acrA: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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{|{{Prettytable}}
{|  id="H46a9b13cad3d5"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''acrA''  
''acrA''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Acridine
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0457, b0463, JW0452, Mb, lir, mbl, mtcA, sipB, nbsA''<ref name='LIB:Riley_2006'/>
''ECK0457, b0463, JW0452, Mb, lir, mbl, mtcA, sipB, nbsA''<ref name='LIB:Riley_2006'/>
|-
 
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===Notes===
===Notes===
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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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10.42 minutes&nbsp;
10.42 minutes&nbsp;
|
|
MG1655: 484843..483650<br />{{GBrowseFigureByCoord|482650|485843|ecoli|MG1655}}
MG1655: 484843..483650<br /><gbrowseImage>
name=NC_000913:483650..484843
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11703 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11703 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:482650..485843 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|482650|485843|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:483650..484843&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|483650|484843|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11703 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11703 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 457686..456493<br /><gbrowseImage>
name=NC_012967:456493..457686
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|456493|457686|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|456493|457686|FASTA Dump}}
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[[BW2952]]
|
 
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NC_012759: 386409..387602<br /><gbrowseImage>
name=NC_012759:386409..387602
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|386409|387602|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|386409|387602|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 484843..483650<br />{{GBrowseFigureByCoord|482650|485843|ecoli_W3110|W3110}}  
W3110: 484843..483650<br /><gbrowseImage>
name=NC_007779:483650..484843
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|482650|485843|GBrowse(W3110)}}  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:482650..485843 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|483650|484843|FASTA Dump}}
|-  
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:483650..484843&plugin_action=Go FASTA Dump]
[[DH10B]]
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DH10B: 424174..422981<br /><gbrowseImage>
name=NC_010473:422981..424174
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|420595|426560|GBrowse(DH10B)}}
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{{GBrowseFastaLink|DH10B|NC_010473|420595|426560|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
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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;acrA (Keio:JW0452)
''acrA(del)'' (Keio:JW0452)
|
|
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]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
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''acrA1''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:6294|CGSC:6294]]
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|-
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''acrA13''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:7201|CGSC:7201]]
|
|-
|
acrA
|
deletion
|
 
|
Sensitivity to
|
decreases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
|-
|
''acrA748(del)''::FRT
|
 
|
 
|
Mutagenesis rate
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
Parental Strain: SMR4562
Experimental Strain: SMR12220
 
|
Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
AcrA mutants grow to higher cell density than wt <ref name='PMID: 16467145'/>
AcrA mutants grow to higher cell density than wt <ref name='PMID: 16467145'/>
==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0452
JW0452
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCAGACTTGGACTGTTCAGGCTG  
Primer 2:CCAGACTTGGACTGTTCAGGCTG  
|-
|-
|
[[:Category:Kohara_Phage:19B7|19B7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=150 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:8C4|8C4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=151 Genobase]
|
PMID:3038334
|-  
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[[ppiD:Gene|zaj-3054::Tn10]]
[[ppiD:Gene|zaj-3054::Tn10]]
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CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zba-3054::Tn10  
Synonyms:zba-3054::Tn10  
|-
|-  
|
|
[[gsk:Gene|gsk-3055::Tn10]]
[[gsk:Gene|gsk-3055::Tn10]]
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CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 54% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10


Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
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===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=EG11703 EcoCyc:EG11703] 
EcoCyc:EG11703
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|
''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=EB1654 EchoBASE:EB1654] 
EcoGene:EG11703
|
|
''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=b0463 EcoliGenExpDB:b0463] 
RegulonDB:ECK120001646
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|
''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=C0581 ECOL199310CYC:C0581]
[http://www.ncbi.nlm.nih.gov/gene?term=945112 GeneID:945112]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11703 EcoGene:EG11703] 
EchoBASE:EB1654
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|
''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=ACRA ECOO157CYC:ACRA] 
ASAP:ABE-0001603
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11491.A46a9b14085b1b&page=11491&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/1045 CGSC:1045]
|
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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:acr genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:31, 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

acrA

Mnemonic

Acridine

Synonyms

ECK0457, b0463, JW0452, Mb, lir, mbl, mtcA, sipB, nbsA[1]

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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

10.42 minutes 

MG1655: 484843..483650
<gbrowseImage> name=NC_000913:483650..484843 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 457686..456493
<gbrowseImage> name=NC_012967:456493..457686 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 386409..387602
<gbrowseImage> name=NC_012759:386409..387602 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 484843..483650
<gbrowseImage> name=NC_007779:483650..484843 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 424174..422981
<gbrowseImage> name=NC_010473:422981..424174 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

acrA(del) (Keio:JW0452)

deletion

deletion

PMID:16738554[2]

Shigen

acrA1

CGSC:6294

acrA13

CGSC:7201

acrA

deletion

Sensitivity to

decreases sensitivity to bicyclomycin

PMID:21357484[3]

fig 2

acrA748(del)::FRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[4]

Parental Strain: SMR4562 Experimental Strain: SMR12220

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

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Notes

AcrA mutants grow to higher cell density than wt [5]


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

JW0452

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAACAAAAACAGAGGGTTTAC

Primer 2:CCAGACTTGGACTGTTCAGGCTG

19B7

Kohara Phage

Genobase

PMID:3038334[7]

8C4

Kohara Phage

Genobase

PMID:3038334[7]

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[8]

est. P1 cotransduction: 40% [9]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[8]

est. P1 cotransduction: 54% [9]
Synonyms:zbb-30-55::TnlO, zba-3055::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:EG11703

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11703

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001646

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945112

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1654

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001603

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. ↑ 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
  3. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  4. ↑ Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  5. ↑ Yang, S et al. (2006) Quorum sensing and multidrug transporters in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103 2386-91 PubMed
  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 CGSC: The Coli Genetics Stock Center
  9. ↑ 9.0 9.1 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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