AluGene: A database of Alu elements incorporated within protein-coding genes

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Dagan, Tal ^a   Sorek, Rotem ^a,b   Sharon, Eilon ^a   Ast, Gil ^a   Graur, Dan ^a,c  

^a TEL AVIV UNIVERSITY   (Israel)

^b Compugen ^*  (Israel)

^c University of Houston   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALU SEQUENCE; ALUGENE; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; EXON; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCATION; GENE STRUCTURE; GENETIC CODE; HUMAN; INFORMATION PROCESSING; INFORMATION SYSTEM; INTRON; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE DATABASE; SHORT INTERSPERSED REPEAT;

ALU ELEMENTS; BASE COMPOSITION; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EXONS; GENES; GENOME, HUMAN; GENOMICS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; INTRONS; MOLECULAR SEQUENCE DATA; PROTEINS; RNA SPLICE SITES; SOFTWARE;

EID: 0347125202     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (18)

1. Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C., Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
2. Mighell,A.J., Markham,A.F. and Robinson,P.A. (1997) Alu sequences. FEBS Lett., 417, 1-5.
3. Kapitonov,V. and Jurka,J. (1996) The age of Alu subfamilies. J. Mol. Evol., 42, 59-65.
4. Lev-Maor,G., Sorek,R., Shomron,N. and Ast,G. (2003) The birth of an alternatively spliced exon: 3′ splice-site selection in Alu exons. Science, 300, 1288-1291.
5. Nekrutenko,A. and Li,W.H. (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet., 17, 619-621.
6. Sorek,R., Ast,G. and Graur,D. (2002) Alu-containing exons are alternatively spliced. Genome Res., 12, 1060-1067.
7. Vervoort,R., Gitzelmann,R., Lissens,W. and Liebaers,I. (1998) A mutation (IVS8+0.6kbdeITC) creating a new donor splice site activates a cryptic exon in an Alu-element in intron 8 of the human β-glucuronidase gene. Hum. Genet., 103, 686-693.
8. Ganguly,A., Dunbar,T., Chen,P., Godmilow,L. and Ganguly,T. (2003) Exon skipping caused by an intronic insertion of a young Alu Yb9 element leads to severe hemophilia A. Hum. Genet., 113, 348-352.
9. Ricci,V., Regis,S., Di Duca,M. and Filocamo,M. (2003) An Alu-mediated rearrangement as cause of exon skipping in Hunter disease. Hum. Genet., 112, 419-425.
10. Hilgard,P., Huang,T., Wolkoff,A.W. and Stockert,R.J. (2002) Translated Alu sequence determines nuclear localization of a novel catalytic subunit of casein kinase 2. Am. J. Physiol. Cell Physiol., 283, C472-C483.
11. Le Goff,W., Guerin,M., Chapman,M.J. and Thillet,J. (2003) A CYP7A promoter binding factor site and Alu repeat in the distal promoter region are implicated in regulation of human CETP gene expression. J. Lipid Res., 44, 902-910.
12. Yi,P., Zhang,W., Zhai,Z., Miao,L., Wang,Y. and Wu,M. (2003) Bcl-rambo β, a special splicing variant with an insertion of an Alu-like cassette, promotes etoposide- and Taxol-induced cell death. FEBS Lett., 534, 61-68.
13. Makalowski,W. (2003) Not junk after all. Science, 300, 1246-1247.
14. Grover,D., Majumder,P.P., Rao,C.B., Brahmachari,S.K. and Mukerji,M. (2003) Non-random distribution of Alu elements in genes of various functional categories: Insight from analysis of human chromosomes 21 and 22. Mol. Biol. Evol., 20, 1420-1424.
15. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
16. Roy-Engel,A.M., Salem,A.H., Oyeniran,O.O., Deininger,L., Hedges,D.J., Kilroy,G.E., Batzer,M.A. and Deininger,P.L. (2002) Active Alu element 'A-tails': Size does matter. Genome Res., 12, 1333-1344.
17. Jurka,J., Krnjajic,M., Kapitonov,V.V., Stenger,J.E. and Kokhanyy,O. (2002) Active Alu elements are passed primarily through paternal germlines. Theor. Popul. Biol., 61, 519-530.
18. Horowitz,D.S. and Krainer,A.R. (1994) Mechanisms for selecting 5′ splice sites in mammalian pre-mRNA splicing. Trends Genet., 10, 100-106.