Gene structure and protein sequence of Rap1GAP2. A complete cDNA corresponding to KIAA1039 was cloned from platelet RNA encoding a protein most closely related to Rap1GAP. Consequently, the new protein was named Rap1GAP2. (A) Rap1GAP2 is expressed in 3 different splice variants. The originally cloned variant, a, is the predominant form in platelets. Rap1GAP2a lacks exons 1 and 6, Rap1GAP2b lacks only exon 1, and Rap1GAP2c (AK124640, cloned from cerebellum) is generated by the splicing of exon 2, resulting in the appearance of a new start codon within exon 3 (asterisk indicates start codons, including Kozak initiation sequences). ▪ indicates noncoding regions. Exon 26 comprises 4351 bp. To the right, the results of RT-PCR analysis of variant expression in platelets are shown. Only the splice variants Rap1GAP2a and Rap1GAP2b are detectable in human platelets. This experiment was performed twice with similar results. (B) Sequence comparison between Rap1GAP1 and Rap1GAP2 reveals a conserved Rap1GAP domain (solid line) and a putative GoLoco domain (dotted line). Differences between variants are marked in gray: the box in Rap1GAP1 marks additional sequences found only in the Rap1GAP1b/Rap1GAPII splice variant, the first N-terminal box in the Rap1GAP2 sequence is missing in variant c, the second box in Rap1GAP2 indicates additional sequences derived from exon 6, present only in Rap1GAP2b and Rap1GAP2c. Asterisks, double dots, and single dots indicate different degrees of amino acid conservation. (C) A phylogenetic tree of all presently known Rap1GAPs, including related uncharacterized cDNAs, shows Rap1GAP1 and Rap1GAP2 as distinct subgroups. Accession numbers of used amino acid sequences are presented in “Materials and methods.” Numbers at the branches represent the confidence limits computed by the bootstrap procedure. Bar indicates 0.1 substitutions per site.