acrE:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
/Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php
touch
 
(14 intermediate revisions by 3 users not shown)
Line 16: Line 16:
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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 45: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3252, b3265, JW3233, G7979''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3252, b3265, JW3233, G7979''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, envC''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 66: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="B46a9f19f63c0c"  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="B46a9f19f63c0c"  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 75: Line 76:
73.54 minutes&nbsp;
73.54 minutes&nbsp;
|
|
MG1655: 3411886..3413043<br />{{GBrowseFigureByCoord|3411886|3413043|ecoli|MG1655}}
MG1655: 3411886..3413043<br /><gbrowseImage>
name=NC_000913:3411886..3413043
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10266 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10266 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3410886|3414043|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3410886|3414043|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3411886|3413043|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3411886|3413043|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10266 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10266 EcoCyc Sequence Dump]  
|-  
|-  
Line 89: Line 95:


|
|
NC_012967: 3341755..3342912<br />{{GBrowseFigureByCoord|3341755|3342912|REL606|NC_012967}}
NC_012967: 3341755..3342912<br /><gbrowseImage>
name=NC_012967:3341755..3342912
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|3341755|3342912|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3341755|3342912|GBrowse (REL606)}}
Line 100: Line 111:


|
|
NC_012759: 3299034..3300191<br />{{GBrowseFigureByCoord|3299034|3300191|BW2952|NC_012759}}
NC_012759: 3299034..3300191<br /><gbrowseImage>
name=NC_012759:3299034..3300191
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|BW2952|012759|3299034|NC_3300191|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3299034|3300191|GBrowse (BW2952)}}
|
|
{{GBrowseFastaLink|BW2952|012759|3299034|NC_3300191|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3299034|3300191|FASTA Dump}}  
|-  
|-  
|
|
Line 111: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 3413719..3414876<br />{{GBrowseFigureByCoord|3413719|3414876|ecoli_W3110|W3110}}
W3110: 3413719..3414876<br /><gbrowseImage>
name=NC_007779:3413719..3414876
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3412719|3415876|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3412719|3415876|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3413719|3414876|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3413719|3414876|FASTA Dump}}  
|-  
|-  
|
|
Line 122: Line 143:


|
|
DH10B: 3509631..3510788<br />{{GBrowseFigureByCoord|3509631|3510788|ecoli_DH10B|DH10B}}
DH10B: 3509631..3510788<br /><gbrowseImage>
name=NC_010473:3509631..3510788
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|3507317|3513102|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3507317|3513102|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3507317|3513102|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3507317|3513102|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 146: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="P46a9f1a0239a1"  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="P46a9f1a0239a1"  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
|-
|
Protein Binding Site (SO:0000410)
|
MG1655
|
-289bps from the translational start site
|
[[Methods: ROMA|ROMA]]
|
PMID:15520470
|
CRP binding site


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 168: Line 207:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="V46a9f1a06bef5"  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="V46a9f1a06bef5"  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 190: Line 229:
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010722 acrE::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010722 acrE::Tn5KAN-I-SceI] (FB21091)
|
|
 
Insertion at nt 611 in Minus orientation
|
|


Line 200: Line 239:


|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21091]
|
|
At position 611 in Minus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB21091
contains [[pKD46]]  
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010722 acrE::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010722 acrE::Tn5KAN-I-SceI] (FB21092)
|
|
 
Insertion at nt 611 in Minus orientation
|
|


Line 217: Line 256:


|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21092]
|
|
At position 611 in Minus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB21092
does not contain [[pKD46]]  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 231: Line 270:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17079.B4e04b6e2187bf-->
<!--
******************************************************************************************
*
*  ** 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="B4e04b6e2187bf"  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.17079.B4e04b6e2187bf&page=17079&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17079.B4e04b6e2187bf--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 241: Line 302:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="I46a9f1a12b862"  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="I46a9f1a12b862"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 259: Line 320:


Primer 2:CCtTTCGATGCAGTATCTGCGGG  
Primer 2:CCtTTCGATGCAGTATCTGCGGG  
|-
|
[[: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
|-  
|-  
|
|
Line 298: Line 377:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="O46a9f1a1c722f"  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="O46a9f1a1c722f"  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=EG10266 EcoCyc:EG10266]
EcoCyc:EG10266
|
|
''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=EB0262 EchoBASE:EB0262]
EcoGene:EG10266
|
|
''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=b3265 EcoliGenExpDB:b3265]
RegulonDB:ECK120000260
|
|
''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=C4031 ECOL199310CYC:C4031]
[http://www.ncbi.nlm.nih.gov/gene?term=947706 GeneID:947706]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10266 EcoGene:EG10266]
EchoBASE:EB0262
|
|
''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=ACRE ECOO157CYC:ACRE]
ASAP:ABE-0010722
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/813 CGSC:813]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0010722&formSubmitReturn=1 ASAP:ABE-0010722]
|


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 376: Line 441:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="J46a70cf4383c5"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a70cf4383c5"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:46, 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

acrE

Mnemonic

Acridine

Synonyms

ECK3252, b3265, JW3233, G7979[1][2], envC

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

73.54 minutes 

MG1655: 3411886..3413043
<gbrowseImage> name=NC_000913:3411886..3413043 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3341755..3342912
<gbrowseImage> name=NC_012967:3341755..3342912 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3299034..3300191
<gbrowseImage> name=NC_012759:3299034..3300191 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3413719..3414876
<gbrowseImage> name=NC_007779:3413719..3414876 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3509631..3510788
<gbrowseImage> name=NC_010473:3509631..3510788 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

Protein Binding Site (SO:0000410)

MG1655

-289bps from the translational start site

ROMA

PMID:15520470[3]

CRP binding site

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

ΔacrE (Keio:JW3233)

deletion

deletion

PMID:16738554[4]

Shigen

acrE::Tn5KAN-I-SceI (FB21091)

Insertion at nt 611 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB21091

contains pKD46

acrE::Tn5KAN-I-SceI (FB21092)

Insertion at nt 611 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB21092

does not contain pKD46

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

JW3233

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCACGAAACATGCCAGGTTTTT

Primer 2:CCtTTCGATGCAGTATCTGCGGG

6G3

Kohara Phage

Genobase

PMID:3038334[7]

6G9

Kohara Phage

Genobase

PMID:3038334[7]

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[8]

est. P1 cotransduction: 11% [9]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[8]

est. P1 cotransduction: 91% [9]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG10266

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10266

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000260

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947706

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0262

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010722

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. ↑ Zheng, D et al. (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res. 32 5874-93 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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 CGSC: The Coli Genetics Stock Center
  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=acrE:Gene&oldid=1479711"