aroF:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
imported>Wikientrybot
Bulk deleting accessions.
touch
 
(2 intermediate revisions by 2 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2598, b2601, JW2582''<ref name='LIB:Riley_2006'/>
''ECK2598, b2601, JW2582''<ref name='LIB:Riley_2006'/>, JW2582''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="M46a9e1e840e28"  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="M46a9e1e840e28"  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 128: Line 128:
|
|
W3110: 2739806..2738736<br /><gbrowseImage>
W3110: 2739806..2738736<br /><gbrowseImage>
name=AC_000091:2738736..2739806
name=NC_007779:2738736..2739806
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
Line 134: Line 134:


|
|
{{GBrowseLink|W3110|AC_000091|2737736|2740806|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2737736|2740806|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|W3110|AC_000091|2738736|2739806|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2738736|2739806|FASTA Dump}}  
|-  
|-  
|
|
Line 172: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="T46a9e1e8eea0f"  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="T46a9e1e8eea0f"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
Line 207: Line 207:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="N46a9e1e940b71"  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="N46a9e1e940b71"  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 298: Line 298:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="X4e04b7af138b7"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X4e04b7af138b7"  class=" tableEdit Genetic_interaction_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
Line 319: Line 319:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="E46a9e1e9eeabf"  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="E46a9e1e9eeabf"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 384: Line 384:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="H46a9e1ea9117c"  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="H46a9e1ea9117c"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|
[[EcoCyc]]
|
EcoCyc:EG10078
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG10078
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120000074
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=947084 GeneID:947084]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EchoBASE]]
|
EchoBASE:EB0076
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[ASAP]]
|
ASAP:ABE-0008549
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 406: Line 448:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="Z46a6fe9521b80"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a6fe9521b80"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:43, 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

aroF

Mnemonic

Aromatic

Synonyms

ECK2598, b2601, JW2582[1], JW2582

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

59.01 minutes 

MG1655: 2739172..2738102
<gbrowseImage> name=NC_000913:2738102..2739172 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2662557..2661487
<gbrowseImage> name=NC_012967:2661487..2662557 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2623914..2624984
<gbrowseImage> name=NC_012759:2623914..2624984 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2739806..2738736
<gbrowseImage> name=NC_007779:2738736..2739806 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2830937..2829867
<gbrowseImage> name=NC_010473:2829867..2830937 source=DH10B 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

Coding Start (SO:0000323)

MG1655

2738102

Edman degradation

PMID:6104668[2]
PMID:6146618[3]


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

ΔaroF (Keio:JW2582)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10050[5]

aroF::Tn5KAN-I-SceI (FB20866)

Insertion at nt 345 in Plus orientation

PMID:15262929[6]

E. coli Genome Project:FB20866

contains pKD46

aroF363

CGSC:11301

ΔaroF764::kan

PMID:16738554[4]

CGSC:100066


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

JW2582

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCAAAAAGACGCGCTGAATAA

Primer 2:CCAGCCACGCGAGCCGTCAGCTG

E8F2

Kohara Phage

Genobase

PMID:3038334[8]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 98% [9]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: % [9]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG10078

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10078

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000074

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947084

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0076

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008549

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. ↑ Herrmann, KM et al. (1980) Sequence homology between the tyrosine-sensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Escherichia coli and hemerythrin from Sipunculida. J. Biol. Chem. 255 7079-81 PubMed
  3. ↑ Shultz, J et al. (1984) The nucleotide sequence of the aroF gene of Escherichia coli and the amino acid sequence of the encoded protein, the tyrosine-sensitive 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase. J. Biol. Chem. 259 9655-61 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  7. ↑ 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
  8. ↑ 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
  9. ↑ 9.0 9.1 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=aroF:Gene&oldid=1479058"