Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

Chromosome 7q22 has been the focus of many cytogenetic and,molecular studie s aimed at delineating regions commonly deleted in myeloid leukemias and my elodysplastic syndromes. We have compared a gene-dense, CC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5, A physical map o f 640 kb of genomic DNA from mouse chromosome 5 was derived from a series o f overlapping bacterial artificial chromosomes, A 296 kb segment from the p hysical map, spanning Ache to Tfr2, was Compared with 267 kb of human seque nce. We identified a conserved linkage of 12 genes including an open readin g frame flanked by Ache and Asr2, a novel cation-chloride cotransporter int eracting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from-o ur comparative sequence analysis. Adjacent unfinished sequence data from th e mouse contains an orthologous block of 10 additional genes including thre e novel cDNA sequences that we subsequently mapped to human 7q22, Methods f or displaying; I comparative genomic information, including unfinished sequ ence data, are becoming increasingly:important. We supplement our printed c omparative analysis with a new, Web-based program called Laj (local alignme nts with java). Laj provides interactive access to archived pairwise sequen ce alignments via the WWW, It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://we b.uvic.ca/similar to bioweb/laj.html. Laj is available at http://bio.cse.ps u.edu/. along with online documentation and additional examples of annotate d genomic regions.