General features of an mRNA transcript as visualized by RNA-seq. This figure shows RNA-seq read coverage plots and individual reads for platelet GP9 mRNA as it appears (ie, with introns removed) in the platelet (A) or as viewed along genomic coordinates in a genome browser (B). The blue annotations along the bottom are the consensus RefSeq annotations of the gene structure. Individual exons are represented by the blue bars, and introns (only in panel B) by the connecting blue lines. The thicker regions of the bars distinguish the coding region from the 5′ and 3′ untranslated regions (UTRs). Arrows indicate the strand orientation (forward [+] or reverse [−]) of the annotation. For GP9, there are 3 exons and 2 introns. In GP9, the 5′ UTR ends just beyond the start of the third exon (at the ATG start codon of the coding region), and the 3′ UTR starts near the end of the third exon (after the TAA stop codon). Above the annotation are the individual reads that align to the transcript. For simplicity, not all reads are shown here. For visualization purposes, the individual reads are colored according to the exon to which they align. Above the reads is the read coverage map. This is generated by plotting the sums of mapped reads that overlap (cover) each nucleotide position along the genomic coordinates (x-axis). The y-axis represents the number of reads. The examples are as illustrated in Integrated Genome Viewer.²²  See it yourself: To see GP9 in platelets via the UCSC Genome Browser, follow the Web link > access instructions for site 1 (see Table 1). For individual reads, follow the Web link > access instructions for site 2 (see Table 1). Search for GP9 in the browser.