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Mutations within lncRNAs are effectively selected against in fruitfly but not in human

Wilfried Haerty* and Chris P Ponting

Author Affiliations

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK

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Genome Biology 2013, 14:R49  doi:10.1186/gb-2013-14-5-r49

Published: 27 May 2013

Additional files

Additional File 1:

Average phastCons scores across protein-coding (blue) and lncRNA (red) gene models in D. melanogaster (A) and human (B, C). Two hundred evenly-spaced nucleotides were randomly sampled per feature. The gray lines represent the 95% confidence intervals computed over 1,000 resampling. Average phastCons score for lncRNAs in human was computed over 200 randomly selected equidistant nucleotides within each of the categories. Confidence intervals were computed using 1,000 resampling of the data.

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Additional File 2:

Median sequence conservation (phastCons) score across protein coding (blue) and positionally equivalent (PE) lncRNA (red) in human.

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Additional File 3:

Comparison of protein-coding (blue) and lncRNA (red) 5' (A) and 3' (B) splice site conservation in D. melanogaster . Only protein coding sequences flanking lncRNAs were used in the analysis. The control set is based on the random selection of 'GT' and 'AG' dinucleotides within the intergenic sequence flanking the lncRNAs in D. melanogaster. The Shannon-Weaver index was computed for each site using the alignments of each splice site and its neighbouring sequences with D. simulans, D. sechellia, D. yakuba and D. erecta with Muscle [102].

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Additional File 4:

Distribution of the distances between consecutive SNPs within protein coding (black) and lncRNA (red) exons in D. melanogaster.

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Additional File 5:

Average (standard deviation) polymorphism estimates for lncRNA and their flanking protein coding genes in human. PE: positional equivalent. A maximum distance threshold between lncRNA loci and ancestral sequences of 5 kb was applied.

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Additional File 6:

Average (standard deviation) polymorphism estimates for lncRNA and their flanking protein coding genes in human. PE: positional equivalent. A maximum distance threshold between lncRNA loci and ancestral sequences of 20 kb was applied.

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Additional File 7:

Comparison of derived allele frequency distribution of SNPs at non-synonymous sites (dark blue), within 3′ UTR (yellow), lncRNA exons (red), 5′ UTR, at four-fold degenerate sites (light blue), and within small introns in D. melanogaster.

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Additional File 8:

Derived allele frequency spectra for 0-fold, four-fold degenerate sites, sites within lncRNA, sites upstream (400 nt) lncRNAs and protein coding genes in D. melanogaster (A) and human (B).

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Additional File 9:

Distribution of average conservation scores for intergenic lncRNAs in human.

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Additional File 10:

Comparison of derived allele frequency distribution of SNPs at 0-fold degenerate sites (blue), GENCODE lncRNA exons (red), ancestral repeats (green) and four-fold degenerate sites (light blue) in human.

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Additional File 11:

Comparison of derived allele frequency distribution of SNPs at 0-fold degenerate sites (blue), GENCODE lncRNA exons (red), ancestral repeats (green) and four-fold degenerate sites (light blue) in individuals of Yoruba origin.

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