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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0053Get Sequence
Gene Name ryhB
Synonyms ECK3426;sraI;psrA18;IS176;b4451;
Position 3578950.....3579039
Length 90 bp
Strand reverse
Gene Class regulatory antisense RNA involved in iron homeostasis
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;Inferred from mutant phenotype;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "SraI acts to reduce iron consumption under low-iron conditions (Masse E,2002). SraI is an antisense RNA that downregulates sdhCDAB RNA abundance (Masse E,2002). SraI also mediates regulation by Fur of acnA, fumA, ftnA, bfr, and sodB; SraI represses expression, and Fur represses this repressor (Masse E,2002). SraI is a small RNA of approximately 90 nt (Wassarman KM,2001) or 91-94 nt in length (Argaman L,2001). SraI and RyhB are reported to be the same RNA species (Gottesman S,2001). An interaction between SraI RNA and Hfq protein has been .....

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References

Massé E, and Gottesman S (2002) "A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli." Proc Natl Acad Sci U S A 99 (7)  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
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
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
Massé E, Escorcia FE, and Gottesman S (2003) "Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli." Genes Dev 17 (19)  PubMed
more..

Literature Records


Species Conditions Experiment Type Regulation PMID
Escherichia coli "poor growth on media containing succinate as a sole carbon source,in minimal media and in late stationary phase" nortern blot and microarray induce PubMed

Computational Records


Gene NameStartEndStrand
IS176 3578549 3578650 reverse

score promoter_score=59.944;terminator_score=8.29
Note GenBank_annotation:ryhB or sraI
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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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_2216_3578437_3582711_rev_f_st
more

External Database Connections

ECK120002584
EB4294
2847761
ABE-0047271
JWR0219
EG31133
G0-8872
b4451
RF00057


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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