Supplementary Materials

Systematic discovery of cap-independent translation sequences in human and viral genomes

Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Alexey A. Gritsenko, Noam Stern-Ginossar, Zohar Yakhini, Adina Weinberger, Eran Segal

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Figs. S1 to S15
  • Table S2 and S9
  • References
  • Data table captions Tables S1 and S3 to S8
Table S1
All tested oligos from full-length IRESs. For each oligo shown information about the IRES name; oligo start position within the full-length reported IRES; the computed eGFP expression levels representing cap-independent translation; and the oligo sequence (including the constant library primer sequence at both ends).
Table S3
All tested human 5' UTRs in our screen. For each oligo shown information about the gene symbol; transcript Refseq; the computed eGFP expression levels representing cap-independent translation; and the oligo sequence. Notes: (1) Oligo sequence includes constant library primer sequence at both ends. (2) Each line represents a human transcript. In cases that two transcripts have the same 5’UTR the same oligo index and sequence are shown in both lines.
Table S4
All tested viral 5' UTRs in our screen from 414 viruses. For each oligo shown information about the virus accession; virus name; ORF start; ORF end; ORF orientation; protein name; protein id; the computed eGFP expression levels representing cap-independent translation; and the oligo sequence (including the constant library primer sequence at both ends).
Table S5
All tested oligos with reverse complementarity to the human 18S rRNA (NR_003286). For each oligo shown information about the oligo start and end positions within the reverse complement sequence of the 18S rRNA; the computed eGFP expression levels representing cap-independent translation; and the oligo sequence (including the constant library primer sequence at both ends).
Table S6
The complementary sequences of all extracted 7-mers from the 18S rRNA active and inactive regions. For each k-mer shown the computed Wilcoxon rank-sum pvalue comparing the expression of native oligos that contain the k-mer sequence (up to 1 mismatch) to oligos that do not. The corrected p-values (Benjamini-Hochberg procedure) are shown in the third column.
Table S7
All tested oligos from 159 human transcripts. For each oligo shown information about the gene symbol; transcript Refseq; CDS start position; CDS end position; oligo start position within the transcript; the computed eGFP expression levels representing cap-independent translation; and the oligo sequence (including the constant library primer sequence at both ends).
Table S8
All tested oligos from 131 [+]ssRNA complete viral genomes. For each oligo shown information about the virus accession; virus name; virus class; ORF start; ORF end; oligo start position within the genome; the computed eGFP expression levels representing cap-independent translation; and the oligo sequence (including the constant library primer sequence at both ends).