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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0041Get Sequence
Gene Name ryeB
Synonyms ECK1839;tkpe79;b4433;
Position 1921188.....1921308
Length 121 bp
Strand reverse
Gene Class small RNA that interacts with Hfq
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "RyeA/SraC and RyeB are small RNAs of approximately 275 nt and 104 nt in length, respectively, and a minor RyeB species of 74 nt has also been detected (Wassarman KM,2001. Vogel J,2003). RyeA and RyeB are encoded within the same inter-ORF region of the genome, between the pphA and yebY genes (Wassarman KM,2001). RyeB is complementary to an internal segment of RyeA (Vogel J,2003). Interactions between RyeA RNA and Hfq protein and between RyeB RNA and Hfq have been detected (Wassarman KM,2001). RyeB levels increase upon entry into stationary .....

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References

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
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
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
Hershberg R, Altuvia S, and Margalit H (2003) "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31 (7)  PubMed

Comparative Genomics by UCSC Genome Browser

Network Visualization

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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_1228_1920997_1921388_rev_st
more

External Database Connections

ECK120002577
EB4515
2847772
ABE-0047253
JWR0238
EG31147
G0-8883
b4433
RF00111


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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