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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0078Get Sequence
Gene Name glmY
Synonyms ECK2554;b4441;tke1;sroF;
Position 2689179.....2689362
Length 184 bp
Strand reverse
Gene Class GlmY small RNA regulator of glmS expression
Species Escherichia coli K12 MG1655
Evidence Inferred from direct assay;Inferred from mutant phenotype;
Source regulonDB

Genome position Promoter site

Structural RNA alignment
(RNALogo)
Get alignment sequences

Descriptions


    "GlmY is a small RNA that specifically increases synthesis of GlmS, encoded by the second open reading frame in the glmUS operon, without affecting GlmU synthesis. The effect of GlmY on GlmS expression requires sequence elements in the intergenic region between glmS and glmU (Urban JH,2007). The GlmY small RNA was first reported to be present as two RNA species of approximately 150 and 180 nt in length (Rivas E,2001). Later, it was shown that the two GlmY RNAs have the same 5" end; thus, the shorter species may be generat.....

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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

Computational Records


Gene NameStartEndStrand
NC082 2689214 2689355 reverse

score Promoter score:53.83;Terminator score:-11.95;Z score-2.73
Note GenBank annotations:tke1/sroF
Methods program pftools2.2 to identify the putative sigma70 promoter; RNAMotif software to identify putative rho-independent terminators; Gapped Markov Model Index.
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

ECK120002620
EB4539
2847700
ABE-0047261
JWR0245
EG31155
G0-8910
b4441
RF00128


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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