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Some broad core promoters exhibit properties of both narrow and broad initiation patterns where they exhibit propensity for one TSS.
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The RefSeq database annotates one TSS for CDKL5 in mouse and two TSSs in human (Additional file 2: Table S2).
TSSs belonging to annotated genes were further categorized into 1,264 single TSSs (a single TSS per gene) and 890 multiple TSSs (more than one TSS per gene), the latter occurring at 365 genes.
Where more than two TSS candidates coexisted within 100-bp either up- or downstream of the TSS, they were counted as one TSS candidate.
For a gene that had more than one TSS identified (e.g., from other libraries), only the TSS furthest away from the start codon was used for analysis.
For genes with more than one TSS, the upstream sequence of the respective gene was only included once in the analysis.
This identified 1126 ESTs with at least one TSS that was predicted to be a binding site for a known, new or one of the 19 23 nt siRNAs.
We classified these genes into three primary groups (genes with one isoform and one TSS; genes with more than one isoform and one TSS; and genes with more than one isoform and more than one TSS) (Fig. 6a and b).
Investigation of the most highly expressed genes revealed that most have more than one TSS with one or two more preferred TSSs.
Experimentally annotated transcription start sites (TSSs) using CAGE data from the FANTOM 5 project (41) show that nearly all eCGIs (98.1%) harbor at least one TSS.
Hence, in comparing our TSS data to published reports, we identified 45 genes with multiple TSS, where just one TSS had been reported before (Additional file 2: Table S5).
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