Skip to main content
. 2014 Sep 16;3:e03523. doi: 10.7554/eLife.03523

Figure 5. Ribosome association in different transcript regions.

(A) Density plot of the relative length of the primary ORF in lncRNA_ribo and codRNA with respect to transcript length. For comparison data for the longest ORF in lncRNA_noribo is also shown (except for fruit fly due to insufficient data). (B) Box-plots of TE distribution in primary ORF, 5′UTR, and 3′UTR regions. The area within the box-plot comprises 50% of the data, and the line represents the median value. The analysis considered all transcripts with 5′UTR and 3′UTR longer than 30 nucleotides and >0.2 FPKM in all three regions. The number of transcripts was 1956 codRNA and 159 lncRNA_ribo in mouse, 3558 codRNA and 139 lncRNA_ribo in human, 5216 codRNA and 252 lncRNA_ribo in zebrafish, and 2019 codRNA and 33 lncRNA_ribo in Arabidopsis. (C) Box-plots of TE distribution in primary ORFs, rest of ORFs with ribosome profiling reads and non-ORF regions (interORF). The analysis considered all transcripts with at least two ORFs and more than 30 nucleotides interORF. The number of transcripts was 3264 codRNA and 204 lncRNA_ribo in mouse, 3104 codRNA and 168 lncRNA_ribo in human, 1646 codRNA and 212 lncRNA_ribo in zebrafish, and 1098 codRNA and 25 lncRNA_ribo in Arabidopsis. Fruit fly and yeast were not included in the last two analyses due to insufficient data (<8 lncRNA_ribo meeting the conditions).

DOI: http://dx.doi.org/10.7554/eLife.03523.011

Figure 5.

Figure 5—figure supplement 1. Absolute nucleotide length of ORFs in different kinds of transcripts.

Figure 5—figure supplement 1.

In codRNAs and lncRNA_ribo, we selected the primary ORF (the ORF with the largest number of ribosome profiling reads), whereas in lncRNA_noribo we selected the longest ORF.
DOI: http://dx.doi.org/10.7554/eLife.03523.012
Figure 5—figure supplement 2. Translational efficiency in single-isoform genes.

Figure 5—figure supplement 2.

(A) Box-plots of TE distribution in primary ORF, 5′UTR, and 3′UTR regions. The analysis considered only genes with one isoform, with UTR and ORF regions expressed at >0.2 FPKM and with 5′UTR and 3′UTR longer than 30 nucleotides. The number of transcripts was 980 codRNA and 97 lncRNA_ribo in mouse, 758 codRNA and 36 lncRNA_ribo in human, 3763 codRNA and 117 lncRNA_ribo in zebrafish, and 1495 codRNA and 32 lncRNA_ribo in Arabidopsis. (B) Box-plots of TE distribution in primary ORFs, other ORFs with ribosome profiling reads and non-ORF regions (interORFs). The analysis only considered genes with one isoform in which these regions were longer than 30 nucleotides and with expression >0.2 FPKM. The number of transcripts was 1691 codRNA and 113 lncRNA_ribo in mouse, 763 codRNA and 54 lncRNA_ribo in human, 1170 codRNA and 108 lncRNA_ribo in zebrafish, and 817 codRNA and 25 lncRNA_ribo in Arabidopsis.
DOI: http://dx.doi.org/10.7554/eLife.03523.013
Figure 5—figure supplement 3. Translational efficiency in annotated transcripts.

Figure 5—figure supplement 3.

(A) Box-plots of TE distribution in primary ORF, 5′UTR, and 3′UTR regions. The analysis considered only annotated transcripts, with UTR and ORF regions expressed at >0.2 FPKM and with 5′UTR and 3′UTR longer than 30 nucleotides. The number of transcripts was 1956 codRNA and 92 lncRNA_ribo in mouse, 3558 codRNA and 138 lncRNA_ribo in human, 5216 codRNA and 54 lncRNA_ribo in zebrafish, and 2019 codRNA and 22 lncRNA_ribo in Arabidopsis. (B) Box-plots of TE distribution in primary ORFs, other ORFs with ribosome profiling reads (rest ORFs) and non-ORF regions (interORF). The analysis only considered annotated transcripts in which these regions were longer than 30 nucleotides and with expression >0.2 FPKM. The number of transcripts was 3264 codRNA and 128 lncRNA_ribo in mouse, 3104 codRNA and 167 lncRNA_ribo in human, 1646 codRNA and 58 lncRNA_ribo in zebrafish, and 1098 codRNA and 18 lncRNA_ribo in Arabidopsis.
DOI: http://dx.doi.org/10.7554/eLife.03523.014
Figure 5—figure supplement 4. Translational efficiency in transcripts expressed at different levels.

Figure 5—figure supplement 4.

We restricted this analysis to transcripts with ORF and UTR regions expressed at >0.2 FPKM and with 5′UTR and 3′UTR longer than 30 nucleotides. (A) Expressed at low levels: transcripts expressed at 0.5–2 FPKM, (B) expressed at high levels: transcripts expressed at 2–10 FPKM. codRNAs were sampled in such a way as to have the same gene expression distribution as the corresponding lncRNA set. Results for species in which all sets contained at least 20 transcripts are shown.
DOI: http://dx.doi.org/10.7554/eLife.03523.015