ribF:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ribF}}{{Tab On|Gene|ribF}}{{Tab|Gene Product(s)|ribF}}{{Tab|Expression|ribF}}{{Tab|Evolution|ribF}}{{Tab|On One Page|ribF}}{{TabsBottom}}
{{Tab|Quickview|ribF}}{{Tab On|Gene|ribF}}{{Tab|Gene Product(s)|ribF}}{{Tab|Expression|ribF}}{{Tab|Evolution|ribF}}{{Tab|On One Page|ribF}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ribF''  
''ribF''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Riboflavin
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0026, b0025, JW0023, yaaC''<ref name='LIB:Riley_2006'/>, yaaC''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10629.V46a9a6c80a1bd&page=10629&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0026, b0025, JW0023, yaaC''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9a6c881e10"  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
|-
|-  
|
|
MG1655
MG1655
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0.46 minutes&nbsp;
0.46 minutes&nbsp;
|
|
MG1655: 21407..22348<br />{{GBrowseFigureByCoord|20407|23348|ecoli|MG1655}}
MG1655: 21407..22348<br /><gbrowseImage>
name=NC_000913:21407..22348
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11079 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11079 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:20407..23348 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|20407|23348|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:21407..22348&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|21407|22348|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11079 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11079 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 25479..26420<br /><gbrowseImage>
name=NC_012967:25479..26420
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|25479|26420|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|25479|26420|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 21407..22348<br /><gbrowseImage>
name=NC_012759:21407..22348
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|21407|22348|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|21407|22348|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 21407..22348<br />{{GBrowseFigureByCoord|20407|23348|ecoli_W3110|W3110}}  
W3110: 21407..22348<br /><gbrowseImage>
name=NC_007779:21407..22348
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|20407|23348|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|21407|22348|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 21407..22348<br /><gbrowseImage>
name=NC_010473:21407..22348
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:20407..23348 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|19525|24230|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:21407..22348&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|19525|24230|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9a6c929802"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9a6c969b93"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L4e04c2808c73e"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0023
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAGCTGATACGCGGCATACA
 
Primer 2:CCAGCCGGTTTTGTTAGCCCAAA
|-
|
[[:Category:Kohara_Phage:6H3|6H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=102 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:22B12|22B12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=103 Genobase]
|
PMID:3038334
|-
|
[[thrA:Gene|thrA34::Tn10]]
|
Linked marker
|
CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:thr-34::Tn10
|-
|
[[carB:Gene|carB96::Tn10]]
|
Linked marker
|
CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 68% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:car-96::Tn10
 
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11079 EcoCyc:EG11079] 
EcoCyc:EG11079
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1071 EchoBASE:EB1071] 
EcoGene:EG11079
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0025 EcoliGenExpDB:b0025] 
RegulonDB:ECK120001067
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0029 ECOL199310CYC:C0029]
[http://www.ncbi.nlm.nih.gov/gene?term=949129 GeneID:949129]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11079 EcoGene:EG11079] 
EchoBASE:EB1071
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=RIBF ECOO157CYC:RIBF] 
ASAP:ABE-0000091
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10629.X46a9a6ca99df8&page=10629&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/35833 CGSC:35833] 
|
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:rib genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:36, 19 September 2013

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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

ribF

Mnemonic

Riboflavin

Synonyms

ECK0026, b0025, JW0023, yaaC[1], yaaC

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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

0.46 minutes 

MG1655: 21407..22348
<gbrowseImage> name=NC_000913:21407..22348 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 25479..26420
<gbrowseImage> name=NC_012967:25479..26420 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 21407..22348
<gbrowseImage> name=NC_012759:21407..22348 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 21407..22348
<gbrowseImage> name=NC_007779:21407..22348 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 21407..22348
<gbrowseImage> name=NC_010473:21407..22348 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
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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

JW0023

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCAAGCTGATACGCGGCATACA

Primer 2:CCAGCCGGTTTTGTTAGCCCAAA

6H3

Kohara Phage

Genobase

PMID:3038334[3]

22B12

Kohara Phage

Genobase

PMID:3038334[3]

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 46% [5]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[4]

est. P1 cotransduction: 68% [5]
Synonyms:car-96::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:EG11079

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11079

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001067

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949129

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1071

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000091

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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. ↑ 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
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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