seqA:Gene: Difference between revisions

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{{Tab|Quickview|seqA}}{{Tab On|Gene|seqA}}{{Tab|Gene Product(s)|seqA}}{{Tab|Expression|seqA}}{{Tab|Evolution|seqA}}{{Tab|On One Page|seqA}}{{TabsBottom}}
{{Tab|Quickview|seqA}}{{Tab On|Gene|seqA}}{{Tab|Gene Product(s)|seqA}}{{Tab|Expression|seqA}}{{Tab|Evolution|seqA}}{{Tab|On One Page|seqA}}{{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
|
||
''seqA''  
''seqA''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Sequestration
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0675, b0687, JW0674''<ref name='LIB:Riley_2006'/>, JW0674''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11927.Z46a9b6803aee3&page=11927&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0675, b0687, JW0674''<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="A46a9b680b293a"  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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MG1655
MG1655
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15.35 minutes&nbsp;
15.35 minutes&nbsp;
|
|
MG1655: 712210..712755<br />{{GBrowseFigureByCoord|711210|713755|ecoli|MG1655}}
MG1655: 712210..712755<br /><gbrowseImage>
name=NC_000913:712210..712755
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12197 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12197 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:711210..713755 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|711210|713755|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:712210..712755&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|712210|712755|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12197 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12197 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 695082..695627<br /><gbrowseImage>
name=NC_012967:695082..695627
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|695082|695627|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|695082|695627|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 614970..615515<br /><gbrowseImage>
name=NC_012759:614970..615515
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|614970|615515|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|614970|615515|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 713409..713954<br />{{GBrowseFigureByCoord|712409|714954|ecoli_W3110|W3110}}  
W3110: 713409..713954<br /><gbrowseImage>
name=NC_007779:713409..713954
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|712409|714954|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|713409|713954|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:712409..714954 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:713409..713954&plugin_action=Go FASTA Dump]
DH10B: 764802..765347<br /><gbrowseImage>
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|763712|766437|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|763712|766437|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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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]]
|
712210
|
Edman degradation
|
PMID:7553853<br />
|
 
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<protect><!--Sequence_notes--></protect>
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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="F46a9b6819a993"  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
|-class='sortbottom'
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&Delta;seqA (Keio:JW0674)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107041 CGSC8760]<ref name='LIB:cgsc'/>
|
|-
|
seqA4
|
 
|
A25T
|
 
|
 
|
PMID:16236133
|
 
|
|-
|
''&#916;seqA735::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102912|CGSC:102912]]
|
|-
|
''&Delta;seqA&Delta;mukB''
|
 
|
 
|
 
|
asynchronous initiation of chromosome replication
|
PMID:10540294
|
 
|
"Temperature sensitivity, anucleate cell production and poor nucleoid folding seen in the ''mukB'' strain were suppressed by the ''seqA'' null mutation, whereas filamentation, asymmetric septation and compact folding of the nucleoids were observed in the ''seqA'' strain were suppressed by inactivation of the ''mukB'' gene function"
 
|- class="tableEdit_footer"
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
SeqA mutants overinitiate and are blind to stringent arrest of replication.


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===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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JW0674
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAAACGATTGAAGTTGATGA
 
Primer 2:CCGATAGTTCCGCAAACCTTCTC
|-
|
[[:Category:Kohara_Phage:3A6|3A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=172 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:11A10|11A10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=173 Genobase]
|
PMID:3038334
|-
|
[[asnB:Gene|asnB3057::Tn10]]
|
Linked marker
|
CAG18433 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39394 CGSC7349]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 67% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.
|-
|
[[nadA:Gene|nadA57::Tn10]]
|
Linked marker
|
CAG12147 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38017 CGSC7351]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 2% <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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==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=EG12197 EcoCyc:EG12197] 
EcoCyc:EG12197
|
|
''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=EB2114 EchoBASE:EB2114] 
EcoGene:EG12197
|
|
''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=b0687 EcoliGenExpDB:b0687] 
RegulonDB:ECK120002086
|
|
''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=C0774 ECOL199310CYC:C0774]
[http://www.ncbi.nlm.nih.gov/gene?term=945272 GeneID:945272]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12197 EcoGene:EG12197] 
EchoBASE:EB2114
|
|
''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=SEQA ECOO157CYC:SEQA] 
ASAP:ABE-0002343
|
|
''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=421aa90e079fa326b6494f812ad13e79.11927.B46a9b682ca989&page=11927&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/31506 CGSC:31506] 
|
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{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:seq genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:34, 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

seqA

Mnemonic

Sequestration

Synonyms

ECK0675, b0687, JW0674[1], JW0674

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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

15.35 minutes 

MG1655: 712210..712755
<gbrowseImage> name=NC_000913:712210..712755 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 695082..695627
<gbrowseImage> name=NC_012967:695082..695627 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 614970..615515
<gbrowseImage> name=NC_012759:614970..615515 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 713409..713954
<gbrowseImage> name=NC_007779:713409..713954 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 764802..765347
<gbrowseImage> name=NC_010473:764802..765347 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

712210

Edman degradation

PMID:7553853[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

ΔseqA (Keio:JW0674)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8760[4]

seqA4

A25T

PMID:16236133[5]

ΔseqA735::kan

PMID:16738554[3]

CGSC:102912

ΔseqAΔmukB

asynchronous initiation of chromosome replication

PMID:10540294[6]

"Temperature sensitivity, anucleate cell production and poor nucleoid folding seen in the mukB strain were suppressed by the seqA null mutation, whereas filamentation, asymmetric septation and compact folding of the nucleoids were observed in the seqA strain were suppressed by inactivation of the mukB gene function"

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Notes

SeqA mutants overinitiate and are blind to stringent arrest of replication.


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

JW0674

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAAAACGATTGAAGTTGATGA

Primer 2:CCGATAGTTCCGCAAACCTTCTC

3A6

Kohara Phage

Genobase

PMID:3038334[8]

11A10

Kohara Phage

Genobase

PMID:3038334[8]

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[4]

est. P1 cotransduction: 67% [9]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[4]

est. P1 cotransduction: 2% [9]

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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:EG12197

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12197

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002086

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945272

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2114

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002343

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. ↑ Slater, S et al. (1995) E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. Cell 82 927-36 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Odsbu, I et al. (2005) Specific N-terminal interactions of the Escherichia coli SeqA protein are required to form multimers that restrain negative supercoils and form foci. Genes Cells 10 1039-49 PubMed
  6. ↑ Weitao, T et al. (1999) Mutual suppression of mukB and seqA phenotypes might arise from their opposing influences on the Escherichia coli nucleoid structure. Mol. Microbiol. 34 157-68 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  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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