Maintenance of transposon-free regions throughout vertebrate evolution

doi:10.1186/1471-2164-8-470

BMC Genomics

Volume 8

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Research article

Maintenance of transposon-free regions throughout vertebrate evolution

Cas Simons , Igor V Makunin , Michael Pheasant and John S Mattick

Australian Research Council Special Research Center for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia QLD 4072, Australia

author email corresponding author email

BMC Genomics 2007, 8:470doi:10.1186/1471-2164-8-470


Published:	20 December 2007

Additional files

Additional File 1:

Chromosomal coordinates of zebrafish TFRs. A tab delimited text file giving the danRer4/Zv6 chromosomal coordinates (Chromosome, start, end, ID) for all zebrafish TFRs. This data is also available in a browsable format with direct links to the UCSC genome browser at: http://jsm-group.imb.uq.edu.au/tfr07/ webcite

Format: TXT Size: 150KB Download file

Additional File 2:

Chromosomal coordinates of human TFRs. A tab delimited text file giving the hg18/NCBI 36 chromosomal coordinates (Chromosome, start, end, ID) for all zebrafish TFRs. This data is also available in a browsable format with direct links to the UCSC genome browser at: http://jsm-group.imb.uq.edu.au/tfr07/ webcite

Format: TXT Size: 287KB Download file

Additional File 3:

Chromosomal coordinates of mouse TFRs. A tab delimited text file giving the mm8/NCBI 36 chromosomal coordinates (Chromosome, start, end, ID) for all zebrafish TFRs. This data is also available in a browsable format with direct links to the UCSC genome browser at: http://jsm-group.imb.uq.edu.au/tfr07/ webcite

Format: TXT Size: 444KB Download file

Additional File 4:

Chromosomal coordinates of opossum TFRs. A tab delimited text file giving the monDom4 chromosomal coordinates (Chromosome, start, end, ID) for all zebrafish TFRs. This data is also available in a browsable format with direct links to the UCSC genome browser at: http://jsm-group.imb.uq.edu.au/tfr07/ webcite

Format: TXT Size: 152KB Download file

Additional File 6:

Supplemental figure S1. Orthologous pair of TFRs in zebrafish and human that have very different GC contents. (A) 30 kb region of the human genome chr22:18,108,001-18,138,000 enclosing the TFR hs22.13 (red bar, 63.9% GC) and the gene TBX1 shown in blue. (B) The syntenic region of zebrafish genome (chr5:30,507,001-30,537,000) showing the 11 kb TFR dr5.101 (35.4% GC) and the ortholog of human tbx1. Above each panel is a smoothed plot describing the percent GC content in 5 bp [31]. Both images are modified screen shots taken from the UCSC genome browser [31].

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Additional File 5:

Supplemental tables S1 and S2. Tables describing the presence of TFRs in X. tropicalis orthologous to the 58 zebrafish TFRs ≥ 10 kb found in all mammals and the pairs of potentially duplicated TFRs found in the zebrafish genome that were removed from the analysis.

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