Figure 3

Comparative analysis of presynaptic genes. (a) Gene names from SynapseDB were used to query RefSeq and ENSEMBL transcript annotations, which were then clustered into gene models defined as groups of overlapping transcripts in the same orientation. The region around the synaptic gene model was extended up to the next annotated upstream and downstream gene models to define gROIs. MCEs were selected and characterized based on their relative genic position into exon-associated and non-exon-associated elements. Exon-associated elements were further subdivided into those that are completely exonic, those that are partially exonic and span exon-intron boundries, and those associated with UTRs; whereas non-exon-associated elements were divided into those that are intergenic and those that are intronic. (b) Individual bases were annotated as CDS, UTR sequence (UTR), intronic (intron), or intergenic (inter) based on gene model annotations. The coverage of MCEs (the proportion of most conserved bases in a gROI) across different annotations is shown. (c) The composition of MCEs (the proportion of MCEs with a given annotation) across CDS, UTR, intronic, and intergenic annotations is shown. CDS, coding sequence; gROI, genomic region of interest; MCR, most conserved element; UTR, untranslated region.