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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0023Get Sequence
Gene Name omrA
Synonyms ECK2833;sraE;psrA12;PAIR2a;t59;b4444;rygA;
Position 2974124.....2974211
Length 88 bp
Strand reverse
Gene Class small RNA that interacts with Hfq
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "SraE is reported to be a small RNA of approximately 88 nt in length (Argaman L,2001), and RygA and RygB are reported to be small RNAs of approximately 89 nt and 83 nt in length, respectively, which are encoded within the same inter-ORF region of the genome (Wassarman KM,2001). SraE and RygA are reported to be the same RNA (Gottesman S,2001). Interactions between RygA RNA and Hfq protein and between RygB RNA and Hfq have been detected (Wassarman KM,2001). RygA and RygB RNAs contain PAIR2 repeats (Wassarman KM,2001). SraE RNA has similarity to .....

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References

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
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
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

Literature Records


Species Conditions Experiment Type Regulation PMID
Escherichia coli addition of procaine nortern blot induce PubMed
Escherichia coli late stationary phase nortern blot induce 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_1846_2974037_2975658_rev_st
more

External Database Connections

ECK120002580
EB4530
2847746
ABE-0047264
JWR0248
EG31157
G0-8868
b4444


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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