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Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

Figure 3

Coding Hairpin near Selenocysteine Insertion Site

(A) Gene structure, EvoFold predictions, and conservation around the selenocysteine insertion site of selenoprotein T (SELT). The pairing regions of the hairpin are shown in dark green and can be seen to start only eight bases downstream of the UGA insertion site (indicated by *). Arrows indicate direction of transcription.

(B) Annotated segment of eight-way alignment spanning the predicted hairpin. SS anno, secondary-structure annotation in parenthesis format (matching parentheses indicate pairs and periods indicate unpaired regions); pair symbol, pairing columns are assigned identical symbols to facilitate navigation; Score, position-specific scores (0–9), which indicate confidence in secondary-structure annotation. Substitutions in predicted pairs are color-coded relative to the human sequence: green is a compensatory double substitution, blue is a compatible single substitution, and red is a noncompatible substitution.

(C) Depiction of hairpin, which is shown with T instead of U to facilitate comparison with the genomic sequences. Pairs are color-coded by presence of substitutions in the eight-way alignment (see b).

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.0020033.g003