arnC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|arnC}}{{Tab On|Gene|arnC}}{{Tab|Gene Product(s)|arnC}}{{Tab|Expression|arnC}}{{Tab|Evolution|arnC}}{{Tab|On One Page|arnC}}{{TabsBottom}}
{{Tab|Quickview|arnC}}{{Tab On|Gene|arnC}}{{Tab|Gene Product(s)|arnC}}{{Tab|Expression|arnC}}{{Tab|Evolution|arnC}}{{Tab|On One Page|arnC}}{{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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{|   id="S46a9d9ae803af"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''arnC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''arnC''
ara4N (4-amino-4-deoxy-L-arabinose)
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''yfbF, ECK2247, b2254, JW2248, pmrF, ORF2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, ORF2''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15069.S46a9d9ae803af&page=15069&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''yfbF, ECK2247, b2254, JW2248, pmrF, ORF2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
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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="H46a9d9af0988c"  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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50.98 minutes&nbsp;
50.98 minutes&nbsp;
|
|
MG1655: 2365093..2366061<br />{{GBrowseFigureByCoord|2364093|2367061|ecoli|MG1655}}
MG1655: 2365093..2366061<br /><gbrowseImage>
name=NC_000913:2365093..2366061
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7167 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7167 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2364093..2367061 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2364093|2367061|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2365093..2366061&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2365093|2366061|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7167 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7167 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2313584..2314552<br /><gbrowseImage>
name=NC_012967:2313584..2314552
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2313584|2314552|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2313584|2314552|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2250898..2251866<br /><gbrowseImage>
name=NC_012759:2250898..2251866
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2250898|2251866|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2250898|2251866|FASTA Dump}}
|-  
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|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2371741..2372709<br />{{GBrowseFigureByCoord|2370741|2373709|ecoli_W3110|W3110}}
W3110: 2371741..2372709<br /><gbrowseImage>
name=NC_007779:2371741..2372709
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2370741..2373709 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2370741|2373709|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2371741..2372709&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2371741|2372709|FASTA Dump}}
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|
[[DH10B]]
|
 
|
DH10B: 2456081..2457049<br /><gbrowseImage>
name=NC_010473:2456081..2457049
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2454145|2458985|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2454145|2458985|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="Q46a9d9afb41cc"  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
|-class='sortbottom'
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9d9b0050ea"  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;yfbF::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
''&#916;arnC735::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:106134|CGSC:106134]]
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15069.S4e04b7a20d87b-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S4e04b7a20d87b"  class=" tableEdit Genetic_interaction_table dataTable" 
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<!-- Genetic Interacdtions Notes -->
===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
|-class='sortbottom'
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|
 
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:4B4|4B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=379 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5H12|5H12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=380 Genobase]
|
PMID:3038334
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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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=G7167 EcoCyc:G7167] 
EcoCyc:G7167
|
|
''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=EB3843 EchoBASE:EB3843] 
EcoGene:EG14090
|
|
''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=b2254 EcoliGenExpDB:b2254] 
RegulonDB:ECK120003743
|
|
''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=C2796 ECOL199310CYC:C2796]
[http://www.ncbi.nlm.nih.gov/gene?term=945275 GeneID:945275]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14090 EcoGene:EG14090] 
EchoBASE:EB3843
|
|
''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=Z3512 ECOO157CYC:Z3512] 
ASAP:ABE-0007458
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:arn genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 19 September 2013

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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

arnC

Mnemonic

ara4N (4-amino-4-deoxy-L-arabinose)

Synonyms

yfbF, ECK2247, b2254, JW2248, pmrF, ORF2[1][2], ORF2

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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

50.98 minutes 

MG1655: 2365093..2366061
<gbrowseImage> name=NC_000913:2365093..2366061 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2313584..2314552
<gbrowseImage> name=NC_012967:2313584..2314552 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2250898..2251866
<gbrowseImage> name=NC_012759:2250898..2251866 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2371741..2372709
<gbrowseImage> name=NC_007779:2371741..2372709 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2456081..2457049
<gbrowseImage> name=NC_010473:2456081..2457049 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

ΔyfbF::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[3]

ΔarnC735::kan

PMID:16738554[4]

CGSC:106134


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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

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

4B4

Kohara Phage

Genobase

PMID:3038334[6]

5H12

Kohara Phage

Genobase

PMID:3038334[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:G7167

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14090

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003743

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945275

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3843

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007458

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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
  4. ↑ 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
  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

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