How do RNA genes overlap with proteincoding genes

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How do RNA genes overlap with protein-coding
genes E. coli K12 genome
Presented by Wenhan Zhu Lab meeting, Sept
9,2005 School of Biology, Georgia Tech
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RNA genes
RNA genes are referred to as noncoding or
non-coding RNAs (ncRNA) other designations
include small RNA (sRNA), non-messenger RNA
(nmRNA), small non-messenger RNA (snmRNA),
functional RNA (fRNA), and the generic
miscellaneous RNA (misc_RNA). Different types
of RNA genes annotated in E. coli tRNA, rRNA,
RNase P, antisense RNA, regulator RNA and unknown
function.
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RNA genes identified by E. coli genome project -
U. Wisconsin Madison
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Proportion in the genome
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Overview RNA genes overlap with protein-coding
genes
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tRNA

• Annotation
• blastp hits only on Shigella flexneri.
• We are not predicting this gene.

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tRNA

• Prediction

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tRNA Overlap with GMS prediction (cont.) Coding
potential
tRNA
tpr 33aa
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Observation 1

• In annotation of E. coli genome, theres no
  experimental validated cases of overlap between
  tRNA genes and protein-coding genes.
• Annotation curators removed all short predictions
  overlapping with tRNA genes.

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rRNA
Prediction
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Miscellaneous RNA Overlap with annotated
protein-coding genes
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Miscellaneous RNA Overlap with GMS predicted
protein-coding genes
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Miscellaneous RNA

• All annotated overlapping cases are
  experimentally verified.
• Our predictions overlapping with RNA genes are
  less than 100 aa.