Open Access Highly Accessed Research article

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes

Albin Sandelin1, Peter Bailey2, Sara Bruce13, Pär G Engström1, Joanna M Klos2, Wyeth W Wasserman4, Johan Ericson2* and Boris Lenhard1*

Author Affiliations

1 Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden

2 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden

3 Department of Biosciences at Novum, Karolinska Institutet, Stockholm, Sweden

4 Centre for Molecular Medicine, Department of Medical Genetics, University of British Columbia, Vancouver, Canada

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BMC Genomics 2004, 5:99  doi:10.1186/1471-2164-5-99

Published: 21 December 2004

Additional files

Additional File 1:

Genescape around 50 randomly selected UCRs. Selected UCRs are shown as yellow triangles, other UCRs as light yellow triangles. Genes are colored after domain (red = Homeobox, green = C2H2 Zink fingers in green, pink = Nuclear receptors, Blue = forkhead).

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Additional File 2:

Genescape around 50 randomly selected genes. UCRs are shown as as light yellow triangles. Color coding of genes as above.

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Additional File 3:

Complete list of protein domains in genes flanking UCRs. Each tested domain is listed along with corrected and uncorrected P-value as in Table 1.

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Additional File 4:

Complete list of protein domains in genes with UCR(s) in intron(s) Each tested domain is listed along with corrected and uncorrected P-value as in Table 1.

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Additional File 5:

UCR distribution in the human genome UCR density (pink) and gene density (blue) is shown for each chromosome. Densities are calculated as described in Methods.

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Additional File 6:

Genes associated with enumerated UCR clusters from Figure 3. UCRs were counted by sliding a 500 kb window along the chromosomes. Overlapping UCR-containing windows were merged into a single cluster span. The cluster span coordinates correspond to the human genome NCBI build 33 (UCSC hg15, April 2003). A more exhaustive list is found in [7]

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Additional File 7:

Extended list of UCR clusters An extended, but less annotated, version of in [6]

Format: HTM Size: 421KB Download file

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