yhaL:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3098, b3107, JW5517''<ref name='LIB:Riley_2006'/>
''ECK3098, b3107, JW5517''<ref name='LIB:Riley_2006'/>, JW5517''


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{|   id="V46a9edce00671"  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="V46a9edce00671"  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: 3253699..3253863<br /><gbrowseImage>
W3110: 3253699..3253863<br /><gbrowseImage>
name=AC_000091:3253699..3253863
name=NC_007779:3253699..3253863
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|3252699|3254863|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3252699|3254863|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|3253699|3253863|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3253699|3253863|FASTA Dump}}  
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{|   id="W46a9edceb2ff5"  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="W46a9edceb2ff5"  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="V46a9edcf075b7"  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="V46a9edcf075b7"  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="K4e04ca0cc84b2"  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="K4e04ca0cc84b2"  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="G46a9edcfba367"  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="G46a9edcfba367"  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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Primer 2:CCtGCGGTAGCTTCATCCTCGGC  
Primer 2:CCtGCGGTAGCTTCATCCTCGGC  
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[[:Category:Kohara_Phage:21D1|21D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=513 Genobase]
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PMID:3038334
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:zgj-203::Tn10, zha-203::Tn10  
Synonyms:zgj-203::Tn10, zha-203::Tn10  
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[[:Category:Kohara_Phage:21D1|21D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=513 Genobase]
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PMID:3038334


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{|   id="N46a9edd060f79"  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="N46a9edd060f79"  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=G7621 EcoCyc:G7621]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2607 EchoBASE:EB2607]
EcoCyc:G7621
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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]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3107 EcoliGenExpDB:b3107]
EcoGene:EG12751
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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]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C3866 ECOL199310CYC:C3866]
RegulonDB:ECK120004174
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12751 EcoGene:EG12751]
[http://www.ncbi.nlm.nih.gov/gene?term=947618 GeneID:947618]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YHAL ECOO157CYC:YHAL]
EchoBASE:EB2607
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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]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0010219&formSubmitReturn=1 ASAP:ABE-0010219]
ASAP:ABE-0010219
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{|   id="J46a7097a236e8"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:46, 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

yhaL

Mnemonic

Systematic nomenclature

Synonyms

ECK3098, b3107, JW5517[1], JW5517

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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

70.11 minutes 

MG1655: 3253065..3253229
<gbrowseImage> name=NC_000913:3253065..3253229 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3188076..3188240
<gbrowseImage> name=NC_012967:3188076..3188240 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3140213..3140377
<gbrowseImage> name=NC_012759:3140213..3140377 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3253699..3253863
<gbrowseImage> name=NC_007779:3253699..3253863 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3350810..3350974
<gbrowseImage> name=NC_010473:3350810..3350974 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

ΔyhaL (Keio:JW5517)

deletion

deletion

PMID:16738554[2]

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

JW5517

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAGTAAAAAATTGGCCAAAAA

Primer 2:CCtGCGGTAGCTTCATCCTCGGC

21D1

Kohara Phage

Genobase

PMID:3038334[4]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: 21% [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: % [6]
Synonyms:zgj-203::Tn10, zha-203::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:G7621

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12751

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004174

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947618

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2607

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010219

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. ↑ 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
  3. ↑ 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
  4. ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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).

Categories

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