yigA:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{|   id="M46a9ff8f754ef" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''yigA''  
''yigA''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Systematic nomenclature
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3805, b3810, JW3783''<ref name='LIB:Riley_2006'/>
''ECK3805, b3810, JW3783''<ref name='LIB:Riley_2006'/>, JW3783''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9ff90030b4"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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86.08 minutes&nbsp;
86.08 minutes&nbsp;
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MG1655: 3993606..3994313<br />{{GBrowseFigureByCoord|3993606|3994313|ecoli|MG1655}}
MG1655: 3993606..3994313<br /><gbrowseImage>
name=NC_000913:3993606..3994313
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11201 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11201 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3992606|3995313|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3992606|3995313|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3993606|3994313|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3993606|3994313|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11201 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11201 EcoCyc Sequence Dump]  
|-
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[[REL606]]
|
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NC_012967: 3957420..3958127<br /><gbrowseImage>
name=NC_012967:3957420..3958127
source=REL606
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|REL606|NC_012967|3957420|3958127|GBrowse (REL606)}}
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&nbsp;
&nbsp;
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W3110: 3641098..3640391<br />{{GBrowseFigureByCoord|3640391|3641098|ecoli_W3110|W3110}}
W3110: 3641098..3640391<br /><gbrowseImage>
name=NC_007779:3640391..3641098
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|3639391|3642098|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3639391|3642098|GBrowse(W3110)}}  
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3640391|3641098|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3640391|3641098|FASTA Dump}}  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9ff911227e"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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Primer 2:CCTACGCGTTCAATCCAACGCTC  
Primer 2:CCTACGCGTTCAATCCAACGCTC  
|-
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[[:Category:Kohara_Phage:12G1|12G1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=553 Genobase]
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PMID:3038334
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Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.  
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.  


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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=EG11201 EcoCyc:EG11201]
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|-
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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=EB1186 EchoBASE:EB1186]
EcoCyc:EG11201
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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=b3810 EcoliGenExpDB:b3810]
EcoGene:EG11201
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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=C4731 ECOL199310CYC:C4731]
RegulonDB:ECK120001181
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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=EG11201 EcoGene:EG11201]
[http://www.ncbi.nlm.nih.gov/gene?term=948359 GeneID:948359]
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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=YIGA ECOO157CYC:YIGA]
EchoBASE:EB1186
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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=0012444&formSubmitReturn=1 ASAP:ABE-0012444]
ASAP:ABE-0012444
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yig genes]][[Category:Gene_List:REL606]]
[[Category:yig genes]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:49, 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

yigA

Mnemonic

Systematic nomenclature

Synonyms

ECK3805, b3810, JW3783[1], JW3783

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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

86.08 minutes 

MG1655: 3993606..3994313
<gbrowseImage> name=NC_000913:3993606..3994313 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3957420..3958127
<gbrowseImage> name=NC_012967:3957420..3958127 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3641098..3640391
<gbrowseImage> name=NC_007779:3640391..3641098 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

Strain DH10B

L156STOP

Nonsense mutation

PMID:18245285[2]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔyigA (Keio:JW3783)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10750[4]

ΔyigA756::kan

PMID:16738554[3]

CGSC:105376


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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

JW3783

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAGCAACCAGGGGAAGAACT

Primer 2:CCTACGCGTTCAATCCAACGCTC

12G1

Kohara Phage

Genobase

PMID:3038334[6]

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[4]

est. P1 cotransduction: 18% [7]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[4]

est. P1 cotransduction: 59% [7]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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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:EG11201

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11201

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001181

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948359

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1186

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012444

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. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  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. ↑ 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
  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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