Potentially expressed RPCs. RPCs were masked and used in a BLAST search against the mRNA and EST databases. (A) HMGA1 RPC lacking exon 2 (vertical line) and with a 33-bp insertion (stippled box) harbors an ORF (red arrow) similar to HMGA1 CDS with an insertion (embedded stippled line) and a premature stop codon (asterisk), as well as one EST (represented by a thin black arrow). (Gray arrow) The CDS of HMGA1. (B) An HMGA1 PS with a 500-bp deletion (vertical line) encodes exons shared with an alternatively spliced mRNA (NM_052844; thin blue arrow) through ESTs (thin black arrows); (dotted lines) introns in transcribed sequence. The HMG insertion ends with poly(A); however, it is internal to the HMGA1 transcript. (C) HMGB1 RPC has an ORF (thick black arrow) in an opposite orientation to EST AW270920, and another ORF (thick red arrow) similar to HMG CDS. (D) An HMGN1 RPC has an ORF within EST AL138207 (thick black arrow) that is not similar to the HMGN1 CDS, and encodes an exon shared with an alternatively spliced mRNA (NM_023071; thin blue arrow) through ESTs. EST AA584308 is part of UniGene cluster Hs.152982. (E) An HMGN2 RPC has an ORF similar to HMG CDS (thick red arrow) and three ESTs in the same orientation. (F) An HMGN2 RPC in the 3′-UTR of cDNA AB037814 provides an alternative poly(A) signal (downward-pointing arrow). ESTs illustrate the use of both signals; a + after EST BF055348 stands for more ESTs at the same position. The gene structure of AB037814 was derived from an alignment with genomic DNA. (Green arrows) Monkey and mouse mRNA sequences similar to AB037814 that do not include an HMG sequence; the black part of the mouse DNA represents nonaligning sequence; (hatched box) a sequence of repetitive elements; (open triangles) TSDs, TSD sequences appear in the inserts, nucleotides in green represent ambiguity; (AAA) poly(A) tracts; (downward-pointing arrowheads) poly(A) signals; (upward-pointing arrowheads) splice sites; (thick arrows) ORFs or CDSs: The position of the HMG CDS is depicted in gray; ORFs similar to HMG CDS are red; ORFs not similar to HMG CDS are black, and CDSs outside the RPC region are blue. (Dotted lines) Intron positions in transcripts; (lines between the boxes) introns in genomic DNA; 3′ EST orientation is reversed to presumed sense; not drawn to scale.