About Search Browse Statistics Tutorial Downloads


sRNA Annotations

2nd structure
(RNAfold)
sRNAG0033Get Sequence
Gene Name rprA
Synonyms ECK1686;b4431;IS083;psrA5;
Position 1768396.....1768500
Length 105 bp
Strand forward
Gene Class small RNA regulator of RpoS
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;Inferred from mutant phenotype;Inferred from experiment;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "RprA RNA is required for wild-type production of RpoS in response to osmotic shock (Majdalani N,2001). DsrA and RsrA RNAs both alter secondary structure in the leader sequence of the RpoS mRNA to facilitate RpoS translation (Majdalani N,2002). RprA is a small RNA of approximately 105 nt in length (Argaman L,2001). The structure of the RprA RNA is discussed (Majdalani N,2001). RprA RNA is subject to endoribonuclease cleavage (Argaman L,2001). The rprA gene contains an internal promoter sequence (Argaman L,2001). An rprA mutant exhibits .....

|

References

Majdalani N, Chen S, Murrow J, St John K, and Gottesman S (2001) "Regulation of RpoS by a novel small RNA: the characterization of RprA." Mol Microbiol 39 (5)  PubMed
Majdalani N, Hernandez D, and Gottesman S (2002) "Regulation and mode of action of the second small RNA activator of RpoS translation, RprA." Mol Microbiol 46 (3)  PubMed
Massé E, Majdalani N, and Gottesman S (2003) "Regulatory roles for small RNAs in bacteria." Curr Opin Microbiol 6 (2)  PubMed
Repoila F, Majdalani N, and Gottesman S (2003) "Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm." Mol Microbiol 48 (4)  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
more..

Literature Records


Species Conditions Experiment Type Regulation PMID
Escherichia coli under conditions of osmotic shock;increasing cell density and are most abundant in stationary phase   induce PubMed

Computational Records


Gene NameStartEndStrand
IS083 1768287 1768506 forward

score promoter_score=53.077;terminator_score=-10.15
Note GenBank_annotation:rprA sRNAgene
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


alt="Your browser understands the <APPLET> tag but isn't running the applet, for some reason." Your browser is completely ignoring the <APPLET> tag! Requires Java Web Start, which is automatically installed when you install JRE/JDK with version 1.4.2 above.
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_1120_1768211_1768611_fwd_st
more

External Database Connections

ECK120002576
EB4292
2847671
ABE-0047251
JWR0203
EG31130
G0-8863
b4431
RF00034


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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