rapA:Gene: Difference between revisions

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{{Tab|Quickview|hepA}}{{Tab On|Gene|hepA}}{{Tab|Gene Product(s)|hepA}}{{Tab|Expression|hepA}}{{Tab|Evolution|hepA}}{{Tab|On One Page|hepA}}{{TabsBottom}}
{{Tab|Quickview|rapA}}{{Tab On|Gene|rapA}}{{Tab|Gene Product(s)|rapA}}{{Tab|Expression|rapA}}{{Tab|Evolution|rapA}}{{Tab|On One Page|rapA}}{{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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{|{{Prettytable}}
{|  id="U46a9a78b7adf8"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''hepA''  
''rapA''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
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|-
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
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''ECK0060, b0059, JW0058, rapA, yabA''<ref name='LIB:Riley_2006'/>
''ECK0060, b0059, JW0058, rapA, yabA'', hepA<ref name='LIB:Riley_2006'/>, hepA, yabA''
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125289'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9a78bf32cb"  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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MG1655
MG1655
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1.3 minutes&nbsp;
1.3 minutes&nbsp;
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MG1655: 63264..60358<br />{{GBrowseFigureByCoord|59358|64264|ecoli|MG1655}}
MG1655: 63264..60358<br /><gbrowseImage>
name=NC_000913:60358..63264
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11083 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11083 EcoCyc]
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{{GBrowseFastaLink|ecoli|NC_000913|60358|63264|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|60358|63264|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11083 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11083 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 66068..63162<br /><gbrowseImage>
name=NC_012967:63162..66068
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|63162|66068|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|63162|66068|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 60358..63264<br /><gbrowseImage>
name=NC_012759:60358..63264
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|60358|NC_63264|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|60358|NC_63264|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 63264..60358<br />{{GBrowseFigureByCoord|59358|64264|ecoli_W3110|W3110}}
W3110: 63264..60358<br /><gbrowseImage>
name=NC_007779:60358..63264
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|59358|64264|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|NC_007779|59358|64264|GBrowse(W3110)}}  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:60358..63264&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli_W3110|NC_007779|60358|63264|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 62378..60358<br /><gbrowseImage>
name=NC_010473:60358..62378
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_DH10B|NC_010473|56318|66418|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|56318|66418|FASTA Dump}}
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125290'
{|  id="F46a9a78c9af45"  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
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Coding Start (SO:0000323)
|
[[MG1655]]
|
60361
|
Edman degradation
|
PMID:9614128<br />PMID:11751638<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====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}}
{| {{Prettytable}}  id="K46a9a78cdb2d3" 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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&Delta;hepA (Keio:JW0058)
''hepA(del)'' (Keio:JW0058)
|
|
deletion
deletion
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106647 CGSC8366]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106647 CGSC8366]<ref name='LIB:cgsc'/>  
|
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''&#916;hepA769::kan''
rapAK183A
|
 
|
K183A
|
 
|
Loss of function. Still interacts with RNAP
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P60240 UniProt:P60240]
|-
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rapADE280AA
|
|


|
DE280AA
|
|
Loss of function. Still interacts with RNAP
|
|


|
|


|
seeded from [http://www.uniprot.org/uniprot/P60240 UniProt:P60240]
|-
|
''hepA769(del)::kan''
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
 
|
 
|
 
|
PMID:16738554
|
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[[cgscmutation:101346|CGSC:101346]]
[[cgscmutation:101346|CGSC:101346]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10697.K46a9a78cdb2d3&page=10697&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===
HepA has a plausible function and reasonable map location to be the gene affected by the [http://cgsc.biology.yale.edu/Mutation.php?ID=75078 psu-1] mutation.
HepA has a plausible function and reasonable map location to be the gene affected by the [http://cgsc.biology.yale.edu/Mutation.php?ID=75078 psu-1] mutation.
==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="S4e04c20234f91"  class=" tableEdit Genetic_interaction_table dataTable" 
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0058
JW0058
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCCTGATGCGTTACAACGATCAA  
Primer 2:CCCTGATGCGTTACAACGATCAA  
|-
|-
|
[[:Category:Kohara_Phage:8D2|8D2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=106 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5H5|5H5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=107 Genobase]
|
PMID:3038334
|-  
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[[carB:Gene|carB96::Tn10]]
[[carB:Gene|carB96::Tn10]]
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CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:car-96::Tn10  
Synonyms:car-96::Tn10  
|-
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|
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leuO3051::Tn10
leuO3051::Tn10
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CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 42% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 42% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).


Synonyms:zab-3051::Tn10
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The start of leuO was reannotated by Riley et al. (2006).
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===Notes===
===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11083 EcoCyc:EG11083]
EcoCyc:EG11083
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1075 EchoBASE:EB1075]
EchoBASE:EB1075
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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]])
[[EcoGene]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11083 EcoGene:EG11083]
EcoGene:EG11083
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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]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000198&formSubmitReturn=1 ASAP:ABE-0000198] 
ASAP:ABE-0000198
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11083 ECOCYC:EG11083]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=948523 GeneID:948523]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001071
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:hep genes]]
[[Category:hep genes]][[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

rapA

Mnemonic
Synonyms

ECK0060, b0059, JW0058, rapA, yabA, hepA[1], hepA, yabA

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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

1.3 minutes 

MG1655: 63264..60358
<gbrowseImage> name=NC_000913:60358..63264 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 66068..63162
<gbrowseImage> name=NC_012967:63162..66068 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 60358..63264
<gbrowseImage> name=NC_012759:60358..63264 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 63264..60358
<gbrowseImage> name=NC_007779:60358..63264 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 62378..60358
<gbrowseImage> name=NC_010473:60358..62378 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

60361

Edman degradation

PMID:9614128[2]
PMID:11751638[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

hepA(del) (Keio:JW0058)

deletion

deletion

PMID:16738554[4]

Shigen

CGSC8366[5]

rapAK183A

K183A

Loss of function. Still interacts with RNAP

seeded from UniProt:P60240

rapADE280AA

DE280AA

Loss of function. Still interacts with RNAP

seeded from UniProt:P60240

hepA769(del)::kan

PMID:16738554[4]

CGSC:101346


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Notes

HepA has a plausible function and reasonable map location to be the gene affected by the psu-1 mutation.


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

JW0058

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCCTTTTACACTTGGTCAACG

Primer 2:CCCTGATGCGTTACAACGATCAA

8D2

Kohara Phage

Genobase

PMID:3038334[7]

5H5

Kohara Phage

Genobase

PMID:3038334[7]

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 34% [8]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 42% [8]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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:EG11083

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1075

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0059

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0070

EcoGene

EcoGene:EG11083

Escherichia coli str. K-12 substr. MG1655

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0067

CGSC (EcoliWiki Page)

CGSC:29491

ASAP

ASAP:ABE-0000198

Escherichia coli str. K-12 substr. MG1655

EcoCyc (EcoliWiki Page)

ECOCYC:EG11083

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948523

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001071

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. ↑ Muzzin, O et al. (1998) Disruption of Escherichia coli hepA, an RNA polymerase-associated protein, causes UV sensitivity. J. Biol. Chem. 273 15157-61 PubMed
  3. ↑ Sukhodolets, MV et al. (2001) RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription. Genes Dev. 15 3330-41 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. ↑ 7.0 7.1 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
  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).

Categories

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