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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0014Get Sequence
Gene Name gadY
Synonyms ECK3500;b4452;IS183;
Position 3662887.....3662991
Length 105 bp
Strand forward
Gene Class GadY small RNA
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;Inferred from expression pattern;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "GadY is a small RNA that is highly expressed during entry into stationary phase (Chen S,2002. Opdyke JA,2004). Full length GadY (GadY(105)) may be processed at the 5" end, resulting in two smaller 90 and 59 base RNA species with identical 3" ends (GadY(90) and GadY(59)). Only GadY(90) remains present during late stationary phase. All three forms of GadY are able to bind Hfq, which is suggested to stabilize the small RNA (Opdyke JA,2004). GadY acts as a positive regulator of gadX, possibly by base-pairing between the 3" UTR of g.....

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References

Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, and Blyn LB () "A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome." Biosystems 65 (2-3)  PubMed
Storz G, Opdyke JA, and Zhang A (2004) "Controlling mRNA stability and translation with small, noncoding RNAs." Curr Opin Microbiol 7 (2)  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
Altuvia S (2004) "Regulatory small RNAs: the key to coordinating global regulatory circuits." J Bacteriol 186 (20)  PubMed
Opdyke JA, Kang JG, and Storz G (2004) "GadY, a small-RNA regulator of acid response genes in Escherichia coli." J Bacteriol 186 (20)  PubMed
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Comparative Genomics by UCSC Genome Browser

Network Visualization

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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
IG_2264_3661158_3667221_fwd_st
more

External Database Connections

ECK120002624
EB4538
2847729
ABE-0047272
JWR0255
EG31164
G0-8914
b4452
RF00122


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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