Identification and Mapping of Paralogous Genes on a Known Genomic DNA Sequence

The completion of whole genome sequencing projects offers the opportunity to exam-ine the organization of genes and the discovery of evolutionarily related genes in a given species. For the beginners in the field, through a specific example, this chapter provides a step-by-step procedure for identifying paralogous genes, using the genome browser at UCSC (http://genome.ucsc.edu/). The example describes identification and mapping in the human genome, the paralogs of TCF12/HTF4. The example identifies TCF3 and TCF4 as paralogs of the TCF12/HTF4 gene. The example also identifies a related sequence, cor-responding to a pseudogene, in one of the introns of the JAK2 gene. The procedure described should be applicable to the discovery and creation of maps of paralogous genes in the gen-omic DNA sequences that are available at the genome browser at UCSC.