Skip to main content
. 2007 Jun;17(6):720–731. doi: 10.1101/gr.5716607

Figure 5.

Figure 5.

Classification of validated promoters with respect to the nearest GENCODE-annotated gene. Exons are indicated by boxes and arrows indicate the 5′ to 3′ direction. (A) (1) Known: the promoter appears within 1 kb upstream of the first exon of any variant of the gene and the transcribed strand is the same as the gene. In case of RACE, the sequence, if spliced, should match the gene splice sites. (2) Pseudogene: like known, but the gene is a pseudogene. (3) 5′-Exon anti-sense: The promoter is within 1 kb of the first exon of some variant of the gene and the transcription is anti-sense to the gene. The transcripts if not present or if short, should at least have a reasonable potential to overlap the exon. (4) 3′-Exon anti-sense: like 5′-exon anti-sense but for the last exon of some variant. (5) Internal exon anti-sense: like 5′-exon anti-sense but for an internal exon. (6) Intron embedded (sense): The promoter overlaps the gene span and transcription is on the same strand as the gene, but the transcripts do not appear to interact with any exons from any variant. (7) Intron embedded (anti-sense): like (5) but for anti-sense direction. (8) New TSS or variant: Transcription is on the same strand as the gene, and the transcribed product overlaps one or more exons of some variant but does not share the same splice sites. (9) Immediate downstream: The promoter is within 2 kb downstream of the last exon and transcription is on the same strand, but the transcripts do not overlap any exons of any variant of the gene. (10) Immediate upstream: The promoter is within 2 kb upstream of the first exon and transcription is on the opposite strand and the transcripts cannot overlap with the first exon of any variant. (11) Intergenic: >2 kb away from any annotated transcript. (B) The 41 regions validated by transient transfection assays. The total number of cases is 48, as some classes (notably intron embedded) can be interpreted as other classes (e.g., new TSS or anti-sense). (C) The 49 regions validated by 5′-RACE. The total number of cases is 59.