Nucleic Acids Research, 1992, Vol. 20, No. 16 4255-4262
© 1992
MOLECULAR BIOLOGY |
Splicing signals in Drosophila: intron size, information content, and consensus sequences
Department of Biological Sciences, Columbia University New York, NY 10027 1Theoretical Biology and Biophysics Group, Los Alamos National Laboratory Los Alamos, NM 87545 2Depeartment of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, CO 80309 3Computing Research Laboratory Box 3000001/3CRL New Mexico State University Las Cruces, NM 8803-0001, USA
Received May 12, 1992. Accepted July 15, 1992.
A database of 209 Drosophila Introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing. A tight distribution of sizes was observed: while the smallest introns in the database are 51 nucleotides, more than half are less than 80 nucleotides in length, and most of these have lengths in the range of 59 – 67 nucleotides. Drosophila splice sites found in large and small introns differ in only minor ways from each other and from those found in vertebrate Introns. However, larger introns have greater pyrimidlne-richness in the region between 11 and 21 nucleotides upstream of 3' splice sites. The Drosophila branchpoint consensus matrix resembles C T A A T (in which branch formation occurs at the underlined A), and differs from the corresponding mammalian signal in the absence of G at the position immediately preceding the branchpoint. The distribution of occurrences of this sequence suggests a minimum distance between 5' splice shies and branchpoints of about 38 nucleotides, and a minimum distance between 3' splice sites and branchpoints of 15 nucleotides. The methods we have used detect no information in exon sequences other than in the few nucleotides immediately adjacent to the splice sites. However, Drosophila resembles many other species in that there is a discontinuity in A + T content between exons and introns, which are A + T rich.
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S. Kim, R. R. McKay, K. Miller, and R. D. Shortridge Multiple Subtypes of Phospholipase C Are Encoded by the norpA Gene of Drosophila melanogaster J. Biol. Chem., June 16, 1995; 270(24): 14376 - 14382. [Abstract] [Full Text] [PDF]
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R Singh, J Valcarcel, and M. Green Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins Science, May 26, 1995; 268(5214): 1173 - 1176. [Abstract] [PDF]
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M. Maroto, J. J. Arredondo, M. S. Román, R. Marco, and M. Cervera Analysis of the Paramyosin/Miniparamyosin Gene J. Biol. Chem., March 3, 1995; 270(9): 4375 - 4382. [Abstract] [Full Text] [PDF]
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S. M. Berget and S. M. Berget Exon Recognition in Vertebrate Splicing J. Biol. Chem., February 10, 1995; 270(6): 2411 - 2414. [Full Text] [PDF]
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G Mardon, N. Solomon, and G. Rubin dachshund encodes a nuclear protein required for normal eye and leg development in Drosophila Development, January 12, 1994; 120(12): 3473 - 3486. [Abstract] [PDF]
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 L.E. Martin-Morris, K. Loughney, E.O. Kershisnik, G. Poortinga, and S. Henikoff Characterization of Sequences Responsible for trans-Inactivation of the Drosophila brown Gene Cold Spring Harb Symp Quant Biol, January 1, 1993; 58(0): 577 - 584. [Abstract] [PDF]
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J. Y.-H. Chan, J. E. Lee-Prudhoe, B. Jorgensen, G. Ihrke, R. Doyonnas, A. C. W. Zannettino, V. J. Buckle, C. J. Ward, P. J. Simmons, and S. M. Watt Relationship between Novel Isoforms, Functionally Important Domains, and Subcellular Distribution of CD164/Endolyn J. Biol. Chem., January 12, 2001; 276(3): 2139 - 2152. [Abstract] [Full Text] [PDF]
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X. Morin, R. Daneman, M. Zavortink, and W. Chia A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila PNAS, December 18, 2001; 98(26): 15050 - 15055. [Abstract] [Full Text] [PDF]
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