nikD: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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{|   id="P46a9f6efbfced" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''nikD''  
''nikD''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Nickel
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3463, b3479, JW3444, hydC, hydD''<ref name='LIB:Riley_2006'/>
''ECK3463, b3479, JW3444, hydC, hydD''<ref name='LIB:Riley_2006'/>, hydD''


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*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|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="T46a9f6f04dcc1"  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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77.92 minutes&nbsp;
77.92 minutes&nbsp;
|
|
MG1655: 3615038..3615802<br />{{GBrowseFigureByCoord|3615038|3615802|ecoli|MG1655}}
MG1655: 3615038..3615802<br /><gbrowseImage>
name=NC_000913:3615038..3615802
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12078 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12078 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3614038|3616802|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3614038|3616802|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3615038|3615802|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3615038|3615802|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12078 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12078 EcoCyc Sequence Dump]  
|-  
|-  
|
|
W3110
[[REL606]]
|
|
&nbsp;
 
|
|
W3110: 4023400..4022636<br />{{GBrowseFigureByCoord|4022636|4023400|ecoli_W3110|W3110}}
NC_012967: 3547703..3548467<br /><gbrowseImage>
name=NC_012967:3547703..3548467
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|4021636|4024400|GBrowse(W3110)}}  
{{GBrowseLink|REL606|NC_012967|3547703|3548467|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|4022636|4023400|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|3547703|3548467|FASTA Dump}}  
|-  
|-  
|
|
[[DH10B]]
[[BW2952]]
|
 
|
|
NC_012759: 3503532..3504296<br /><gbrowseImage>
name=NC_012759:3503532..3504296
source=BW2952
preset=GeneLocation
</gbrowseImage>


|
|
DH10B: 3712783..3713547<br />{{GBrowseFigureByCoord|3712783|3713547|ecoli_DH10B|DH10B}}
{{GBrowseLink|BW2952|NC_012759|3503532|3504296|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3503532|3504296|FASTA Dump}}  
|-
|
W3110
|
&nbsp;
|
W3110: 4023400..4022636<br /><gbrowseImage>
name=NC_007779:4022636..4023400
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3711255|3715075|GBrowse(DH10B)}}
{{GBrowseLink|W3110|NC_007779|4021636|4024400|GBrowse(W3110)}}  
|
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3711255|3715075|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|4022636|4023400|FASTA Dump}}  
|-  
|-  
|
|
[[REL606]]
[[DH10B]]
|
|


|
|
NC_012967: 3547703..3548467<br />{{GBrowseFigureByCoord|3547703|3548467|REL606|NC_012967}}
DH10B: 3712783..3713547<br /><gbrowseImage>
name=NC_010473:3712783..3713547
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|3547703|3548467|GBrowse (REL606)}}
{{GBrowseLink|DH10B|NC_010473|3711255|3715075|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|3547703|3548467|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3711255|3715075|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_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;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|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="U46a9f6f15a897"  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.17501.H4e04c01fbba34-->
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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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Primer 2:CCTGATGCCAGCTCCATACCGTA  
Primer 2:CCTGATGCCAGCTCCATACCGTA  
|-
|
[[:Category:Kohara_Phage:10D10|10D10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=610 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5F2|5F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=611 Genobase]
|
PMID:3038334
|-  
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12078 EcoCyc:EG12078]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2003 EchoBASE:EB2003]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3479 EcoliGenExpDB:b3479]
EcoCyc:EG12078
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4272 ECOL199310CYC:C4272]
EcoGene:EG12078
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12078 EcoGene:EG12078]
RegulonDB:ECK120001984
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=NIKD ECOO157CYC:NIKD]
[http://www.ncbi.nlm.nih.gov/gene?term=947989 GeneID:947989]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33186 CGSC:33186]
EchoBASE:EB2003
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011360&formSubmitReturn=1 ASAP:ABE-0011360]
ASAP:ABE-0011360
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:nik genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:nik genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:48, 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

nikD

Mnemonic

Nickel

Synonyms

ECK3463, b3479, JW3444, hydC, hydD[1], hydD

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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

77.92 minutes 

MG1655: 3615038..3615802
<gbrowseImage> name=NC_000913:3615038..3615802 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3547703..3548467
<gbrowseImage> name=NC_012967:3547703..3548467 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3503532..3504296
<gbrowseImage> name=NC_012759:3503532..3504296 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4023400..4022636
<gbrowseImage> name=NC_007779:4022636..4023400 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3712783..3713547
<gbrowseImage> name=NC_010473:3712783..3713547 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

ΔnikD (Keio:JW3444)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10555[3]

ΔnikD733::kan

PMID:16738554[2]

CGSC:102072


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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

JW3444

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCCGCAACAGATTGAACTACG

Primer 2:CCTGATGCCAGCTCCATACCGTA

10D10

Kohara Phage

Genobase

PMID:3038334[5]

5F2

Kohara Phage

Genobase

PMID:3038334[5]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[3]

est. P1 cotransduction: 41% [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[3]

est. P1 cotransduction: % [6]

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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:EG12078

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12078

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001984

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947989

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2003

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011360

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).

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