bax:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|bax}}{{Tab On|Gene|bax}}{{Tab|Gene Product(s)|bax}}{{Tab|Expression|bax}}{{Tab|Evolution|bax}}{{Tab|On One Page|bax}}{{TabsBottom}}
{{Tab|Quickview|bax}}{{Tab On|Gene|bax}}{{Tab|Gene Product(s)|bax}}{{Tab|Expression|bax}}{{Tab|Evolution|bax}}{{Tab|On One Page|bax}}{{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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="G46a9f95081038"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''bax''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''bax''
Between avtA and xyl
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3559, b3570, JW5653''<ref name='LIB:Riley_2006'/>, JW5653''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17693.G46a9f95081038&page=17693&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3559, b3570, JW5653''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="S46a9f9510e3b5"  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
|-
|-  
|
|
MG1655
MG1655
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80.49 minutes&nbsp;
80.49 minutes&nbsp;
|
|
MG1655: 3735200..3734376<br />{{GBrowseFigureByCoord|3733376|3736200|ecoli|MG1655}}
MG1655: 3735200..3734376<br /><gbrowseImage>
name=NC_000913:3734376..3735200
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11360 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11360 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3733376..3736200 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3733376|3736200|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3734376..3735200&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3734376|3735200|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11360 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11360 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3667633..3666809<br /><gbrowseImage>
name=NC_012967:3666809..3667633
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3666809|3667633|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3666809|3667633|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3622702..3623526<br /><gbrowseImage>
name=NC_012759:3622702..3623526
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3622702|3623526|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3622702|3623526|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3903238..3904062<br />{{GBrowseFigureByCoord|3902238|3905062|ecoli_W3110|W3110}}  
W3110: 3903238..3904062<br /><gbrowseImage>
name=NC_007779:3903238..3904062
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3902238|3905062|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3903238|3904062|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3902238..3905062 GBrowse(W3110)]
DH10B: 3832777..3831953<br /><gbrowseImage>
name=NC_010473:3831953..3832777
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3903238..3904062&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|3830305|3834425|GBrowse(DH10B)}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9f951c5086"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="M46a9f9521a67c"  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;bax (Keio:JW5653)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011655 bax::Tn5KAN-I-SceI] (FB21296)
|
Insertion at nt 345 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21296]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0011655 bax::Tn5KAN-I-SceI] (FB21297)
|
Insertion at nt 345 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21297]
|
does not contain [[pKD46]]
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C4e04b81b7fb89"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW5653
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:cloned as old JW
 
Primer 1:GCCATTTTGACTCCCATACGACG
 
Primer 2:CCCATATGCGCCGCGATTAACCG
|-
|
[[:Category:Kohara_Phage:7C3|7C3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=579 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10C8|10C8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=580 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6F2|6F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=601 Genobase]
|
PMID:3038334
|-
|
zhg-50::Tn10
|
Linked marker
|
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhf-50::Tn10, zhf-5::Tn10
|-
|
zic-4901::Tn10
|
Linked marker
|
CAG18492 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38944 CGSC7457]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
 
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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=EG11360 EcoCyc:EG11360] 
EcoCyc:EG11360
|
|
''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=EB1335 EchoBASE:EB1335] 
EcoGene:EG11360
|
|
''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=b3570 EcoliGenExpDB:b3570] 
RegulonDB:ECK120001329
|
|
''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=C4390 ECOL199310CYC:C4390]
[http://www.ncbi.nlm.nih.gov/gene?term=948089 GeneID:948089]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11360 EcoGene:EG11360] 
EchoBASE:EB1335
|
|
''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=BAX ECOO157CYC:BAX] 
ASAP:ABE-0011655
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
==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:bax genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:48, 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

bax

Mnemonic

Between avtA and xyl

Synonyms

ECK3559, b3570, JW5653[1], JW5653

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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

80.49 minutes 

MG1655: 3735200..3734376
<gbrowseImage> name=NC_000913:3734376..3735200 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3667633..3666809
<gbrowseImage> name=NC_012967:3666809..3667633 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3622702..3623526
<gbrowseImage> name=NC_012759:3622702..3623526 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3903238..3904062
<gbrowseImage> name=NC_007779:3903238..3904062 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3832777..3831953
<gbrowseImage> name=NC_010473:3831953..3832777 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

Δbax (Keio:JW5653)

deletion

deletion

PMID:16738554[2]

Shigen

bax::Tn5KAN-I-SceI (FB21296)

Insertion at nt 345 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB21296

contains pKD46

bax::Tn5KAN-I-SceI (FB21297)

Insertion at nt 345 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB21297

does not contain pKD46

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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

JW5653

Plasmid clone

Shigen

PMID:16769691[4]

Status:cloned as old JW

Primer 1:GCCATTTTGACTCCCATACGACG

Primer 2:CCCATATGCGCCGCGATTAACCG

7C3

Kohara Phage

Genobase

PMID:3038334[5]

10C8

Kohara Phage

Genobase

PMID:3038334[5]

6F2

Kohara Phage

Genobase

PMID:3038334[5]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[6]

est. P1 cotransduction: % [7]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[6]

est. P1 cotransduction: % [7]

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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:EG11360

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11360

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001329

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948089

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1335

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011655

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. ↑ 3.0 3.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ 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
  5. ↑ 5.0 5.1 5.2 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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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