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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0027Get Sequence
Gene Name psrN
Synonyms ECK3078;sraF;psrA14;tpk1;b4448;IS160;
Position 3236396.....3236583
Length 188 bp
Strand forward
Gene Class PsrN small RNA
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


            "SraF is a small RNA reported to be approximately 189 nt in length (Argaman L,2001), and also reported to be found as two species of 120 and 180 nt in length (Rivas E,2001). SraF RNA is subject to RNase III cleavage (Argaman L,2001). SraF RNA has similarity to sequences from Salmonella and Klebsiella pneumoniae (Argaman L,2001). Sra: small RNA (Argaman L,2001). PsrA: predicted small RNA (Argaman L,2001). Reviews: (Gottesman S,2001. Hershberg R,2003)."
 

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

Computational Records


Gene NameStartEndStrand
IS160 3236011 3236135 forward

score promoter_score=61.088;terminator_score=-7.20
Note GenBank_annotation:sraF
Methods "profile-based search method(profile search program, pftools2.2) to identify putative promoters in the E. coli genome."
Species Escherichia coli K12 MG1655
Sequence Get Sequence
PMID PubMed

Comparative Genomics by UCSC Genome Browser

Network Visualization

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External Database Connections

ECK120002581
EB4535
2847692
ABE-0047268
JWR0252
EG31161
G0-8869
b4448


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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