Genomic annotation of the CDR of the 5q− syndrome.

(A) The CDR of the 5q− syndrome showing all known genes9,11-13 and novel genes predicted by Ensembl. (B) Table showing all known genes and novel (predicted) genes assigned to the CDR of the 5q− syndrome with the use of the Ensembl program and their expression profiling. Each of the Ensembl gene numbers shown is preceded by ENSG00000. Sequence data (comprising draft and finished sequence under the GenBank accession numbers shown) was obtained from a complete BAC tiling path from the CDR of the 5q− syndrome (http://www-gsd.lbl.gov/∼j_martin/ and LBNL) and analyzed by means of the Ensembl gene prediction program (http://www.ensembl.org/) for the presence of coding exons. The genes were predicted by the Ensembl analysis pipeline from either a GeneWise or a Genscan prediction followed by confirmation of the exons by comparisons with protein, cDNA, and EST databases (Ensembl v1.2.0 and previous versions). Genes identical to known human genes or protein sequences are referred to as known genes (shaded boxes); genes homologous to, or containing a region of similarity to, gene or protein sequences from human or other species or sequences homologous to only ESTs are referred to as novel genes. Expression profiling was performed on all known and novel genes by means of RT-PCR. Primers were designed to span at least one intron in all cases, and optimal conditions were determined for each primer pair. PBL indicates peripheral blood leukocyte. Expression status is indicated as follows: +, RT-PCR product obtained on at least 2 occasions; −, no RT-PCR product obtained on at least 2 occasions. Note that Ensembl genes 145870 (predicted) and 145906 (predicted) were shown to be positive for expression in human colon and prostate, respectively.