ybaB: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="H46a9b17dbb56b"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ybaB''  
''ybaB''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0465, b0471, JW0460, dnaZ''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''ECK0465, b0471, JW0460, dnaZ''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='127721'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9b17e6d02f"  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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|-  
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MG1655
MG1655
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10.63 minutes&nbsp;
10.63 minutes&nbsp;
|
|
MG1655: 493300..493629<br />{{GBrowseFigureByCoord|492300|494629|ecoli|MG1655}}
MG1655: 493300..493629<br /><gbrowseImage>
name=NC_000913:493300..493629
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11100 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11100 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:492300..494629 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|492300|494629|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:493300..493629&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|493300|493629|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11100 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11100 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 466143..466472<br /><gbrowseImage>
name=NC_012967:466143..466472
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|466143|466472|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|466143|466472|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 396059..396388<br /><gbrowseImage>
name=NC_012759:396059..396388
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|396059|396388|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|396059|396388|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 493300..493629<br />{{GBrowseFigureByCoord|492300|494629|ecoli_W3110|W3110}}  
W3110: 493300..493629<br /><gbrowseImage>
name=NC_007779:493300..493629
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|492300|494629|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|493300|493629|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 432631..432960<br /><gbrowseImage>
name=NC_010473:432631..432960
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:492300..494629 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|431973|433618|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:493300..493629&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|431973|433618|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;ybaB (Keio:JW0460)
''ybaB(del)'' (Keio:JW0460)
|
|
deletion
deletion
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106895 CGSC8614]<ref name='LIB:cgsc'/>
|
|-
|
''ybaB755(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[[cgscmutation:103626|CGSC:103626]]
|
|
   
   
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|
ybaB
|
deletion
|
 
|
Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11507.J4e04c63c26cc6-->
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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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JW0460
JW0460
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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:CCGAACGGCATCTTAAAGCCAGG  
Primer 2:CCGAACGGCATCTTAAAGCCAGG  
|-
|-
|
[[:Category:Kohara_Phage:12H5|12H5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=152 Genobase]
|
PMID:3038334
|-  
|
|
[[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: 25% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 25% <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: 77% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 77% <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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!Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11100 EcoCyc:EG11100] 
EcoCyc:EG11100
|
|
''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=EB1092 EchoBASE:EB1092] 
EcoGene:EG11100
|
|
''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=b0471 EcoliGenExpDB:b0471] 
RegulonDB:ECK120001088
|
|
''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=C0591 ECOL199310CYC:C0591]
[http://www.ncbi.nlm.nih.gov/gene?term=945104 GeneID:945104]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11100 EcoGene:EG11100] 
EchoBASE:EB1092
|
|
''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=YBAB ECOO157CYC:YBAB] 
ASAP:ABE-0001636
|
|
''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 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:yba genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

ybaB

Mnemonic

Systematic nomenclature

Synonyms

ECK0465, b0471, JW0460, dnaZ[1][2]

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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

10.63 minutes 

MG1655: 493300..493629
<gbrowseImage> name=NC_000913:493300..493629 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 466143..466472
<gbrowseImage> name=NC_012967:466143..466472 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 396059..396388
<gbrowseImage> name=NC_012759:396059..396388 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 493300..493629
<gbrowseImage> name=NC_007779:493300..493629 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 432631..432960
<gbrowseImage> name=NC_010473:432631..432960 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

ybaB(del) (Keio:JW0460)

deletion

deletion

PMID:16738554[3]

Shigen

CGSC8614[4]

ybaB755(del)::kan

PMID:16738554[3]

CGSC:103626

ybaB

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[5]

fig 2

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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

JW0460

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTTTGGTAAAGGCGGTCTGGG

Primer 2:CCGAACGGCATCTTAAAGCCAGG

12H5

Kohara Phage

Genobase

PMID:3038334[7]

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[4]

est. P1 cotransduction: 25% [8]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[4]

est. P1 cotransduction: 77% [8]
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:EG11100

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11100

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001088

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945104

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1092

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001636

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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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. ↑ 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
  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. ↑ 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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