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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0024Get Sequence
Gene Name omrB
Synonyms ECK2834;t59;rygB;b4445;PAIR2b;
Position 2974332.....2974407
Length 76 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


    "RygA and RygB are 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). The nucleotide position of the rygB gene has been predicted (Hershberg R,2003). The precise location of the rygB gene has been reported (Vogel J,2003). RygA and RygB RNAs contain PAIR2 repeats (Wassarman KM,2001). RygB has 77% sequence identity to SraE/RygA, but their expression patterns are complementary; RygB levels increase at the onset of stationary phase and decre.....

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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
Hershberg R, Altuvia S, and Margalit H (2003) "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31 (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
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

Literature Records


Species Conditions Experiment Type Regulation PMID
Escherichia coli addition of procaine nortern blot induce PubMed
Escherichia coli early 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

ECK120002593
EB4531
2847747
ABE-0047265
JWR0249
EG31158
G0-8882
b4445


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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