EcoliHub logo

Try the new EcoliHub and let us know what you'd like to see.

sgrS:On One Page

From EcoliWiki

Jump to: navigation, search
Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]



See Help:Quickview for help with entering information in the Quickview table.

Standard Name

sgrS

Gene Synonym(s)

ECK0071, b4577, JWR0259, ryaA[1]

Product Desc.

SgrS[2][3]

Product Synonyms(s)

small antisense RNA[1], RyaA[2][1], B4577[2][1]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sgrS[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(sgrS)    Textpresso(sgrS)

edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]



Gene

[back to top]


Nomenclature

[back to top]


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

Standard name

sgrS

Mnemonic

SuGar transport-Related sRNA

Synonyms

ECK0071, b4577, JWR0259, ryaA[1]

edit table

Notes

Location(s) and DNA Sequence

[back to top]


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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

1.67 minutes 

MG1655: 77367..77593
gbrowse_img.php?coord=77367..77593&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 77367..77593
gbrowse_img.php?coord=77367..77593&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 77366..77592
gbrowse_img.php?coord=77366..77592&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

edit table

Notes

Sequence Features

[back to top]


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

Feature typeLocationDescription
edit table

Notes

Alleles and Phenotypes

[back to top]


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

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments
edit table

Notes

Genetic Resources

[back to top]


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

ResourceResource TypeSourceNotes/Reference

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[4]

est. P1 cotransduction: 14% [5]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 81% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G0-9941

EchoBASE (EcoliWiki Page)

EchoBASE:EB4546


edit table

Notes

Links

[back to top]



Product(s)

[back to top]



Nomenclature

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

Standard name

SgrS RNA

Synonyms

small antisense RNA[1], RyaA[2][1], B4577[2][1]

Product description

SgrS[2][3]

EC number (for enzymes)


edit table

Notes

Function

[back to top]


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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0016246

RNA interference

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005515

protein binding

PMID:14622403

IDA: Inferred from Direct Assay

UniProtKB:P0A6X3

F

Seeded from EcoCyc [6]

complete

GO:0006950

response to stress

PMID:15522088

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [6]

complete

GO:0030423

RNA interference, targeting of mRNA for destruction

PMID:15522088

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [6]

complete

GO:0040033

negative regulation of translation, ncRNA-mediated

PMID:16549791

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [6]

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence
edit table

Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
edit table

Notes

Structure and Physical Properties

[back to top]


Physical Properties

Type

sRNA

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


edit table

SgrS RNA - Image courtesy of RFam
Domains/Motifs/Modification Sites

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

TypeResiduesDescriptionNotesReferences
edit table


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

Structures
Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource typeSourceNotes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:RNA0-241


edit table

Notes

Links

[back to top]




Expression

[back to top]



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

[back to top]


See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


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

Transcription unit(s)

sgrS

edit table
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

[back to top]


gbrowse_img.php?coord=77347..77387&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
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

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

[back to top]


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

Allele NameMutationPhenotypeReference
edit table


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

TypeReferenceNotes
edit table


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

Resource NameResource TypeDescriptionSourceNotes
edit table

Notes

Accessions Related to sgrS Expression

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G0-9941

EchoBASE (EcoliWiki Page)

EchoBASE:EB4546


edit table

Notes

Links

[back to top]



Evolution

[back to top]



Homologs in Other Organisms

[back to top]



Do-It-Yourself Web Tools

Notes

Families

[back to top]


DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00496

edit table

Notes

Links

[back to top]



References

[back to top]


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

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 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. ↑ 6.0 6.1 6.2 6.3 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

Categories

[back to top]


Retrieved from "http://ecoliwiki.net/colipedia/index.php/sgrS:On_One_Page"
Personal tools