cmoB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Fixing Gbrowse links (bug #119)
touch
 
(4 intermediate revisions by 2 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''yecP, ECK1872, b1871, JW1860''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''yecP, ECK1872, b1871, JW1860''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, JW1860''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="L46a9d0e91dc0a"  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="L46a9d0e91dc0a"  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: 1955156..1956127<br /><gbrowseImage>
W3110: 1955156..1956127<br /><gbrowseImage>
name=AC_000091:1955156..1956127
name=NC_007779:1955156..1956127
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
Line 134: Line 134:


|
|
{{GBrowseLink|W3110|AC_000091|1954156|1957127|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1954156|1957127|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|W3110|AC_000091|1955156|1956127|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1955156|1956127|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 156: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="D46a9d0e9c52e6"  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="D46a9d0e9c52e6"  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 178: Line 178:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="F46a9d0ea14d96"  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="F46a9d0ea14d96"  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 218: Line 218:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="E4e04b8d9cdb79"  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="E4e04b8d9cdb79"  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 239: Line 239:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="Q46a9d0eabc74d"  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="Q46a9d0eabc74d"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 257: Line 257:


Primer 2:  
Primer 2:  
|-
|
[[:Category:Kohara_Phage:20H4|20H4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=337 Genobase]
|
PMID:3038334


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 276: Line 285:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="H46a9d0eb598c4"  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="H46a9d0eb598c4"  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=G7021 EcoCyc:G7021]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3788 EchoBASE:EB3788]
EcoCyc:G7021
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1871 EcoliGenExpDB:b1871]
EcoGene:EG14034
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2285 ECOL199310CYC:C2285]
RegulonDB:ECK120003608
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14034 EcoGene:EG14034]
[http://www.ncbi.nlm.nih.gov/gene?term=946387 GeneID:946387]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YECP ECOO157CYC:YECP]
EchoBASE:EB3788
|
|
''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=0006241&formSubmitReturn=1 ASAP:ABE-0006241]
ASAP:ABE-0006241
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 347: Line 349:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="V46a6ee430c943"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a6ee430c943"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:39, 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

cmoB

Mnemonic

CarboxylMethOxy

Synonyms

yecP, ECK1872, b1871, JW1860[1][2], JW1860

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

42.06 minutes 

MG1655: 1951466..1952437
<gbrowseImage> name=NC_000913:1951466..1952437 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1932212..1933183
<gbrowseImage> name=NC_012967:1932212..1933183 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1843525..1844496
<gbrowseImage> name=NC_012759:1843525..1844496 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1955156..1956127
<gbrowseImage> name=NC_007779:1955156..1956127 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

ΔcmoB725::kan

PMID:16738554[3]

CGSC:106146


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

Plasmid clone

Shigen

PMID:16769691[4]

Status:

Primer 1:

Primer 2:

20H4

Kohara Phage

Genobase

PMID:3038334[5]

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:G7021

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14034

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003608

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946387

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3788

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006241

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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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. ↑ 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
  5. ↑ 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

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=cmoB:Gene&oldid=1478333"