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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0040Get Sequence
Gene Name ryeA
Synonyms ECK1838;IS091;b4432;tkpe79;sraC;psrA8;sraCryeA;
Position 1921090.....1921338
Length 249 bp
Strand forward
Gene Class small RNA that interacts with Hfq
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;
Source regulonDB

Genome position Promoter site

NO conserved alignment determine the structure

Descriptions


    "RyeA and SraC are reported to be the same RNA (Gottesman S,2001). SraC is reported to be a small RNA of approximately 234-249 nt in length (Argaman L,2001), and RyeA and RyeB are reported to be small RNAs of approximately 275 nt and 100 nt in length, respectively (and shorter species have also been detected) (Wassarman KM,2001) RyeA and RyeB are encoded within the same inter-ORF region of the genome (Wassarman KM,2001), with RyeB being complementary to an internal segment of RyeA (Vogel J,2003). Interactions between RyeA RNA and Hfq prote.....

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References

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
Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, and Altuvia S (2001) "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli." Curr Biol 11 (12)  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
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
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
more..

Computational Records


Gene NameStartEndStrand
IS091 1921086 1921365 forward

score promoter_score=61.661;terminator_score=-5.12
Note GenBank_annotation:ryeA and ryeBa or sraCb
Methods "profile-based search method(profile search program, pftools2.2) to identify putative promoters in the E. coli genome."
Species Escherichia coli K12 MG1655
Sequence Get Sequence
PMID 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_1227_1920337_1923131_fwd_st
more

External Database Connections

ECK120002594
EB4516
2847771
ABE-0047252
JWR0237
G0-8865
b4432
RF00101


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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