selU:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|ybbB}}{{Tab On|Gene|ybbB}}{{Tab|Gene Product(s)|ybbB}}{{Tab|Expression|ybbB}}{{Tab|Evolution|ybbB}}{{Tab|On One Page|ybbB}}{{TabsBottom}}
{{Tab|Quickview|selU}}{{Tab On|Gene|selU}}{{Tab|Gene Product(s)|selU}}{{Tab|Expression|selU}}{{Tab|Evolution|selU}}{{Tab|On One Page|selU}}{{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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{|   id="Q46a9b22acf8dd" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''ybbB''  
''selU''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Selenium
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0496, b0503, JW0491''<ref name='LIB:Riley_2006'/>
''ECK0496, b0503, JW0491'', ybbB<ref name='LIB:Riley_2006'/>, JW0491, selE, ybbB''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9b22b53696"  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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11.41 minutes&nbsp;
11.41 minutes&nbsp;
|
|
MG1655: 530450..529356<br />{{GBrowseFigureByCoord|528356|531450|ecoli|MG1655}}
MG1655: 530450..529356<br /><gbrowseImage>
name=NC_000913:529356..530450
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11768 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11768 EcoCyc]
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{{GBrowseFastaLink|ecoli|NC_000913|529356|530450|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|529356|530450|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11768 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11768 EcoCyc Sequence Dump]  
|-
|
[[BW2952]]
|
|
NC_012759: 432115..433209<br /><gbrowseImage>
name=NC_012759:432115..433209
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|012759|432115|NC_433209|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|432115|NC_433209|FASTA Dump}}
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&nbsp;
&nbsp;
|
|
W3110: 530450..529356<br />{{GBrowseFigureByCoord|528356|531450|ecoli_W3110|W3110}}  
W3110: 530450..529356<br /><gbrowseImage>
name=NC_007779:529356..530450
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|528356|531450|GBrowse(W3110)}}
|
{{GBrowseFastaLink|ecoli_W3110|NC_007779|529356|530450|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|528356|531450|GBrowse(W3110)}}
 
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|529356|530450|FASTA Dump}}
DH10B: 469781..468687<br /><gbrowseImage>
name=NC_010473:468687..469781
source=DH10B
preset=GeneLocation
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|466499|471969|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|466499|471969|FASTA Dump}}
 
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{|   id="M46a9b22befd41" 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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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| {{Prettytable}}  id="U46a9b22c3bbb1" 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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|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001740 ybbB::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001740 ybbB::Tn5KAN-I-SceI] (FB20189)
|
Insertion at nt 1013 in Minus orientation
|
|


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|
|


|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20190]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001740 ybbB::Tn5KAN-I-SceI] (FB20189)
|
Insertion at nt 1013 in Minus orientation
|
|


|
|
PMID:12519969
 
|
 
|
|
[[asapstrains:ASAP|ASAP]]
PMID:15262929
|
|
At position 1013 in Minus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20190
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20191]
|
contains [[pKD46]]  
|-  
|-  
|
|
''&#916;ybbB786::kan''
selUC96S
|
 
|
C96S
|
 
|
No change in activity
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P33667 UniProt:P33667]
|-
|
selUC97S
|
 
|
C97S
|
|


|
In vivo, abolishes 2-selenouridine synthase activity. In vitro, reduces activity by only 50%
|
|


|
|


|
seeded from [http://www.uniprot.org/uniprot/P33667 UniProt:P33667]
|-
|
&Delta;ybbB::kan
|
deletion
|
|


|
|
PMID:16738554
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketoglutarate]]
|
PMID:16095938
|
|
[[cgscmutation:103658|CGSC:103658]]
 
|
|
   
   
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0001740 ybbB::Tn5KAN]
''&#916;ybbB786::kan''
|
|


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|
|
PMID:12519969
PMID:16738554
|
|
[[asapstrains:ASAP|ASAP]]
[[cgscmutation:103658|CGSC:103658]]
|
|
At position 1013 in Minus orientation, contains plasmid [[pKD46]].<br />ASAP strain name: FB20191
   


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


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11569.N4e04c3af219e6-->
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|- {{table_heading_style}}
!|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
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Primer 2:CCCCGCGCCTTAACCCATTCCGC  
Primer 2:CCCCGCGCCTTAACCCATTCCGC  
|-
|
[[: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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Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  


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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=EG11768 EcoCyc:EG11768]
EcoCyc:EG11768
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1718 EchoBASE:EB1718]
EchoBASE:EB1718
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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|-  
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11768 EcoGene:EG11768]
EcoGene:EG11768
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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|-  
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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=0001740&formSubmitReturn=1 ASAP:ABE-0001740]
ASAP:ABE-0001740
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11768 ECOCYC:EG11768]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=947063 GeneID:947063]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001704
|
''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 Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ybb genes]]
[[Category:ybb genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:sel genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

selU

Mnemonic

Selenium

Synonyms

ECK0496, b0503, JW0491, ybbB[1], JW0491, selE, ybbB

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

11.41 minutes 

MG1655: 530450..529356
<gbrowseImage> name=NC_000913:529356..530450 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 432115..433209
<gbrowseImage> name=NC_012759:432115..433209 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 530450..529356
<gbrowseImage> name=NC_007779:529356..530450 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 469781..468687
<gbrowseImage> name=NC_010473:468687..469781 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

ΔybbB (Keio:JW0491)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8636[3]

ybbB::Tn5KAN-I-SceI (FB20189)

Insertion at nt 1013 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20190

does not contain pKD46

ybbB::Tn5KAN-I-SceI (FB20189)

Insertion at nt 1013 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20191

contains pKD46

selUC96S

C96S

No change in activity

seeded from UniProt:P33667

selUC97S

C97S

In vivo, abolishes 2-selenouridine synthase activity. In vitro, reduces activity by only 50%

seeded from UniProt:P33667

ΔybbB::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ΔybbB786::kan

PMID:16738554[2]

CGSC:103658


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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

JW0491

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCAAGAGAGACACACGGAACA

Primer 2:CCCCGCGCCTTAACCCATTCCGC

8E4

Kohara Phage

Genobase

PMID:3038334[7]

9E5

Kohara Phage

Genobase

PMID:3038334[7]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 34% [8]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 43% [8]
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

EcoCyc

EcoCyc:EG11768

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1718

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0503

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0618

EcoGene

EcoGene:EG11768

Escherichia coli str. K-12 substr. MG1655

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBBB

ASAP

ASAP:ABE-0001740

Escherichia coli str. K-12 substr. MG1655

EcoCyc (EcoliWiki Page)

ECOCYC:EG11768

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947063

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001704

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. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 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).

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