arnF:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G46a9d9cbb5a99"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7171 ECOCYC:G7171]
EcoCyc:G7171
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG14094 EcoGene:EG14094]
EcoGene:EG14094
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120003747
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB3847
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0007466
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:23, 27 May 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

arnF

Mnemonic

ara4N (4-amino-4-deoxy-L-arabinose)

Synonyms

ECK2252, b2258, JW5373, pmrL, yfbJ[1][2], pbgE3, pmrM, yfbJ

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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

51.1 minutes 

MG1655: 2370914..2371300
<gbrowseImage> name=NC_000913:2370914..2371300 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2319405..2319791
<gbrowseImage> name=NC_012967:2319405..2319791 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2256719..2257105
<gbrowseImage> name=NC_012759:2256719..2257105 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2377562..2377948
<gbrowseImage> name=AC_000091:2377562..2377948 source=W3110 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

ΔyfbJ (Keio:JW5373)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC11348[4]

ΔyfbJ740::kan

PMID:16738554[3]

CGSC:104644


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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

JW5373

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGGCCTGATGTGGGGATTATT

Primer 2:CCGTAACGTTGTTTTGTCGTGGG

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[4]

est. P1 cotransduction: 34% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[4]

est. P1 cotransduction: 51% [6]
Synonyms:zej-223::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:G7171

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14094

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945344

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003747

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3847

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007466

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  6. ↑ 6.0 6.1 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).

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