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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0075Get Sequence
Gene Name ssrA
Synonyms ECK2617;sipB;b2621;
Position 2753615.....2753977
Length 363 bp
Strand forward
Gene Class tmRNA
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay
Source regulonDB

Genome position Promoter site

NO conserved alignment determine the structure

Descriptions


    "SsrA RNA functions to release a stalled ribosome from the end of a broken mRNA that has no stop codon by acting both as a tRNA and as an mRNA, using a trans-translation mechanism (Muto A,1996). SsrA also mediates release of a ribosome that has stalled due to lack of an appropriate tRNA (Roche ED,1999. Hayes CS,2002). Other translation problems can also lead to SsrA activity (Ueda K,2002. Abo T,2002. Hayes CS,2002. Sunohara T,2002. Christensen SK,2003). In addition, SsrA RNA stimulates degradation of defective mRNAs (Yamamoto Y,2003). Th.....

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References

Muto A, Sato M, Tadaki T, Fukushima M, Ushida C, and Himeno H (1996) "Structure and function of 10Sa RNA: trans-translation system." Biochimie 78 (11-1)  PubMed
Roche ED, and Sauer RT (1999) "SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity." EMBO J 18 (16)  PubMed
Hayes CS, Bose B, and Sauer RT (2002) "Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli." Proc Natl Acad Sci U S A 99 (6)  PubMed
Abo T, Ueda K, Sunohara T, Ogawa K, and Aiba H (2002) "SsrA-mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coli." Genes Cells 7 (7)  PubMed
Sunohara T, Abo T, Inada T, and Aiba H (2002) "The C-terminal amino acid sequence of nascent peptide is a major determinant of SsrA tagging at all three stop codons." RNA 8 (11)  PubMed
more..

Computational Records


Gene NameStartEndStrand
NC084 2753612 2754061 forward

score Promoter score:59.76;Terminator score:-19.94;Z score-2.95
Note GenBank annotations:ssrA
Methods program pftools2.2 to identify the putative sigma70 promoter; RNAMotif software to identify putative rho-independent terminators; Gapped Markov Model Index.
Species Escherichia coli K12 MG1655
Sequence Get Sequence
PMID PubMed

Network Visualization

Regulators/sRNAs


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sRNAs/Targets


sRNA Expression Profiles

TitleF plasmid induced changes in expression levels in E. coli
Citation(s)16432259;16981998;SeriesGSE1154
Samples
1:MG1655_replicate12:MG1655_replicate23:MG1655F_replicate1
4:MG1655F_replicate25:DH5alpha_replicate16:DH5alpha_replicate2
7:DH5alphaF_replicate18:DH5alphaF_replicate2
ssrA_b2621_st
more

External Database Connections

ECK120002542
EB4263
3433106
ABE-0008624
JWR0055
EG30100
b2621
331
RF00023


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

Contact with: bryan@mail.NCTU.edu.tw