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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0038Get Sequence
Gene Name rydB
Synonyms ECK1681;b4430;IS082;tpe7;
Position 1762737.....1762804
Length 68 bp
Strand reverse
Gene Class small RNA regulator of RpoS
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay
Source regulonDB

Genome position

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


            "RydB is a small RNA reported to be approximately 60 nt (Wassarman KM,2001), 65 nt (Rivas E,2001) , or 67 nt (Hershberg R,2003) in length. High-copy expression causes decreased expression of rpoS at stationary phase in LB (Wassarman KM,2001). Ryx: RNA of unknown function at X position ARRAY(0x421bac) in the genome (Wassarman KM,2001). Regulation has been described (Wassarman KM,2001). Reviews: (Gottesman S,2001. Hershberg R,2003)."
 

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
Rivas E, Klein RJ, Jones TA, and Eddy SR (2001) "Computational identification of noncoding RNAs in E. coli by comparative genomics." Curr Biol 11 (17)  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

Computational Records


Gene NameStartEndStrand
IS082 1762690 1762847 reverse
NC052 1762744 1762848 reverse

score promoter_score=53.649;terminator_score=-13.26
Note GenBank_annotation:rydB or tpe7
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

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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_1118_1762411_1762957_rev_st
more

External Database Connections

ECK120002588
EB4514
2847670
ABE-0047250
JWR0236
EG31145
G0-8876
b4430
RF00118


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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