Highly conserved G runs, G1M2 and ISE, regulate the proteolipid protein (PLP)/DM20 ratio. We have investigated recruitment of U1 small nuclear ribonuclear protein (snRNP) by G1M2 and ISE and examined the effect of splice site strength, distance, and context on G run function. G1M2 is necessary for initial recruitment of U1snRNP to the DM20 5 splice site independent of the strength of the splice site. G1M2 regulates E complex formation and supports DM20 splicing when functional U1snRNP is reduced. By contrast, the ISE is not required for the initial recruitment of U1snRNP to the PLP 5 splice site. However, in close proximity to either the DM20 or the PLP 5 splice site, the ISE recruits U1snRNP to both splice sites. The ISE enhances DM20 splicing, whereas close to the PLP 5 splice site, it inhibits PLP splicing. Splicing enhancement and inhibition are mediated by heterogeneous nuclear ribonuclear protein (hnRNP)H/F. The data show that recognition of the DM20 5 splice site depends on G run-mediated recruitment of U1snRNA, whereas a complex interaction between the ISE G runs, context and position determines the functional outcome on splicing. The data suggest that different mechanisms underlie G run-mediated recognition of 5 splice sites and that context and position play a critical role.Alternative splicing is broadly utilized to generate multiple protein isoforms from a single transcript in a cell-and development-dependent fashion. Genome-wide analyses have shown that alternatively spliced sites are generally weak and that flanking regulatory sequences orchestrate their selection through the interaction with auxiliary splicing factors (for review, see Refs. 1 and 2).Removal of introns from pre-mRNAs takes place within the spliceosome, a ribonuclear complex of RNA, and proteins whose assembly occurs in a stepwise fashion (reviewed in Refs. 3-5). The first step is the formation of the commitment complex, or E complex, that contains the U1snRNP bound to the 5Ј splice site, U2AF bound to the 3Ј acceptor site and at least one member of the SR (serine arginine) proteins. The second step is the formation of the prespliceosome, termed complex A, characterized by the ATP-dependent addition of U2 snRNP. Next, U1 snRNP is replaced by U5 and U6 snRNPs, which base pair with the 5Ј splice site, and the splicing reaction is completed (6, 7).U1snRNP is composed of the U1snRNA, U1-specific proteins (U1 70K, U1A, and U1C), and general Sm spliceosomal proteins that are also present in the U2, U5, and U6 snRNP complexes (8). The recognition of the 5Ј splice site by the RNA moiety of the U1snRNP, through direct base pairing between the 5Ј end of the U1snRNA and the 5Ј splice site of the pre-RNA, commits the pre-RNA to splicing. However, in some genes, interactions other than direct base pairing of the U1snRNA with the 5Ј splice site contribute significantly to the first step of splicing, and removal of the first 7 nucleotides of the U1snRNA does not prevent formation of the E complex (9 -11). G runs, of which the G triplet is the basi...