RegulonDB

Gene
Name:	ssrA
Synonym(s):	ECK2617, EG30100, b2621, sipB
Genome position(nucleotides):	2755593 --> 2755955 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.89
External database links:

ASAP:	ABE-0008624
CGSC:	35783
ECHOBASE:	EB4263
OU-MICROARRAY:	b2621
PORTECO:	ssrA
REGULONDB:	b2621
M3D:	ssrA
COLOMBOS:	ssrA
PortEco:	b2621

Product

Name:

TmRNA

Synonym(s):

"ssrA, 10Sa RNA, 10Sa", SipB, SsrA, tmRNA, transfer-messenger RNA

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
		2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
		2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation
		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
		5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity
		6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)
	molecular_function	GO:0005515 - protein binding GO:0043022 - ribosome binding
	biological_process	GO:0070929 - trans-translation GO:0070930 - trans-translation-dependent protein tagging GO:0072344 - rescue of stalled ribosome

Note(s):

Note(s): ...[more].

Evidence:

[IDA] Inferred from direct assay

Reference(s):

[1] Kirby JE., et al., 1994
[2] Muto A., et al., 1996
[3] Nakano H., et al., 2001
[4] Oh BK., et al., 1990
[5] Ray BK, et al., 1979
[6] Roche ED., et al., 1999
[7] Williams KP. 2003

External database links:

ECOCYC:

SSRA-RNA

ECOLIWIKI:

b2621

Operon

Name:

ssrA

Operon arrangement:

Transcription unit	Promoter
ssrA	ssrAp

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	ssrAp2	2755507		forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.658. P-value: 3.013e-5 Read more >	[ICWHO]	[8]
	promoter	TSS_2971	2756133		forward	nd	[RS-EPT-CBR]	[9]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Kirby JE., Trempy JE., Gottesman S., 1994, Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli., J Bacteriol 176(7):2068-81
[2] Muto A., Sato M., Tadaki T., Fukushima M., Ushida C., Himeno H., 1996, Structure and function of 10Sa RNA: trans-translation system., Biochimie 78(11-12):985-91
[3] Nakano H., Goto S., Nakayashiki T., Inokuchi H., 2001, Temperature-sensitive mutations in various genes of Escherichia coli K12 can be suppressed by the ssrA gene for 10Sa RNA (tmRNA)., Mol Genet Genomics 265(4):615-21
[4] Oh BK., Chauhan AK., Isono K., Apirion D., 1990, Location of a gene (ssrA) for a small, stable RNA (10Sa RNA) in the Escherichia coli chromosome., J Bacteriol 172(8):4708-9
[5] Ray BK, Apirion D., 1979, Characterization of 10S RNA: a new stable rna molecule from Escherichia coli., Mol Gen Genet. Jul 2;174(1):25-32.
[6] Roche ED., Sauer RT., 1999, SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity., EMBO J 18(16):4579-89
[7] Williams KP., 2003, Traffic at the tmRNA gene., J Bacteriol 185(3):1059-70
[8] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[9] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.