ssrA:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

ssrA

Gene Synonym(s)

ECK2617, b2621, JWR0055, sipB[1], sipB

Product Desc.

tmRNA[2][3]

Product Synonyms(s)

10Sa RNA SsrA (tmRNA)[1], SsrA[2][1], tmRNA[2][1], 10Sa RNA[2][1], transfer-messenger RNA[2][1], SipB[2][1], B2621[2][1]

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ssrA[2]

Regulation/Activity
Quick Links



     

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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ssrA

Mnemonic

Small stable RNA

Synonyms

ECK2617, b2621, JWR0055, sipB[1], sipB

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

59.35 minutes, 59.35 minutes 

MG1655: 2753615..2753977
<gbrowseImage> name=NC_000913:2753615..2753977 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2639427..2639789
<gbrowseImage> name=NC_012759:2639427..2639789 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2754249..2754611
<gbrowseImage> name=NC_007779:2754249..2754611 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2845380..2845742
<gbrowseImage> name=NC_010473:2845380..2845742 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments
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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

E8F2

Kohara Phage

Genobase

PMID:3038334

22D7

Kohara Phage

Genobase

PMID:3038334

24G1

Kohara Phage

Genobase

PMID:3038334

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[4]

est. P1 cotransduction: 56% [5]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[4]

est. P1 cotransduction: 1% [5]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG30100

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30100

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002542

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945053

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4263

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008624

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

SsrA RNA

Synonyms

10Sa RNA SsrA (tmRNA)[1], SsrA[2][1], tmRNA[2][1], 10Sa RNA[2][1], transfer-messenger RNA[2][1], SipB[2][1], B2621[2][1]

Product description

tmRNA[2][3]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

SmpB


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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Physical Properties

<protect>

Type

tmRNA

Sequence 
GGGGCUGAUU CUGGAUUCGA CGGGAUUUGC GAAACCCAAG GUGCAUGCCG AGGGGCGGUU
GGCCUCGUAA AAAGCCGCAA AAAAUAGUCG CAAACGACGA AAACUACGCU UUAGCAGCUU
AAUAACCUGC UUAGAGCCCU CUCUCCCUAG CCUCCGCUCU UAGGACGGGG AUCAAGAGAG
GUCAAACCCA AAAGAGAUCG CGUGGAAGCC CUGCCUGGGG UUGAAGCGUU AAAACUUAAU
CAGGCUAGUU UGUUAGUGGC GUGUCCGUCC GCAGCUGGCA AGCGAAUGUA AAGACUGACU
AAGCAUGUAG UACCGAGGAU GUAGGAAUUU CGGACGCGGG UUCAACUCCC GCCAGCUCCA CCA
Mol. Wt


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tmRNA - Image courtesy of RFam

Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ssrA taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

Notes

Gene Product Resources


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG30100

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30100

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002542

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4263

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008624

Escherichia coli str. K-12 substr. MG1655

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Notes

Links




Expression


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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)
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Notes

Transcription and Transcriptional Regulation


See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

ssrA

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Figure courtesy of RegulonDB


Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation


<gbrowseImage> name=NC_000913:2753595..2753635 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental


Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b2621 (EcoliWiki Page)

NCBI GEO profiles for ssrA

microarray

GenExpDB:b2621 (EcoliWiki Page)

Summary of data for ssrA from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (2753299..2753570) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ19; Well:F12[6]

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<protect>

Notes

Accessions Related to ssrA Expression


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG30100

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4263

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2621

EcoGene

EcoGene:EG30100

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002542

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008624

Escherichia coli str. K-12 substr. MG1655

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Notes

Links



Evolution


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Homologs in Other Organisms


See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments
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Do-It-Yourself Web Tools


Notes

Families


Database Accession Notes

PFAM (EcoliWiki Page)

PFAM:PF01668

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Notes

Families


See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes
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Notes

Links



References


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  6. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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