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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0050Get Sequence
Gene Name rygD
Synonyms ECK3041;tp8;C0730;QUAD1d;b4447;IS156;
Position 3192743.....3192887
Length 145 bp
Strand reverse
Gene Class RygD small RNA
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;
Source regulonDB

Genome position

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


            "RygD is a small RNA reported to be two species of 110 and 140 nt in length. The gene position corresponds to that of the predicted site of the gene, which would encode an RNA of 254 nt (Rivas E,2001). (Wassarman KM,2001) did not detect transcription in the intergenic region between yqiK and rfaE, while (Tjaden B,2002) and (Rivas E,2001) did. Review: (Hershberg R,2003)"
 

References

Hershberg R, Altuvia S, and Margalit H (2003) "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31 (7)  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

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_1981_3189956_3192960_rev_st
more

External Database Connections

ECK120002623
EB4534
2847684
ABE-0047267
JWR0251
EG31160
G0-8913
b4447


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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