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Many small RNAs contribute essential activities to eukaryotic cells. In mammalian genomes dispersed repetitive sequences which exhibit homology to small RNAs often exist as pseudogenes which can complicate identification, localization, and analysis of the authentic gene. We mapped a productive human 7SK small nuclear RNA gene to human chromosome 6 by analyzing Northern blots derived from a panel of somatic cell hybrids that contain single human chromosomes. In order to avoid crossreactivity of the probe with rodent 7SK RNA, which is 98% identical to human 7SK, a method termed homolog exclusion probing was developed. This method uses an excess of non-labelled rodent-specific oligodeoxynucleotide to block the rodent 7SK RNA from hybridizing with the human-specific oligodeoxynucleotide probe. The effectiveness of this method to enhance the human 7SK RNA signal is demonstrated. The potential to map and subsequently isolate other small RNA genes by this approach and the use of homolog exclusion probing to discriminate among family members of highly related RNAs and DNAs in a single species is discussed.

The conserved 7SK snRNA gene localizes to human chromosome 6 by homolog exclusion probing of somatic cell hybrid RNA