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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0043Get Sequence
Gene Name ryeD
Synonyms ECK2069;QUAD1b;tpe60;b4437;
Position 2151668.....2151803
Length 136 bp
Strand forward
Gene Class RyeD small RNA
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;
Source regulonDB

Genome position

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


            "RyeC and RyeD are small RNAs of approximately 107-143 nt and 102-137 nt in length, respectively, which are encoded within the same inter-ORF region of the genome (between the yegL and yegM genes) (Wassarman KM,2001). RyeC and RyeD contain QUAD repeats (Wassarman KM,2001). Ryx: RNA of unknown function at X position ARRAY(0x45c4cc) 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
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
Hershberg R, Altuvia S, and Margalit H (2003) "A survey of small RNA-encoding genes in Escherichia coli." Nucleic Acids Res 31 (7)  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_1368_2149669_2151890_fwd_st
more

External Database Connections

ECK120002596
EB4521
2847674
ABE-0047257
JWR0242
EG31152
G0-8885
b4437


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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