uidB:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Edited by wikibot
touch
 
(7 intermediate revisions by 2 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1611, b1616, JW1608, gusB, uidP''<ref name='LIB:Riley_2006'/>
''ECK1611, b1616, JW1608, gusB, uidP''<ref name='LIB:Riley_2006'/>, uidP''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="R46a9cae8c7869"  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="R46a9cae8c7869"  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 84: Line 84:
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11658 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11658 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1689914|1693287|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1689914|1693287|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|1690914|1692287|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1690914|1692287|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11658 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11658 EcoCyc Sequence Dump]  
|-  
|-  
Line 112: Line 112:
|
|
W3110: 1695977..1694604<br /><gbrowseImage>
W3110: 1695977..1694604<br /><gbrowseImage>
name=AC_000091:1694604..1695977
name=NC_007779:1694604..1695977
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1693604|1696977|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1693604|1696977|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1694604|1695977|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1694604|1695977|FASTA Dump}}  
|-  
|-  
|
|
Line 129: Line 129:
DH10B: 1783248..1781875<br /><gbrowseImage>
DH10B: 1783248..1781875<br /><gbrowseImage>
name=NC_010473:1781875..1783248
name=NC_010473:1781875..1783248
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1779129|1785994|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1779129|1785994|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1779129|1785994|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1779129|1785994|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 156: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="W46a9cae97887e"  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="W46a9cae97887e"  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 191: Line 191:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="N46a9cae9bb845"  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="N46a9cae9bb845"  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 282: Line 282:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="B4e04c540596c0"  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="B4e04c540596c0"  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 303: Line 303:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="G46a9caea6c43e"  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="G46a9caea6c43e"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 321: Line 321:


Primer 2:CCATTAGTGATATCGCTGATTAA  
Primer 2:CCATTAGTGATATCGCTGATTAA  
|-
|
[[:Category:Kohara_Phage:6A5|6A5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=314 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 360: Line 369:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="X46a9caeb083db"  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="X46a9caeb083db"  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=EG11658 EcoCyc:EG11658]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1610 EchoBASE:EB1610]
EcoCyc:EG11658
|
|
''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=b1616 EcoliGenExpDB:b1616]
EcoGene:EG11658
|
|
''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=C2008 ECOL199310CYC:C2008]
RegulonDB:ECK120001601
|
|
''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=EG11658 EcoGene:EG11658]
[http://www.ncbi.nlm.nih.gov/gene?term=947484 GeneID:947484]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=UIDB ECOO157CYC:UIDB]
EchoBASE:EB1610
|
|
''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=0005407&formSubmitReturn=1 ASAP:ABE-0005407]
ASAP:ABE-0005407
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 431: Line 433:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="B46a6e8525b39c"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a6e8525b39c"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:28, 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

uidB

Mnemonic

hexUronIDes

Synonyms

ECK1611, b1616, JW1608, gusB, uidP[1], uidP

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

36.44 minutes 

MG1655: 1692287..1690914
<gbrowseImage> name=NC_000913:1690914..1692287 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1671458..1670085
<gbrowseImage> name=NC_012967:1670085..1671458 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1695977..1694604
<gbrowseImage> name=NC_007779:1694604..1695977 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1783248..1781875
<gbrowseImage> name=NC_010473:1781875..1783248 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

1690914

Edman degradation

PMID:15774881[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

ΔuidB (Keio:JW1608)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9369[4]

uidB::Tn5KAN-2 (FB20390)

Insertion at nt 333 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20390

does not contain pKD46

uidB::Tn5KAN-2 (FB20391)

Insertion at nt 333 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20391

contains pKD46

ΔuidB764::kan

PMID:16738554[3]

CGSC:103300


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

JW1608

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAATCAACAACTCTCCTGGCG

Primer 2:CCATTAGTGATATCGCTGATTAA

6A5

Kohara Phage

Genobase

PMID:3038334[7]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[4]

est. P1 cotransduction: % [8]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[4]

est. P1 cotransduction: % [8]
Synonyms:zdh-925::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:EG11658

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11658

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001601

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947484

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1610

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005407

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. ↑ Liang, WJ et al. (2005) The gusBC genes of Escherichia coli encode a glucuronide transport system. J. Bacteriol. 187 2377-85 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. ↑ 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. ↑ 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=uidB:Gene&oldid=1476033"