fis:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|fis}}{{Tab On|Gene|fis}}{{Tab|Gene Product(s)|fis}}{{Tab|Expression|fis}}{{Tab|Evolution|fis}}{{Tab|On One Page|fis}}{{TabsBottom}}
{{Tab|Quickview|fis}}{{Tab On|Gene|fis}}{{Tab|Gene Product(s)|fis}}{{Tab|Expression|fis}}{{Tab|Evolution|fis}}{{Tab|On One Page|fis}}{{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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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''fis''  
''fis''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Factor for inversion stimulation
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3248, b3261, JW3229, nbp''<ref name='LIB:Riley_2006'/>, nbp''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17071.O46a9f1852adf3&page=17071&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3248, b3261, JW3229, nbp''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="K46a9f185ab7ff"  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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73.48 minutes&nbsp;
73.48 minutes&nbsp;
|
|
MG1655: 3409293..3409589<br />{{GBrowseFigureByCoord|3408293|3410589|ecoli|MG1655}}
MG1655: 3409293..3409589<br /><gbrowseImage>
name=NC_000913:3409293..3409589
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10317 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10317 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3408293..3410589 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3408293|3410589|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3409293..3409589&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3409293|3409589|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10317 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10317 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3339162..3339458<br /><gbrowseImage>
name=NC_012967:3339162..3339458
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3339162|3339458|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3339162|3339458|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3296441..3296737<br /><gbrowseImage>
name=NC_012759:3296441..3296737
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3296441|3296737|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3296441|3296737|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3411126..3411422<br />{{GBrowseFigureByCoord|3410126|3412422|ecoli_W3110|W3110}}  
W3110: 3411126..3411422<br /><gbrowseImage>
name=NC_007779:3411126..3411422
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3410126|3412422|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3411126|3411422|FASTA Dump}}  
|-
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[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3410126..3412422 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3411126..3411422&plugin_action=Go FASTA Dump]
DH10B: 3507038..3507334<br /><gbrowseImage>
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3506446|3507926|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3506446|3507926|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="Y46a9f1866b941"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
3409293
|
Edman degradation
|
PMID:2835774<br />PMID:2837762<br />PMID:8809757<br />
|
 
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<protect><!--Sequence_notes--></protect>
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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="V46a9f186b452f"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;fis (Keio:JW3229)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108724 CGSC10443]<ref name='LIB:cgsc'/>
|
|-
|
&Delta;fis::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
 
|
|-
|
''&#916;fis-779::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100880|CGSC:100880]]
|
|-
|
''fis''(del)-767::''khan''
|
 
|
 
|
Growth Phenotype
|
Growth rate regulation of the amount of the ''pdxA-ksgA'' contranscript was abolished by mutation, figure 7.
|
PMID:11844765
|
 
|
Strain: TX3333
 
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<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="Y4e04bb07819ee"  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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JW3229
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCTTCGAACAACGCGTAAATTC
 
Primer 2:CCGTTCATGCCGTATTTTTTCAA
|-
|
[[:Category:Kohara_Phage:6G3|6G3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=529 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6G9|6G9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=530 Genobase]
|
PMID:3038334
|-
|
[[yhcF:Gene|zhc-6::Tn10]]
|
Linked marker
|
CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zha-6::Tn10
|-
|
[[acrF:Gene|acrF3083::Tn10]]
|
Linked marker
|
CAG12075 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40247 CGSC7447]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 83% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10317 EcoCyc:EG10317] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0313 EchoBASE:EB0313] 
EcoCyc:EG10317
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3261 EcoliGenExpDB:b3261] 
EcoGene:EG10317
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4027 ECOL199310CYC:C4027] 
RegulonDB:ECK120000311
|
|
''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=EG10317 EcoGene:EG10317]
[http://www.ncbi.nlm.nih.gov/gene?term=947697 GeneID:947697]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=FIS ECOO157CYC:FIS] 
EchoBASE:EB0313
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/18328 CGSC:18328] 
ASAP:ABE-0010703
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
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===Notes===
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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:fis genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

fis

Mnemonic

Factor for inversion stimulation

Synonyms

ECK3248, b3261, JW3229, nbp[1], nbp

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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

73.48 minutes 

MG1655: 3409293..3409589
<gbrowseImage> name=NC_000913:3409293..3409589 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3339162..3339458
<gbrowseImage> name=NC_012967:3339162..3339458 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3296441..3296737
<gbrowseImage> name=NC_012759:3296441..3296737 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3411126..3411422
<gbrowseImage> name=NC_007779:3411126..3411422 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3507038..3507334
<gbrowseImage> name=NC_010473:3507038..3507334 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

Coding Start (SO:0000323)

MG1655

3409293

Edman degradation

PMID:2835774[2]
PMID:2837762[3]
PMID:8809757[4]


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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

Δfis (Keio:JW3229)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC10443[6]

Δfis::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[7]

Δfis-779::kan

PMID:16738554[5]

CGSC:100880

fis(del)-767::khan

Growth Phenotype

Growth rate regulation of the amount of the pdxA-ksgA contranscript was abolished by mutation, figure 7.

PMID:11844765[8]

Strain: TX3333

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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

JW3229

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCTTCGAACAACGCGTAAATTC

Primer 2:CCGTTCATGCCGTATTTTTTCAA

6G3

Kohara Phage

Genobase

PMID:3038334[10]

6G9

Kohara Phage

Genobase

PMID:3038334[10]

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[6]

est. P1 cotransduction: 13% [11]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[6]

est. P1 cotransduction: 83% [11]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG10317

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10317

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000311

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947697

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0313

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010703

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. ↑ Johnson, RC et al. (1988) Isolation of the gene encoding the Hin recombinational enhancer binding protein. Proc. Natl. Acad. Sci. U.S.A. 85 3484-8 PubMed
  3. ↑ Koch, C et al. (1988) Escherichia coli host factor for site-specific DNA inversion: cloning and characterization of the fis gene. Proc. Natl. Acad. Sci. U.S.A. 85 4237-41 PubMed
  4. ↑ Green, J et al. (1996) The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis. Mol. Microbiol. 20 1043-55 PubMed
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 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
  8. ↑ Pease, AJ et al. (2002) Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12. J. Bacteriol. 184 1359-69 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 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
  11. ↑ 11.0 11.1 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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