amn:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Convert to gbrowse_img.php extension.
touch
 
(11 intermediate revisions by 2 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
||
||
''ECK1977, b1982, JW1963''<ref name='LIB:Riley_2006'/>
''ECK1977, b1982, JW1963''<ref name='LIB:Riley_2006'/>, JW1963''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 66: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="U46a9d367cf4ac"  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="U46a9d367cf4ac"  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 82: Line 83:


|
|
{{GBrowseLink|BW2952|012759|1945568|NC_1947022|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1945568|1947022|GBrowse (BW2952)}}
|
|
{{GBrowseFastaLink|BW2952|012759|1945568|NC_1947022|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|1945568|1947022|FASTA Dump}}  
|-  
|-  
|
|
Line 93: Line 94:
MG1655: 2053085..2054539<br /><gbrowseImage>
MG1655: 2053085..2054539<br /><gbrowseImage>
name=NC_000913:2053085..2054539
name=NC_000913:2053085..2054539
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
Line 99: Line 100:
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10039 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10039 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2052085|2055539|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2052085|2055539|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2053085|2054539|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2053085|2054539|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10039 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10039 EcoCyc Sequence Dump]  
|-  
|-  
Line 127: Line 128:
|
|
W3110: 2057198..2058652<br /><gbrowseImage>
W3110: 2057198..2058652<br /><gbrowseImage>
name=AC_000091:2057198..2058652
name=NC_007779:2057198..2058652
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2056198|2059652|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2056198|2059652|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2057198|2058652|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2057198|2058652|FASTA Dump}}  
|-  
|-  
|
|
Line 144: Line 145:
DH10B: 2144093..2145547<br /><gbrowseImage>
DH10B: 2144093..2145547<br /><gbrowseImage>
name=NC_010473:2144093..2145547
name=NC_010473:2144093..2145547
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|2141185|2148455|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|2141185|2148455|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2141185|2148455|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2141185|2148455|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 171: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="C46a9d3688358b"  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="C46a9d3688358b"  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 206: Line 207:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="Q46a9d368c75ff"  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="Q46a9d368c75ff"  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 228: Line 229:
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006579 amn]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0006579 amn::Tn5KAN-2] (FB20556)
|
|
 
Insertion at nt 239 in Minus orientation
|
|


Line 238: Line 239:


|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20556]
|
|
At position 239 in Minus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20556
contains [[pKD46]]  
|-  
|-  
|
|
Line 269: Line 270:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14529.A4e04b748045bb-->
<!--
******************************************************************************************
*
*  ** 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="A4e04b748045bb"  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.14529.A4e04b748045bb&page=14529&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14529.A4e04b748045bb--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 279: Line 302:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="N46a9d3697b862"  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="N46a9d3697b862"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 297: Line 320:


Primer 2:CCTCGGAACGGCGGCTCATTAAA  
Primer 2:CCTCGGAACGGCGGCTCATTAAA  
|-
|
[[:Category:Kohara_Phage:7D4|7D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=346 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9B2|9B2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=347 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 335: Line 376:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="H46a9d36a196c0"  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="H46a9d36a196c0"  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=EG10039 EcoCyc:EG10039]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0037 EchoBASE:EB0037]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1982 EcoliGenExpDB:b1982]
EcoCyc:EG10039
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2444 ECOL199310CYC:C2444]
EcoGene:EG10039
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10039 EcoGene:EG10039]
RegulonDB:ECK120000035
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=AMN ECOO157CYC:AMN]
[http://www.ncbi.nlm.nih.gov/gene?term=946508 GeneID:946508]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17764 CGSC:17764]
EchoBASE:EB0037
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0006579&formSubmitReturn=1 ASAP:ABE-0006579]
ASAP:ABE-0006579
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 413: Line 440:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="O46a6f0bb7cc1a"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a6f0bb7cc1a"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:40, 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

amn

Mnemonic

AMP nucleosidase

Synonyms

ECK1977, b1982, JW1963[1], JW1963

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

BW2952

NC_012759: 1945568..1947022
<gbrowseImage> name=NC_012759:1945568..1947022 source=BW2952 preset=GeneLocation </gbrowseImage>

MG1655

44.25 minutes 

MG1655: 2053085..2054539
<gbrowseImage> name=NC_000913:2053085..2054539 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1993060..1994514
<gbrowseImage> name=NC_012967:1993060..1994514 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2057198..2058652
<gbrowseImage> name=NC_007779:2057198..2058652 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2144093..2145547
<gbrowseImage> name=NC_010473:2144093..2145547 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

2053085

Edman degradation

PMID:2690948[2]


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

Δamn (Keio:JW1963)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9628[4]

amn::Tn5KAN-2 (FB20556)

Insertion at nt 239 in Minus orientation

PMID:15262929[5]

E. coli Genome Project:FB20556

contains pKD46

Δamn-756::kan

PMID:16738554[3]

CGSC:99996


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

JW1963

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAATAATAAGGGCTCCGGTCT

Primer 2:CCTCGGAACGGCGGCTCATTAAA

7D4

Kohara Phage

Genobase

PMID:3038334[7]

9B2

Kohara Phage

Genobase

PMID:3038334[7]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[4]

est. P1 cotransduction: 56% [8]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: 31% [8]
Synonyms:zee-3129::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:EG10039

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10039

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000035

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946508

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0037

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006579

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. ↑ Leung, HB et al. (1989) Structure and regulation of the AMP nucleosidase gene (amn) from Escherichia coli. Biochemistry 28 8726-33 PubMed
  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. ↑ 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 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=amn:Gene&oldid=1478438"