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sRNA Annotations

2nd structure
(RNAfold)
sRNAG0015Get Sequence
Gene Name gcvB
Synonyms ECK2804;b4443;IS145;psrA11;
Position 2940718.....2940922
Length 205 bp
Strand forward
Gene Class small regulatory RNA
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


    "GcvB is a small RNA of approximately 205 nt in length (Argaman L,2001) that is involved in transcriptional repression of the dppA gene and in translational repression of OppA synthesis (Urbanowski ML,2000). A gcvB mutant exhibits overproduction of OppA and DppA, compared to wild type (Urbanowski ML,2000). A gcvB mutant does not exhibit a defect in glycine cleavage system activity (Urbanowski ML,2000). GcvB RNA has similarity to sequences from Salmonella, Yersinia pestis, and Klebsiella pneumoniae (Argaman L,2001). PsrA: .....

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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
Urbanowski ML, Stauffer LT, and Stauffer GV (2000) "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." Mol Microbiol 37 (4)  PubMed

Computational Records


Gene NameStartEndStrand
IS145 2940715 2940928 forward

score promoter_score=63.377;terminator_score=-10.75
Note GenBank_annotation:gcvB sRNA gene
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

Regulators/sRNAs


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sRNAs/Targets


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_1826_2938122_2941358_fwd_st
more

External Database Connections

ECK120002579
EB4291
2847720
ABE-0047263
JWR0247
EG31129
G0-8867
b4443
RF00022


Department of Biological Science and Technology,

Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan

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