allen DR, Dahlke CE, Sanders R, Li K, Liu X, Levitsky AA, Majoros WH, Chen Q, Xia AC, Lopez JR, Donnelly MT, Newman MH, Glodek A, Kraft CL, Nodell M, Ali F, An HJ, Baldwin-Pitts D, Beeson KY, Cai S, Carnes M, Carver A, Caulk PM, Center A, Chen YH, Cheng ML, Coyne MD, Crowder M, Danaher S, Davenport LB, Desile s R8 Dietz SM, Doup L, Dullaghan P, Ferriera S, Fosler CR, Gire HC, Glueclosmann A, Gocayne JD, Gray J, Hart B, Haynes J, Hoover J, Howland T, Ibegwam C,!Jalali M, Johns D, Kline L, Ma DS, MacCawley S, Magoon A, Mann F, May D, McIntosi TC, Mehta S, Moy L, Moy MC, Murphy BJ, Murphy SD, Nelson KA, Nuri Z, Parker KA- Prudhomme AC, Puri VN, Qureshi H, Raley JC, Reardon MS, Regier MA, Rogers YH,!Romblad DL, Schutz J, Scott JL, Scott R, Sitter CD, Smallwood M, Sprague AC, Suewart E, Strong RV, Suh E, Sylvester K, Thomas R, Tint NN, Tsonis C, Wang G,!Wang G, Williams MS, Williams SM, Windsor SM, Wolfe K, Wu MM, Zaveri J, Chatvrvedi K, Gabrielian AE, Ke Z, Sun J, Subramanian G, Pfannkoch CM, Branstead M- Stephenson LD, Vender JC (2002) A comparison of whole-genome shotgun-derived nouse chromosome 16 and the human genome. Science 31:296:1661-1671
12. Murphy WJ, Sun S, Chen Z, Yuhki N, Hirschmann D, Menottio Raymond M, O'Brien SJ (2000) A radiation hybrid map of the cat genome: Implications for comparative mapping. Genome Res 10:691-702
13. Murphy WJ, Stanyon R, O'Brien SJ (2001) Evolution of mammalian genome organization inferred from comparative gene mapping. Genome Biol 2:5
14. Nadeau JH, Sankoff D (1998) The lengths of undiscovered conserved segments in comparative maps. Mamm Genome 9:491-495
15. Nadeau JH, Davisson MT, Doolittle DP, Grant P, Hillyard AL, Kosowsky M, Roderick TH (1991) Comparative map for mice and humans. Mamm Genome 1:S461-S515
16. Needleman S, Wunsch C (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J Mol Biol 48:443-453
17. O'Brien SJ, Womack JE, Lyons LA, Moore KJ, Jenkins NA, Copeland NG (1993) Anchored reference loci for comparative genome mapping in mammals. Nat Genet 3:103-112
18. Ovchinnikov I, Troxel AB, Swergold GD (2001) Genomic characterization of recent human LINE-1 insertions: Evidence supporting random insertion. Genome Res 11:2050-2058
19. Schibler L, Vaiman D, Oustry A, Giraud-Delville C, Cribiu, EP (1998) Comparative gene mapping: A fine-scale survey of chromosome rearrangements between ruminants and humans. Genome Res 8:901-915
20. Schughart K, Kappen C, Ruddle FH (1989) Duplication of large genomic regions during the evolution of vertebrate homeobox genes. Proc Natl Acad Sci USA 86:7067-7071
21. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker - A web server for aligning two genomic DNA sequences. Genome Res 10:577-86
22. Seldin MF, Saunders AM, Rochell JM, Howard TA (1991) A proximal mouse chromosome 9 linkage map that further defines linkage groups homologous with segments of human chromosomes 11, 15, and 19. Genomics 9:678-685
23. Smit AFA (1993) Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res 21:1863-1872
24. Smit AFA (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Devel 9:657-663
25. Smit AFA, Toth G, Riggs AD, Jurka J (1995) Ancestral, mammalian wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 246:401-417