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EcogeneTopic Page

TopicPage for sRNA of Escherichia coli K-12

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Description:

The sRNAs of E. coli are small regulatory non-protein coding ncRNAs that can work as antisense regulators base-pairing to mRNA translation signals, activating or inhibiting translation and/or by increasing RNA degradation. Hfq or other sRNA-binding proteins can be involved as sRNA-mRNA interaction chaperones that may also promote RNA degradation of Hfq/sRNA/mRNA complexes.


Details:

Currently 61 sRNA genes and one sRNA pseudogene, sokA, are annotated in EcoGene although many more sRNAs have been predicted. This sRNA gene set does not include the small tmRNA gene ssrA, which has its own RNA category as a hybrid tRNA/mRNA molecule. Even though a small protein mRNA can also function as an sRNA (e.g. sgrT/sgrS), this has not been shown for two mRNAs (ryfB encoding ShoB and IS0192(isrB) encoding AzuC) encoding small proteins that were initially identified as sRNAs, so these mRNAs have been removed as sRNAs although they may be replaced later if there is evidence that they are dual function mRNA/sRNAs.

In order to be included in EcoGene, the sRNA gene should:

1) not be transcribed as part of an mRNA , or be antisense to an mRNA

2) have evidence of expression as a discete small RNA with a size estimate, usually from a Northern blot or cDNA sequence.

and

3) have a 5' end determination to the bp level, usually primer extension or 5' RACE.

These inclusion criteria allow accurate annotation of the sRNA interval on the genome sequence an reduce spurious gene annotation.

Note: the last 15 bp pf the ryeE sRNA gene are derived from the P2-like prophage PR-X, but it is not annotated as a fusion pseudogene.


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