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Open Access Research article

Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals

Chun-Hsi Chen1, Ben-Yang Liao1* and Feng-Chi Chen123*

Author Affiliations

1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan

2 Department of Life Science, National Chiao-Tung University, Hsinchu, 300 Taiwan

3 Department of Dentistry, Chinese Medical University, Taichung, 404 Taiwan

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BMC Evolutionary Biology 2011, 11:192  doi:10.1186/1471-2148-11-192

Published: 5 July 2011

Additional files

Additional file 1:

The indel selection index in 5'UTRs without uAUGs. The X-axis indicates the relative distance from the 5'-cap to the reference point in terms of percentage of the 5'UTR length. The results were derived from the genes with randomly selected transcripts.

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Open Data

Additional file 2:

Distributions of ISI values according to Pecan-aligned sequences, with reference to the gene annotations of (A) human; and (B) mouse. The numbers in the parentheses following G0 indicate the median distances of the uAUGs from 5' cap in terms of percentage of 5'UTR length in the non-G0 transcripts. These proportions of length are referenced to determine which G0 distributions to use in the comparisons. The P values of pair-wise differences (calculated by using the Mann-Whitney U test) are shown at the top. The symbols "*", "**", and "***" represent 0.01 ≦ P < 0.05, 0.001 ≦ P < 0.01, and P < 0.001, respectively.

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Additional file 3:

The ISI distributions of Gv transcripts with different uAUG locations. Each GV dataset is divided into three equal-sized subgroups according to the relative locations of uAUGs. The numbers in the parentheses following G0 indicate the median distances of the uAUGs from 5' cap in terms of percentage of 5'UTR length in the GV transcripts. The P values (by the Mann-Whitney U test) for the ISI differences between GV and the corresponding G0 transcripts are shown at the top.

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Open Data

Additional file 4:

The five alternatively spliced transcript isoforms of human gene ENSG00000119125. Only the 5' proximal regions of the transcripts are shown here. Among the isoforms, ENST00000358399 is the only one that contains a pure 5'UTR, which includes no uAUGs at all. Note that this pure 5'UTR is also the shortest one. In comparison, ENST00000238018 contains the longest 5'UTR, which encompasses as many as 15 uAUGs. The exons are represented as blue bars (not to the scale). The black, red, green, and blue inverted triangles represent translation initiation sites, AISs ("A"), VuAUGs ("V"), and SuAUGs ("S"), respectively.

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Additional file 5:

The numbers and percentages of transcripts analyzed in this study. "Gam", "Gsm", and "Gvm" indicate transcripts with multiple AISs, SuAUGs, and VuAUGs, respectively. In the Gm group, more than one type of uORF is found in the 5'UTRs. The subscripts "a", "s", and "v", indicate the presence of AIS, SuAUG, and VuAUG, respectively. Note that only Ga, Gs, and Gv are analyzed in this study.

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Additional file 6:

The distributions of R values using different pseudocounts. "c" stands for the pseudocount. The black bar represents a 5'UTR, where solid and open circles indicate the locations of non-3n and 3n indels, respectively. The reference point is used to differentiate the upstream and downstream region of a 5'UTR.

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