ybbD: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
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''ybbD''  
''ybbD''
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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|-
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0494, b0500, JW0489''<ref name='LIB:Riley_2006'/>
''ECK0494, b0500, JW0489''<ref name='LIB:Riley_2006'/>, JW0489, b0501''
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===Notes===
===Notes===
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<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="C46a9b22204dc1"  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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MG1655
MG1655
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11.38 minutes&nbsp;
11.38 minutes&nbsp;
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MG1655: 527864..528124<br />{{GBrowseFigureByCoord|526864|529124|ecoli|MG1655}}
MG1655: 527864..528124<br /><gbrowseImage>
name=NC_000913:527864..528124
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11770 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11770 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:526864..529124 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|526864|529124|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:527864..528124&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|527864|528124|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11770 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11770 EcoCyc Sequence Dump]  
|-
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[[REL606]]
|
 
|
NC_012967: 500807..501067<br /><gbrowseImage>
name=NC_012967:500807..501067
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|500807|501067|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|500807|501067|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 527864..528124<br />{{GBrowseFigureByCoord|526864|529124|ecoli_W3110|W3110}}  
W3110: 527864..528124<br /><gbrowseImage>
name=NC_007779:527864..528124
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|526864|529124|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|527864|528124|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 467195..467685<br /><gbrowseImage>
name=NC_010473:467195..467685
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:526864..529124 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|466215|468665|GBrowse(DH10B)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:527864..528124&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|466215|468665|FASTA Dump}}
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9b222a14e3"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9b222e15c9"  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!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;ybbD (Keio:JW0489)
&Delta;ybbD (Keio:JW0489)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106916 CGSC8635]<ref name='LIB:cgsc'/>  
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''&#916;ybbD783::kan''
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]  
 
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PMID:16738554
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[[cgscmutation:103660|CGSC:103660]]
|
 
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{{Gene_alleles_help}}
 
<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="T4e04c64e0a693"  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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JW0489
JW0489
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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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGGGAAAAATAAGAAAAAAATA  
Primer 2:CCGGGAAAAATAAGAAAAAAATA  
|-
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[[:Category:Kohara_Phage:8E4|8E4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=155 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9E5|9E5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=156 Genobase]
|
PMID:3038334
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[[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: 36% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 36% <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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[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
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CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:purE79::Tn10


Synonyms:purE79::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoGene]]
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EcoGene:EG11770
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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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=EG11770 EcoCyc:EG11770] 
EcoCyc:EG11770
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1720 EchoBASE:EB1720]
[http://www.ncbi.nlm.nih.gov/gene?term=945133 GeneID:945133]
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0500 EcoliGenExpDB:b0500] 
RegulonDB:ECK120001706
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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]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG11770 EcoGene:EG11770] 
EchoBASE:EB1720
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YBBD ECOO157CYC:YBBD] 
ASAP:ABE-0001731
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:ybb genes]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]

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

ybbD

Mnemonic
Synonyms

ECK0494, b0500, JW0489[1], JW0489, b0501

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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

11.38 minutes 

MG1655: 527864..528124
<gbrowseImage> name=NC_000913:527864..528124 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 500807..501067
<gbrowseImage> name=NC_012967:500807..501067 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 527864..528124
<gbrowseImage> name=NC_007779:527864..528124 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 467195..467685
<gbrowseImage> name=NC_010473:467195..467685 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

ΔybbD (Keio:JW0489)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8635[3]

ΔybbD783::kan

PMID:16738554[2]

CGSC:103660


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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

JW0489

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCTGGCTATCTCAAGTAATCT

Primer 2:CCGGGAAAAATAAGAAAAAAATA

8E4

Kohara Phage

Genobase

PMID:3038334[5]

9E5

Kohara Phage

Genobase

PMID:3038334[5]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 36% [6]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 40% [6]
Synonyms:purE79::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

EcoGene

EcoGene:EG11770

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11770

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945133

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001706

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1720

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001731

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. ↑ 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 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 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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