||The promoter and transcriptional start site for each gene was predicted by Weiner, Hermann, and Browning using a PSS matrix developed by sequencing the 5' ends of several M. pneumoniae transcripts [PUB_0411].
The transcription unit structure was compiled by mapping the reported M. pneumoniae transcription structure to M. genitalium [PUB_0418 Table S5 Suboperons] with three modifications:
r/s/tRNAs were assigned to transcription units according to their reference operons [PUB_0418 Table s4]
mRNAs not assigned to suboperons because of insufficient evidence where assigned to separate transcription units.
The 5 non-homologous genes were were assigned to separate transcription units. These genes occur outside other transcription units.
We considered several additional data set when compiling the the transcription unit structure:
Primary reports of cotranscribed genes [PUB_0176, PUB_0182, PUB_0186, PUB_0188, PUB_0188, PUB_0244, PUB_0247, PUB_0248, PUB_0249, PUB_0251]
OperonDB database of cotranscribed genes [PUB_0250]
Conservation of gene order across multiple species
Related function of adjacent genes
Expression levels as measured by microarrays of adjacent genes [PUB_0569]
Strandedness of adjacent genes
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