alkB:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2204, b2212, JW2200, aidD''<ref name='LIB:Riley_2006'/>
''ECK2204, b2212, JW2200, aidD''<ref name='LIB:Riley_2006'/>, aidD''


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{|   id="L46a9d8a764cee"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9d8a764cee"  class=" tableEdit Gene_location_table"   
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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: 2307363..2306713<br /><gbrowseImage>
MG1655: 2307363..2306713<br /><gbrowseImage>
name=NC_000913:2306713..2307363
name=NC_000913:2306713..2307363
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10037 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10037 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2305713|2308363|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2305713|2308363|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|2306713|2307363|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2306713|2307363|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10037 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10037 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2192518|NC_2193168|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2192518|2193168|GBrowse (BW2952)}}
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W3110: 2312675..2312025<br /><gbrowseImage>
W3110: 2312675..2312025<br /><gbrowseImage>
name=AC_000091:2312025..2312675
name=NC_007779:2312025..2312675
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|2311025|2313675|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2311025|2313675|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2312025|2312675|FASTA Dump}}  
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DH10B: 2398351..2397701<br /><gbrowseImage>
DH10B: 2398351..2397701<br /><gbrowseImage>
name=NC_010473:2397701..2398351
name=NC_010473:2397701..2398351
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|2396401|2399651|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|2396401|2399651|GBrowse(DH10B)}}
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{|   id="L46a9d8a81b025"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9d8a81b025"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="Y46a9d8a85ff11"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9d8a85ff11"  class=" tableEdit Gene_allele_table dataTable"   
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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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{|   id="C4e04b72f3d3a5"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C4e04b72f3d3a5"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="X46a9d8a916045"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9d8a916045"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTCTTTTTTACCTGCCTGACG  
Primer 2:CCTTCTTTTTTACCTGCCTGACG  
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[[:Category:Kohara_Phage:19D1|19D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=372 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:22A6|22A6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=373 Genobase]
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PMID:3038334
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{|   id="S46a9d8a9a9e43"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a9d8a9a9e43"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10037 EcoCyc:EG10037]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0036 EchoBASE:EB0036]
EcoCyc:EG10037
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2212 EcoliGenExpDB:b2212]
EcoGene:EG10037
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C2753 ECOL199310CYC:C2753]
RegulonDB:ECK120000034
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10037 EcoGene:EG10037]
[http://www.ncbi.nlm.nih.gov/gene?term=946708 GeneID:946708]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=ALKB ECOO157CYC:ALKB]
EchoBASE:EB0036
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/18544 CGSC:18544]
ASAP:ABE-0007308
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007308&formSubmitReturn=1 ASAP:ABE-0007308]
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:41, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

alkB

Mnemonic

Alkylation

Synonyms

ECK2204, b2212, JW2200, aidD[1], aidD

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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

49.72 minutes, 49.72 minutes 

MG1655: 2307363..2306713
<gbrowseImage> name=NC_000913:2306713..2307363 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2259445..2258795
<gbrowseImage> name=NC_012967:2258795..2259445 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2192518..2193168
<gbrowseImage> name=NC_012759:2192518..2193168 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2312675..2312025
<gbrowseImage> name=NC_007779:2312025..2312675 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2398351..2397701
<gbrowseImage> name=NC_010473:2397701..2398351 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

2306713

Edman degradation

PMID:3536913[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

ΔalkB (Keio:JW2200)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9779[4]

alkB::Tn5KAN-2 (FB20706)

Insertion at nt 334 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20706

contains pKD46

alkB::Tn5KAN-2 (FB20707)

Insertion at nt 334 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20707

does not contain pKD46

ΔalkB765::kan

PMID:16738554[3]

CGSC:99968


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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

JW2200

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTTGGATCTGTTTGCCGATGC

Primer 2:CCTTCTTTTTTACCTGCCTGACG

19D1

Kohara Phage

Genobase

PMID:3038334[7]

22A6

Kohara Phage

Genobase

PMID:3038334[7]

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[4]

est. P1 cotransduction: 83% [8]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[4]

est. P1 cotransduction: 63% [8]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

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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:EG10037

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10037

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000034

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946708

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0036

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007308

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ Kondo, H et al. (1986) Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA. J. Biol. Chem. 261 15772-7 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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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 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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