cbl:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|cbl}}{{Tab On|Gene|cbl}}{{Tab|Gene Product(s)|cbl}}{{Tab|Expression|cbl}}{{Tab|Evolution|cbl}}{{Tab|On One Page|cbl}}{{TabsBottom}}
{{Tab|Quickview|cbl}}{{Tab On|Gene|cbl}}{{Tab|Gene Product(s)|cbl}}{{Tab|Expression|cbl}}{{Tab|Evolution|cbl}}{{Tab|On One Page|cbl}}{{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
|
||
''cbl''  
''cbl''
|-
!align=left {{table_heading_style}} |Mnemonic
||
cysB-like
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1982, b1987, JW1966''<ref name='LIB:Riley_2006'/>, JW1966''


|-
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!{{table_heading_style}} |Synonyms
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''ECK1982, b1987, JW1966''<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="A46a9d3840893e"  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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44.36 minutes&nbsp;
44.36 minutes&nbsp;
|
|
MG1655: 2058938..2057988<br />{{GBrowseFigureByCoord|2056988|2059938|ecoli|MG1655}}
MG1655: 2058938..2057988<br /><gbrowseImage>
name=NC_000913:2057988..2058938
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7071 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7071 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2056988..2059938 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2056988|2059938|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2057988..2058938&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2057988|2058938|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7071 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7071 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1998914..1997964<br /><gbrowseImage>
name=NC_012967:1997964..1998914
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1997964|1998914|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1997964|1998914|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 1950471..1951421<br /><gbrowseImage>
name=NC_012759:1950471..1951421
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1950471|1951421|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1950471|1951421|FASTA Dump}}
|-  
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|
W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 2063051..2062101<br />{{GBrowseFigureByCoord|2061101|2064051|ecoli_W3110|W3110}}
W3110: 2063051..2062101<br /><gbrowseImage>
name=NC_007779:2062101..2063051
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2061101..2064051 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2061101|2064051|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2062101..2063051&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2062101|2063051|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2149946..2148996<br /><gbrowseImage>
name=NC_010473:2148996..2149946
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2147096|2151846|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2147096|2151846|FASTA Dump}}
 
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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="U46a9d384b0e96"  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="G46a9d38500eb2"  class=" tableEdit Gene_allele_table dataTable" 
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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;cbl (Keio:JW1966)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107911 CGSC9630]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006590 cbl::Tn5KAN-2] (FB20557)
|
Insertion at nt 399 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20557]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006590 cbl::Tn5KAN-2] (FB20558)
|
Insertion at nt 399 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20558]
|
does not contain [[pKD46]]
|-
|
''&#916;cbl-759::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100242|CGSC:100242]]
|
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==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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JW1966
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAATTTCCAACAACTAAAGAT
 
Primer 2:CCTATCTGATAATCAATTTCCTC
|-
|
[[:Category:Kohara_Phage:7D4|7D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=346 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9B2|9B2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=347 Genobase]
|
PMID:3038334
|-
|
[[yedZ:Gene|zed-3069::Tn10]]
|
Linked marker
|
CAG18451 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39990 CGSC7395]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
zef-3129::Tn10
|
Linked marker
|
CAG12099 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39996 CGSC7397]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 39% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zee-3129::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9d3864741b"  class=" tableEdit Gene_accessions_table" 
|- {{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=G7071 EcoCyc:G7071] 
EcoCyc:G7071
|
|
''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=EB4012 EchoBASE:EB4012] 
EcoGene:EG14264
|
|
''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=b1987 EcoliGenExpDB:b1987] 
RegulonDB:ECK120003657
|
|
''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=C2447 ECOL199310CYC:C2447]
[http://www.ncbi.nlm.nih.gov/gene?term=946502 GeneID:946502]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14264 EcoGene:EG14264] 
EchoBASE:EB4012
|
|
''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=CBL ECOO157CYC:CBL] 
ASAP:ABE-0006590
|
|
''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:cbl genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:40, 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

cbl

Mnemonic

cysB-like

Synonyms

ECK1982, b1987, JW1966[1], JW1966

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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

44.36 minutes 

MG1655: 2058938..2057988
<gbrowseImage> name=NC_000913:2057988..2058938 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1998914..1997964
<gbrowseImage> name=NC_012967:1997964..1998914 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1950471..1951421
<gbrowseImage> name=NC_012759:1950471..1951421 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2063051..2062101
<gbrowseImage> name=NC_007779:2062101..2063051 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2149946..2148996
<gbrowseImage> name=NC_010473:2148996..2149946 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

Δcbl (Keio:JW1966)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9630[3]

cbl::Tn5KAN-2 (FB20557)

Insertion at nt 399 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20557

contains pKD46

cbl::Tn5KAN-2 (FB20558)

Insertion at nt 399 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20558

does not contain pKD46

Δcbl-759::kan

PMID:16738554[2]

CGSC:100242


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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

JW1966

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAATTTCCAACAACTAAAGAT

Primer 2:CCTATCTGATAATCAATTTCCTC

7D4

Kohara Phage

Genobase

PMID:3038334[6]

9B2

Kohara Phage

Genobase

PMID:3038334[6]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[3]

est. P1 cotransduction: 46% [7]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[3]

est. P1 cotransduction: 39% [7]
Synonyms:zee-3129::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:G7071

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14264

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003657

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946502

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4012

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006590

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  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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