aroG:Gene: Difference between revisions

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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0743, b0754, JW0737''<ref name='LIB:Riley_2006'/>
''ECK0743, b0754, JW0737''<ref name='LIB:Riley_2006'/>, JW0737''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="A46a9b7f1a34b3"  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="A46a9b7f1a34b3"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
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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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16.92 minutes&nbsp;
16.92 minutes&nbsp;
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MG1655: 784856..785908<br />{{GBrowseFigureByCoord|784856|785908|ecoli|MG1655}}
MG1655: 784856..785908<br /><gbrowseImage>
name=NC_000913:784856..785908
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10079 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10079 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|783856|786908|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|783856|786908|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|784856|785908|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|784856|785908|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10079 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10079 EcoCyc Sequence Dump]  
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NC_012967: 766262..767314<br />{{GBrowseFigureByCoord|766262|767314|REL606|NC_012967}}
NC_012967: 766262..767314<br /><gbrowseImage>
name=NC_012967:766262..767314
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|766262|767314|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|766262|767314|GBrowse (REL606)}}
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NC_012759: 687824..688876<br />{{GBrowseFigureByCoord|687824|688876|BW2952|NC_012759}}
NC_012759: 687824..688876<br /><gbrowseImage>
name=NC_012759:687824..688876
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|687824|NC_688876|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|687824|688876|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|687824|NC_688876|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|687824|688876|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 786055..787107<br />{{GBrowseFigureByCoord|786055|787107|ecoli_W3110|W3110}}
W3110: 786055..787107<br /><gbrowseImage>
name=NC_007779:786055..787107
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|785055|788107|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|785055|788107|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|786055|787107|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|786055|787107|FASTA Dump}}  
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DH10B: 837448..838500<br />{{GBrowseFigureByCoord|837448|838500|ecoli_DH10B|DH10B}}
DH10B: 837448..838500<br /><gbrowseImage>
name=NC_010473:837448..838500
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|835344|840604|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|835344|840604|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|835344|840604|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|835344|840604|FASTA Dump}}  


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{|   id="T46a9b7f24bcaf"  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="T46a9b7f24bcaf"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="M46a9b7f28bbdc"  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="M46a9b7f28bbdc"  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}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12063.J4e04b7b0c82ee-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04b7b0c82ee"  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.12063.J4e04b7b0c82ee&page=12063&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="N46a9b7f334618"  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="N46a9b7f334618"  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:CCCCCGCGACGCGCTTTTACTGC  
Primer 2:CCCCCGCGACGCGCTTTTACTGC  
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[[:Category:Kohara_Phage:4H1|4H1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=179 Genobase]
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PMID:3038334
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{|   id="W46a9b7f3bcd3c"  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="W46a9b7f3bcd3c"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=EG10079 EcoCyc:EG10079]
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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=EB0077 EchoBASE:EB0077]
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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=b0754 EcoliGenExpDB:b0754]
EcoCyc:EG10079
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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]])
[[EcoGene]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0830 ECOL199310CYC:C0830]
EcoGene:EG10079
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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]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10079 EcoGene:EG10079]
RegulonDB:ECK120000075
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=AROG ECOO157CYC:AROG]
[http://www.ncbi.nlm.nih.gov/gene?term=945605 GeneID:945605]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/1002 CGSC:1002]
EchoBASE:EB0077
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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=0002560&formSubmitReturn=1 ASAP:ABE-0002560]
ASAP:ABE-0002560
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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 20:33, 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

aroG

Mnemonic

Aromatic

Synonyms

ECK0743, b0754, JW0737[1], JW0737

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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

16.92 minutes 

MG1655: 784856..785908
<gbrowseImage> name=NC_000913:784856..785908 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 766262..767314
<gbrowseImage> name=NC_012967:766262..767314 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 687824..688876
<gbrowseImage> name=NC_012759:687824..688876 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 786055..787107
<gbrowseImage> name=NC_007779:786055..787107 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 837448..838500
<gbrowseImage> name=NC_010473:837448..838500 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

784856

Edman degradation

PMID:9298646[2]
PMID:9740056[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

ΔaroG (Keio:JW0737)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC8801[5]

aroG365

CGSC:11321

ΔaroG726::kan

PMID:16738554[4]

CGSC:100068


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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

JW0737

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAATTATCAGAACGACGATTT

Primer 2:CCCCCGCGACGCGCTTTTACTGC

4H1

Kohara Phage

Genobase

PMID:3038334[7]

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[5]

est. P1 cotransduction: 84% [8]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: 22% [8]
Synonyms:zbi-29::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:EG10079

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10079

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000075

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945605

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0077

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002560

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. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  3. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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
  7. ↑ 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
  8. ↑ 8.0 8.1 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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