Splicing signals inDrosophila: intron size, information content, and consensus sequences

Abstract

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 pyrimidine-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 sites 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.

A primordial dopamine D1‐like adenylyl cyclase‐linked receptor from Drosophila melanogaster displaying poor affinity for benzazepines

“…Consensus sequences for 3' and 5' splice sites were present in this fragment before and after the small coding region [33]. Due to the presence of introns, a PstI-ClaI 250 bp coding fragment was used to screen a Drosophila adult head cDNA library.…”

Multiple products from the shavenbaby-ovo gene region of Drosophila melanogaster: relationship to genetic complexity.

“…Second, we identified an additional G following position 4283. Although the published sequence (23) (24), N is any nucleotide at the indicated position and y is either pyrimidine at the indicated position. Note also that exon la is found in its entirety at the 5' end of one of the cDNA clones isolated from the 0-to 4-h embryonic cDNA library.…”

Isolation, characterization and expression of the eclosion hormone gene of Drosophila melanogaster

“…This region was identical in both classes of subclones, and potentially encodes an open reading frame which has 68% amino acid identity (34/50) to the corresponding sequence of Manduca EH (78% similar if conservative substitutions are allowed). The DNA sequence spanning the 5' limit of similarity between the Munduca and Drosophila sequences resembled that of a splice acceptor site [37], indicating that DNA encoding the N-terminus of the peptide is located on an upstream exon. The genomic clone that contained the most upstream sequence (AG2) was analyzed further, and the sequence of 7.1 kb upstream from the splice junction was determined (Fig.…”