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. 2006 Jan 1;34(Database issue):D86-9.
doi: 10.1093/nar/gkj129.

DBTSS: DataBase of Human Transcription Start Sites, Progress Report 2006

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Free PMC article

DBTSS: DataBase of Human Transcription Start Sites, Progress Report 2006

Riu Yamashita et al. Nucleic Acids Res. .
Free PMC article

Abstract

DBTSS was first constructed in 2002 based on precise, experimentally determined 5' end clones. Several major updates and additions have been made since the last report. First, the number of human clones has drastically increased, going from 190,964 to 1,359,000. Second, information about potential alternative promoters is presented because the number of 5' end clones is now sufficient to determine several promoters for one gene. Namely, we defined putative promoter groups by clustering transcription start sites (TSSs) separated by <500 bases. A total of 8308 human genes and 4276 mouse genes were found to have putative multiple promoters. Third, DBTSS provides detailed sequence comparisons of user-specified TSSs. Finally, we have added TSS information for zebrafish, malaria and schyzon (a red algae model organism). DBTSS is accessible at http://dbtss.hgc.jp.

Figures

Figure 1
Figure 1
An example of alternative promoter view. Here we show AKAP1 (NM_003488) as an example. (A) The putative promoter clusters are given using different colors; therefore, there are three putative promoters in human AKAP1. We observed several patterns of first exon in promoter type 1, so we clustered them and show them as ‘First exon variant type A–F’. (B) Comparative analysis between human and mouse alternative promoters. There are two putative promoters in mouse. The best match between two promoters is available in ‘Promoter Comparison’. (C) Clicking the ‘Comparative View’, the user can obtain the alignment between these promoters.
Figure 2
Figure 2
An example of comparative analysis with any pair of TSSs. We show paralogous genes, protamine 1 (PRM1: NM_002761) and protamine 2 (PRM2: NM_002762), as an example. (A) By inputting the IDs of clones of PRM1 (TST01431) and PRM2 (TST00906) representative TSSs, users can obtain the results (B and C). (B) LALIGN analysis between two sequences. Note: smaller numbers indicate more highly conserved blocks. In this figure, the most conserved region between a pair is block 0; however, it includes Alu repeats. (C) The detail of the alignment of block 7. The putative TATA-boxes are marked with boxes.

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