matC: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="T46a9aca877f79"  class=" tableEdit Gene_nomenclature_table"   
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
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''yagY, ECK0291, b0292, JW0286''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''yagY, ECK0291, b0292, JW0286''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, JW0286''


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*  
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{|   id="V46a9aca8f0bbd"  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="V46a9aca8f0bbd"  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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6.65 minutes&nbsp;
6.65 minutes&nbsp;
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|
MG1655: 309250..308582<br />{{GBrowseFigureByCoord|308582|309250|ecoli|MG1655}}
MG1655: 309250..308582<br /><gbrowseImage>
name=NC_000913:308582..309250
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6163 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6163 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|307582|310250|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|307582|310250|GBrowse(MG1655)}}
   
   
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|
{{GBrowseFastaLink|ecoli|NC_000913|308582|309250|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|308582|309250|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6163 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6163 EcoCyc Sequence Dump]  
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NC_012967: 279540..280208<br />{{GBrowseFigureByCoord|279540|280208|REL606|NC_012967}}
NC_012967: 279540..280208<br /><gbrowseImage>
name=NC_012967:279540..280208
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|279540|280208|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|279540|280208|GBrowse (REL606)}}
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&nbsp;
&nbsp;
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W3110: 309250..308582<br />{{GBrowseFigureByCoord|308582|309250|ecoli_W3110|W3110}}
W3110: 309250..308582<br /><gbrowseImage>
name=NC_007779:308582..309250
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|307582|310250|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|307582|310250|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|308582|309250|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|308582|309250|FASTA Dump}}  
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DH10B: 284800..284132<br />{{GBrowseFigureByCoord|284132|284800|ecoli_DH10B|DH10B}}
DH10B: 284800..284132<br /><gbrowseImage>
name=NC_010473:284132..284800
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_DH10B|NC_010473|282796|286136|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|282796|286136|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|282796|286136|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|282796|286136|FASTA Dump}}  


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{|   id="A46a9aca99ab32"  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="A46a9aca99ab32"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11159.A46a9aca99ab32&page=11159&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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{| {{Prettytable}} id="D46a9aca9dbb30"  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="D46a9aca9dbb30"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001007 yagY::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001007 yagY::Tn5KAN-I-SceI] (FB20130)
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Insertion at nt 426 in Minus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20130]
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At position 426 in Minus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20130
does not contain [[pKD46]]  
|-  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001007 yagY::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001007 yagY::Tn5KAN-I-SceI] (FB20131)
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Insertion at nt 426 in Minus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20131]
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At position 426 in Minus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20131
contains [[pKD46]]  
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11159.A4e04bee4b07ee-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04bee4b07ee"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.11159.A4e04bee4b07ee&page=11159&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="N46a9acaa857c8"  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="N46a9acaa857c8"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:5E5|5E5]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=132 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:3E3|3E3]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=133 Genobase]
|
PMID:3038334
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[[:Category:Kohara_Phage:9G4|9G4]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=134 Genobase]
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PMID:3038334


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{|   id="W46a9acab1bdf0"  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="W46a9acab1bdf0"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6163 EcoCyc:G6163]
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|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3334 EchoBASE:EB3334]
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|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0292 EcoliGenExpDB:b0292]
[http://www.ncbi.nlm.nih.gov/gene?term=948806 GeneID:948806]
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Escherichia coli str. K-12 substr. 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=C0403 ECOL199310CYC:C0403]
RegulonDB:
|
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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]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13564 EcoGene:EG13564]
EchoBASE:
|
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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=YAGY ECOO157CYC:YAGY]
ASAP:
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:37, 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

matC

Mnemonic

Meningitis-Associated

Synonyms

yagY, ECK0291, b0292, JW0286[1][2], JW0286

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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

6.65 minutes 

MG1655: 309250..308582
<gbrowseImage> name=NC_000913:308582..309250 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 279540..280208
<gbrowseImage> name=NC_012967:279540..280208 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 309250..308582
<gbrowseImage> name=NC_007779:308582..309250 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 284800..284132
<gbrowseImage> name=NC_010473:284132..284800 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

yagY::Tn5KAN-I-SceI (FB20130)

Insertion at nt 426 in Minus orientation

PMID:15262929[3]

E. coli Genome Project:FB20130

does not contain pKD46

yagY::Tn5KAN-I-SceI (FB20131)

Insertion at nt 426 in Minus orientation

PMID:15262929[3]

E. coli Genome Project:FB20131

contains pKD46

ΔmatC736::kan

PMID:16738554[4]

CGSC:106236


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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

[back to top]


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

Resource Resource Type Source Notes/Reference

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

5E5

Kohara Phage

Genobase

PMID:3038334[6]

3E3

Kohara Phage

Genobase

PMID:3038334[6]

9G4

Kohara Phage

Genobase

PMID:3038334[6]

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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

NCBI (EcoliWiki Page)

GeneID:948806

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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 6.2 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

Categories

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