Splicing and mouse-human conservation patterns for sense and antisense ESTs from UniGene cluster Hs.47313. The graph depicts the exon-intron splicing structures of transcript sequences belonging to UniGene cluster Hs.47313. SIM4  was used to map the exons of a single mRNA sequence (GenBank accession number NM_014785) and directionally cloned ESTs belonging to UniGene cluster Hs.47313 to genomic contig Hs9_28427_24 of the NCBI draft of the assembled human genome. The x-axis reflects base-pair positions along the genomic contig. Each position along the y-axis is assigned to a single EST or mRNA sequence. GenBank accession numbers are listed along with the UniLib ID of the library from which the EST was derived. Rectangular boxes indicate the locations of complete or partial exons. Individual exons of the BOU representative of this cluster (mRNA sequence NM_014785) are represented in blue and green, with annotated coding regions of the transcript shaded blue and untranslated regions shaded green. In this case, the mRNA is oriented from left to right with respect to the genomic contig. Immediately below the mRNA mapping, we have indicated the regions of the genome indicated to be highly conserved in HUMMUS , a set of around 1.15 million 'islands' of strong mouse-human conservation (in gold). The heights of individual bars in this row are proportional to the percent nucleotide identity over a 50-bp window centered on each base-pair. In the upper portion of the graph (all horizontal bars above the BOU mRNA sequence and HUMMUS rows), the exon mappings of sense ESTs are represented in yellow. In the lower portion of the graph (all horizontal bars below the BOU mRNA sequence and HUMMUS rows), exon mappings of antisense ESTs are represented in pink. Similar graphical representations for all 217 candidates (generated with GNUPLOT ) are available from our website . The sense transcript (represented by the mRNA and sense ESTs) encodes KIAA0258, a protein of unknown function. Not unexpectedly, there is a strong correlation between the locations of sense transcript exons and the peaks in the strength of mouse-human conservation. It is also evident that the antisense ESTs are spliced in a consistent pattern that differs significantly from that of the mRNA and sense ESTs. This strengthens the claim that these represent a distinct RNA species inadvertently co-clustered into a single UniGene cluster by virtue of an antisense overlap. Observed regions of sense-antisense overlap are restricted to the 3' UTR of the sense transcript. Also striking is the observation that the islands of conservation in the 3' UTR of the BOU mRNA are largely coincident with the positions of exons of the putative antisense transcript, providing at least a potential explanation for the conserved elements observed in the 3' UTR of the sense mRNA. In this case, the antisense mRNA species does have strong homology to a known protein, suggesting that it is also a coding mRNA.