preA:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2140, b2147, JW2134, yeiA'''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, yeiA''
''ECK2140, b2147, JW2134, yeiA'''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, yeiA, dpdB''


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{|   id="N46a9d71d68cac"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9d71d68cac"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 2238599..2239834<br /><gbrowseImage>
W3110: 2238599..2239834<br /><gbrowseImage>
name=AC_000091:2238599..2239834
name=NC_007779:2238599..2239834
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|2237599|2240834|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2237599|2240834|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|2238599|2239834|FASTA Dump}}  
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{|   id="E46a9d71e23db8"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9d71e23db8"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="Y46a9d71e6872e"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9d71e6872e"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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{|   id="M4e04c8b44e2cb"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04c8b44e2cb"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="V46a9d71f1e4d5"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9d71f1e4d5"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="E46a9d71fb1a59"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9d71fb1a59"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|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=EG11289 EcoCyc:EG11289]
EcoCyc:EG11289
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1266 EchoBASE:EB1266]
EcoGene:EG11289
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2147 EcoliGenExpDB:b2147]
RegulonDB:ECK120001262
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C2680 ECOL199310CYC:C2680]
[http://www.ncbi.nlm.nih.gov/gene?term=949037 GeneID:949037]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG11289 EcoGene:EG11289]
EchoBASE:EB1266
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=YEIA ECOO157CYC:YEIA]
ASAP:ABE-0007098
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007098&formSubmitReturn=1 ASAP:ABE-0007098]
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!|Name!!URL!!Comments
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Latest revision as of 20:40, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

preA

Mnemonic

Systematic nomenclature

Synonyms

ECK2140, b2147, JW2134, yeiA[1][2], yeiA, dpdB

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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

48.13 minutes 

MG1655: 2233287..2234522
<gbrowseImage> name=NC_000913:2233287..2234522 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2186503..2187738
<gbrowseImage> name=NC_012967:2186503..2187738 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2125770..2127005
<gbrowseImage> name=NC_012759:2125770..2127005 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2238599..2239834
<gbrowseImage> name=NC_007779:2238599..2239834 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2324295..2325530
<gbrowseImage> name=NC_010473:2324295..2325530 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

Coding Start (SO:0000323)

MG1655

2233287

Edman degradation

PMID:18482579[3]


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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

ΔyeiA (Keio:JW2134)

deletion

deletion

PMID:16738554[4]

Shigen


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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

JW2134

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTAACGAAAGATCTTTCGAT

Primer 2:CCtAACGTTACCGGGTGTTCTTT

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[6]

est. P1 cotransduction: 6% [7]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[6]

est. P1 cotransduction: 2% [7]
Synonyms:zeg-722, zei-722::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:EG11289

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11289

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001262

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949037

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1266

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007098

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ Mihara, H et al. (2008) The iscS gene deficiency affects the expression of pyrimidine metabolism genes. Biochem. Biophys. Res. Commun. 372 407-11 PubMed
  4. ↑ 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
  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 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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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