Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression

Pavel V Baranov¹^,2 , Andrew W Hammer¹ , Jiadong Zhou¹^,3 , Raymond F Gesteland¹ and John F Atkins¹^,2

¹Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA

²Bioscience Institute, University College Cork, Cork, Ireland

³Current address: Gene Technology Division, Nitto Denko Technical Corporation, 401 Jones Road, Oceanside, CA 92054, USA

author email corresponding author email

Genome Biology 2005, 6:R25doi:10.1186/gb-2005-6-3-r25


Published:	15 February 2005

Subject areas: Molecular biology, Microbiology and parasitology, Genetics

Additional files

Additional File 1:

Numbers of occurrences of A and T runs in bacterial genomes. Column A is used for the names of analyzed files and row 1 indicates the length of A/T run. Sheet 'whole genomes' corresponds to occurrences in entire genomes, sheet 'coding sequences' corresponds to occurrences in coding regions and sheet 'ATRatio' corresponds to the ratio between these numbers

Format: XLS Size: 122KB Download file

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Additional File 2:

Information about genes where 9A or 9T patterns were found. These genes correspond to the pool of genes selected for comparative analysis. The table contains representatives from 98 gene groups selected in step 4 of the scheme in Figure 3. Column A is used for accession numbers. B is for coordinates of the corresponding gene. C indicates whether it is a run of A or T in a sense strand. D shows the functional status of a gene. The functional status is annotated by text and by color. The red color is used for genes with potential positive role of transcriptional slippage, blue is for those where there is no positive functional role, green is for genes where transcriptional slippage might restore a disrupted ORF and grey is used for ORFans, where functional status cannot be assessed. Column E contains nucleotide sequences of mRNAs produced via transcriptional slippage with ORFs longer than those in the original DNA templates. Column F contains the corresponding protein sequences

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