intZ: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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****************************************************************************************** -->{{Gene_nomenclature_help}}
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{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="A46a9de22a0dd5" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''intZ''  
''intZ''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Integrase
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2437, b2442, unique to MG1655''<ref name='LIB:Riley_2006'/>
''ECK2437, b2442, unique to MG1655''<ref name='LIB:Riley_2006'/>


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9de232a7fb"  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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55.11 minutes&nbsp;
55.11 minutes&nbsp;
|
|
MG1655: 2556793..2558088<br />{{GBrowseFigureByCoord|2555793|2559088|ecoli|MG1655}}
MG1655: 2556793..2558088<br /><gbrowseImage>
name=NC_000913:2556793..2558088
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7272 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7272 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2555793|2559088|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2555793|2559088|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2556793|2558088|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2556793|2558088|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7272 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7272 EcoCyc Sequence Dump]  
|-
|
[[BW2952]]
|
|
NC_012759: 2442685..2443893<br /><gbrowseImage>
name=NC_012759:2442685..2443893
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2442685|2443893|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2442685|2443893|FASTA Dump}}
|-
|
[[DH10B]]
|
|
DH10B: 2648558..2649853<br /><gbrowseImage>
name=NC_010473:2648558..2649853
source=DH10B
preset=GeneLocation
</gbrowseImage>


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{{GBrowseLink|DH10B|NC_010473|2645968|2652443|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2645968|2652443|FASTA Dump}}
 
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*  
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9de237a451"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!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="D46a9de23bff63"  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


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15449.I4e04bdf4651d9-->
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|- {{table_heading_style}}
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<!-- Genetic Interacdtions Notes -->
===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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|
|
[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:
Status:
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est. P1 cotransduction: 22% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 22% <ref name='LIB:Nichols_linked_Tn'/>  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7272 EcoCyc:G7272]
EcoCyc:G7272
|
|
''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=EB3924 EchoBASE:EB3924]
EcoGene:EG14172
|
|
''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=b2442 EcoliGenExpDB:b2442]
RegulonDB:ECK120003846
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14172 EcoGene:EG14172]
[http://www.ncbi.nlm.nih.gov/gene?term=946923 GeneID:946923]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z5890 ECOO157CYC:Z5890]
EchoBASE:EB3924
|
|
''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]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0008052&formSubmitReturn=1 ASAP:ABE-0008052]
ASAP:ABE-0008052
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:Eut/CPZ-55 prophage]]
[[Category:Gene List:Eut/CPZ-55 prophage]]
[[Category:int genes]]
[[Category:int genes]][[Category:Gene_List:DH10B]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

intZ

Mnemonic

Integrase

Synonyms

ECK2437, b2442, unique to MG1655[1]

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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

55.11 minutes 

MG1655: 2556793..2558088
<gbrowseImage> name=NC_000913:2556793..2558088 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2442685..2443893
<gbrowseImage> name=NC_012759:2442685..2443893 source=BW2952 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2648558..2649853
<gbrowseImage> name=NC_010473:2648558..2649853 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
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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

Plasmid clone

Shigen

PMID:16769691[2]

Status:

Primer 1:

Primer 2:

nupC510::Tn10

Linked marker

CAG18468 = CGSC7410[3]

est. P1 cotransduction: 12% [4]

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[3]

est. P1 cotransduction: 22% [4]

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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:G7272

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14172

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003846

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946923

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3924

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008052

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

[back to top]


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. ↑ 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
  3. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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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