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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0037Get Sequence
Gene Name rybB
Synonyms ECK0837;p25;b4417;
Position 887200.....887280
Length 81 bp
Strand reverse
Gene Class small RNA involved in envelope stress response
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;Inferred from expression pattern;Inferred from mutant phenotype;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "RybB is a small RNA 81 nt in length (Vogel J,2003). Expression of RybB increases in stationary phase, when its half life is 8 minutes (Wassarman KM,2001. Vogel J,2003), and is dependent on the alternative sigma factor σE, which is activated by cell envelope stress (Johansen J,2006. Thompson KM,2007). Repression of σE synthesis by RybB creates an autoregulatory loop (Thompson KM,2007). An efficient interaction between RybB RNA and Hfq protein has been detected (Wassarman KM,2001). Overexpression of rybB<.....

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References

Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, and Wagner EG (2003) "RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria." Nucleic Acids Res 31 (22)  PubMed
Hershberg R, Altuvia S, and Margalit H (2003) "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31 (7)  PubMed
Gottesman S, Storz G, Rosenow C, Majdalani N, Repoila F, and Wassarman KM (2001) "Small RNA regulators of translation: mechanisms of action and approaches for identifying new small RNAs." Cold Spring Harb Symp Quant Biol 66 ()  PubMed
Wassarman KM, Repoila F, Rosenow C, Storz G, and Gottesman S (2001) "Identification of novel small RNAs using comparative genomics and microarrays." Genes Dev 15 (13)  PubMed

Literature Records


Species Conditions Experiment Type Regulation PMID
Escherichia coli in stationary phase nortern blot induce PubMed

Comparative Genomics by UCSC Genome Browser

Network Visualization

Regulators/sRNAs


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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
IG_563_886563_887356_rev_st
more

External Database Connections

ECK120002591
EB4506
2847774
ABE-0047241
JWR0227
EG31137
G0-8880
b4417
RF00110


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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