arnF:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Added to the category for BW2952 genes.
touch
 
(12 intermediate revisions by 2 users not shown)
Line 14: Line 14:
|{{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]]
Line 31: Line 33:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{| id="Q46a9d9ca3c2ec"  class=" tableEdit Gene_nomenclature_table"   
{|   id="Q46a9d9ca3c2ec"  class=" tableEdit Gene_nomenclature_table"   


|-
|-
Line 44: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2252, b2258, JW5373, pmrL'', yfbJ<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2252, b2258, JW5373, pmrL'', yfbJ<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, pbgE3, pmrM, yfbJ''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 65: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="I46a9d9cab9810"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9d9cab9810"  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
Line 74: Line 76:
51.1 minutes&nbsp;
51.1 minutes&nbsp;
|
|
MG1655: 2370914..2371300<br />{{GBrowseFigureByCoord|2370914|2371300|ecoli|MG1655}}
MG1655: 2370914..2371300<br /><gbrowseImage>
name=NC_000913:2370914..2371300
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7171 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7171 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2369914|2372300|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2369914|2372300|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2370914|2371300|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2370914|2371300|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7171 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7171 EcoCyc Sequence Dump]  
|-  
|-  
Line 88: Line 95:


|
|
NC_012967: 2319405..2319791<br />{{GBrowseFigureByCoord|2319405|2319791|REL606|NC_012967}}
NC_012967: 2319405..2319791<br /><gbrowseImage>
name=NC_012967:2319405..2319791
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|2319405|2319791|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|2319405|2319791|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|2319405|2319791|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|2319405|2319791|FASTA Dump}}  
|-
|
[[BW2952]]
|
|
NC_012759: 2256719..2257105<br /><gbrowseImage>
name=NC_012759:2256719..2257105
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2256719|2257105|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2256719|2257105|FASTA Dump}}
|-  
|-  
|
|
Line 99: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 2377562..2377948<br />{{GBrowseFigureByCoord|2377562|2377948|ecoli_W3110|W3110}}
W3110: 2377562..2377948<br /><gbrowseImage>
name=NC_007779:2377562..2377948
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2376562|2378948|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2376562|2378948|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2377562|2377948|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2377562|2377948|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 123: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="O46a9d9cb70588"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9d9cb70588"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15079.O46a9d9cb70588&page=15079&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15079.O46a9d9cb70588&page=15079&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15079.O46a9d9cb70588-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15079.O46a9d9cb70588-->
Line 145: Line 178:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="G46a9d9cbb5a99"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G46a9d9cbb5a99"  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
Line 191: Line 224:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15079.J4e04b7a57374e-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04b7a57374e"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.15079.J4e04b7a57374e&page=15079&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15079.J4e04b7a57374e--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 201: Line 256:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="C46a9d9cc6c3cc"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9d9cc6c3cc"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 258: Line 313:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="V46a9d9cd1707f"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9d9cd1707f"  class=" tableEdit Gene_accessions_table"   
|- {{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=G7171 EcoCyc:G7171]
EcoCyc:G7171
|
|
''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=EB3847 EchoBASE:EB3847]
EcoGene:EG14094
|
|
''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=b2258 EcoliGenExpDB:b2258]
RegulonDB:ECK120003747
|
|
''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=C2801 ECOL199310CYC:C2801]
[http://www.ncbi.nlm.nih.gov/gene?term=945344 GeneID:945344]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14094 EcoGene:EG14094]
EchoBASE:EB3847
|
|
''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=Z3517 ECOO157CYC:Z3517]
ASAP:ABE-0007466
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 322: Line 377:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="N46a6f6f2a8666"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a6f6f2a8666"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:41, 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

arnF

Mnemonic

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

Synonyms

ECK2252, b2258, JW5373, pmrL, yfbJ[1][2], pbgE3, pmrM, yfbJ

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

51.1 minutes 

MG1655: 2370914..2371300
<gbrowseImage> name=NC_000913:2370914..2371300 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2319405..2319791
<gbrowseImage> name=NC_012967:2319405..2319791 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2256719..2257105
<gbrowseImage> name=NC_012759:2256719..2257105 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2377562..2377948
<gbrowseImage> name=NC_007779:2377562..2377948 source=W3110 preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔyfbJ (Keio:JW5373)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC11348[4]

ΔyfbJ740::kan

PMID:16738554[3]

CGSC:104644


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW5373

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGGCCTGATGTGGGGATTATT

Primer 2:CCGTAACGTTGTTTTGTCGTGGG

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[4]

est. P1 cotransduction: 34% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[4]

est. P1 cotransduction: 51% [6]
Synonyms:zej-223::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G7171

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14094

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003747

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945344

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3847

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007466

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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 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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=arnF:Gene&oldid=1478712"