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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0045Get Sequence
Gene Name ryfA
Synonyms ECK2518;tp1;b4440;PAIR3;
Position 2651877.....2652180
Length 304 bp
Strand forward
Gene Class RyfA small RNA
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay
Source regulonDB

Genome position

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


            "RyfA is a small RNA reported to be approximately 320 nt (Wassarman KM,2001), 302 nt (Hershberg R,2003), or 300 nt (Rivas E,2001) in length. RyfA RNA contains a PAIR3 repeat (Wassarman KM,2001). RyfA may be identical to IS128 (Chen S,2002). Ryx: RNA of unknown function at X position ARRAY(0x4b32a0) in the genome (Wassarman KM,2001). Regulation has been described (Wassarman KM,2001). Reviews: (Gottesman S,2001. Hershberg R,2003)."
 

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
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
Rivas E, Klein RJ, Jones TA, and Eddy SR (2001) "Computational identification of noncoding RNAs in E. coli by comparative genomics." Curr Biol 11 (17)  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
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Comparative Genomics by UCSC Genome Browser

Network Visualization

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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_1646_2651360_2661461_fwd_f_st
more

External Database Connections

ECK120002590
EB4526
2847714
ABE-0047260
JWR0244
EG31154
G0-8879
b4440
RF00126


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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