psd: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="G46aa08ae62b42"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''psd''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''psd''
Phosphatidylserine decarboxylase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4156, b4160, JW4121''<ref name='LIB:Riley_2006'/>, JW4121''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18885.G46aa08ae62b42&page=18885&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK4156, b4160, JW4121''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18885.G46aa08ae62b42&page=18885&pagename={{FULLPAGENAMEE}} edit table]
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='149866'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46aa08aee66c7"  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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MG1655
MG1655
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94.56 minutes&nbsp;
94.56 minutes&nbsp;
|
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MG1655: 4388383..4387415<br />{{GBrowseFigureByCoord|4386415|4389383|ecoli|MG1655}}
MG1655: 4388383..4387415<br /><gbrowseImage>
name=NC_000913:4387415..4388383
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10775 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10775 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4386415..4389383 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4386415|4389383|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4387415..4388383&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4387415|4388383|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10775 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10775 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4368515..4367547<br /><gbrowseImage>
name=NC_012967:4367547..4368515
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4367547|4368515|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4367547|4368515|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 4326150..4327118<br /><gbrowseImage>
name=NC_012759:4326150..4327118
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4326150|4327118|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4326150|4327118|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4395040..4394072<br />{{GBrowseFigureByCoord|4393072|4396040|ecoli_W3110|W3110}}
W3110: 4395040..4394072<br /><gbrowseImage>
name=NC_007779:4394072..4395040
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4393072..4396040 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4393072|4396040|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4394072..4395040&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4394072|4395040|FASTA Dump}}
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|
[[DH10B]]
|
 
|
DH10B: 4488745..4487777<br /><gbrowseImage>
name=NC_010473:4487777..4488745
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4485841|4490681|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4485841|4490681|FASTA Dump}}
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46aa08afae96f"  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]]
|
4387415
|
Edman degradation
|
PMID:3042771<br />
|
 
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<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====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}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="K46aa08b005d94"  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
|-
|
psdS254A
|
|
S254A
|
|
No processing of the proenzyme, complete loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A8K1 UniProt:P0A8K1]
|-
|
psdS254C
|
|
S254C
|
|
Reduced processing, 16% wild-type activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A8K1 UniProt:P0A8K1]
|-
|
psdS254T
|
|
S254T
|
|
Reduced processing, 2% wild-type activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A8K1 UniProt:P0A8K1]
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|
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18885.K46aa08b005d94&page=18885&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18885.M4e04c1962eda2-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04c1962eda2"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW4121
JW4121
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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:CCGACCTGGTCTTTTTTGTCGTC  
Primer 2:CCGACCTGGTCTTTTTTGTCGTC  
|-
|-
|
[[:Category:Kohara_Phage:3H6|3H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=651 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3A1|3A1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=652 Genobase]
|
PMID:3038334
|-  
|
|
[[cadB:Gene|cadB2231::Tn10]]
[[cadB:Gene|cadB2231::Tn10]]
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CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjd-2231::Tn10  
Synonyms:zjd-2231::Tn10  
|-
|-  
|
|
[[cycA:Gene|cycA30::Tn10]]
[[cycA:Gene|cycA30::Tn10]]
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|
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est. P1 cotransduction: 20% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 20% <ref name='LIB:Nichols_linked_Tn'/>  
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa08b170ac0"  class=" tableEdit Gene_accessions_table"   
|- {{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=EG10775 EcoCyc:EG10775]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0768 EchoBASE:EB0768]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4160 EcoliGenExpDB:b4160]
EcoCyc:EG10775
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5247 ECOL199310CYC:C5247]
EcoGene:EG10775
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10775 EcoGene:EG10775]
RegulonDB:ECK120000766
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z5766 ECOO157CYC:Z5766]
[http://www.ncbi.nlm.nih.gov/gene?term=948673 GeneID:948673]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/356 CGSC:356]
EchoBASE:EB0768
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013623&formSubmitReturn=1 ASAP:ABE-0013623] 
ASAP:ABE-0013623
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:psd genes]]
[[Category:psd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 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

psd

Mnemonic

Phosphatidylserine decarboxylase

Synonyms

ECK4156, b4160, JW4121[1], JW4121

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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

94.56 minutes 

MG1655: 4388383..4387415
<gbrowseImage> name=NC_000913:4387415..4388383 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4368515..4367547
<gbrowseImage> name=NC_012967:4367547..4368515 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4326150..4327118
<gbrowseImage> name=NC_012759:4326150..4327118 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4395040..4394072
<gbrowseImage> name=NC_007779:4394072..4395040 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4488745..4487777
<gbrowseImage> name=NC_010473:4487777..4488745 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

4387415

Edman degradation

PMID:3042771[2]


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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

psdS254A

S254A

No processing of the proenzyme, complete loss of activity

seeded from UniProt:P0A8K1

psdS254C

S254C

Reduced processing, 16% wild-type activity

seeded from UniProt:P0A8K1

psdS254T

S254T

Reduced processing, 2% wild-type activity

seeded from UniProt:P0A8K1

psd-2(ts)

temperature sensitive

CGSC:8626


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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

JW4121

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCTTAAATTCATTTAAACTTTC

Primer 2:CCGACCTGGTCTTTTTTGTCGTC

3H6

Kohara Phage

Genobase

PMID:3038334[4]

3A1

Kohara Phage

Genobase

PMID:3038334[4]

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[5]

est. P1 cotransduction: 30% [6]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[5]

est. P1 cotransduction: 20% [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

EcoCyc

EcoCyc:EG10775

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10775

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000766

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948673

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0768

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013623

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. ↑ Li, QX & Dowhan, W (1988) Structural characterization of Escherichia coli phosphatidylserine decarboxylase. J. Biol. Chem. 263 11516-22 PubMed
  3. ↑ 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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