A FASTA alignment (Pearson and Lipman 1988) between three EST clones associated with cDNA 37 and their corresponding genomic DNA (only 90 bp of the 3′ end of each EST are shown). (A) An authentic EST corresponding to the end of cDNA 37 that possesses a poly(A)+addition signal (AATAAA). Note that the poly(A) tail has not been completely trimmed. (B) An EST that is associated with the end of cDNA 37, but does not have a poly(A)+ addition signal and appears to have arisen by internal priming. The sequence starts 180 bp 5′ of the true end of the clone. Analysis of the sequence trace does not suggest that this sequence read was excessively trimmed to produce the 180-bp difference (data not shown). The underlined sequence immediately 3′ to the end of the alignment is an Alu sequence. (C) An EST that aligns to the intron of cDNA 37 and contains no poly(A)+addition signal (this EST sequence was edited from the available sequence traces files) The alignment begins 5 bp 5′ of a stretch of poly(A) (in italics). The underlined sequence represents anAlu sequence.
