preA:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
No edit summary
Fixing Gbrowse links (bug #119)
Line 84: Line 84:
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11289 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11289 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2232287|2235522|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2232287|2235522|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2233287|2234522|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2233287|2234522|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11289 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11289 EcoCyc Sequence Dump]  
|-  
|-  
Line 118: Line 118:


|
|
{{GBrowseLink|BW2952|012759|2125770|NC_2127005|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2125770|2127005|GBrowse (BW2952)}}
|
|
{{GBrowseFastaLink|BW2952|012759|2125770|NC_2127005|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|2125770|2127005|FASTA Dump}}  
|-  
|-  
|
|
Line 134: Line 134:


|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2237599|2240834|GBrowse(W3110)}}  
{{GBrowseLink|W3110|AC_000091|2237599|2240834|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2238599|2239834|FASTA Dump}}  
{{GBrowseFastaLink|W3110|AC_000091|2238599|2239834|FASTA Dump}}  
|-  
|-  
|
|
Line 150: Line 150:


|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|2321825|2328000|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|2321825|2328000|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2321825|2328000|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2321825|2328000|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  

Revision as of 20:17, 17 August 2011

{{#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

preA

Mnemonic

Systematic nomenclature

Synonyms

ECK2140, b2147, JW2134, yeiA[1][2], yeiA

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

48.13 minutes 

MG1655: 2233287..2234522
<gbrowseImage> name=NC_000913:2233287..2234522 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2186503..2187738
<gbrowseImage> name=NC_012967:2186503..2187738 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2125770..2127005
<gbrowseImage> name=NC_012759:2125770..2127005 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2238599..2239834
<gbrowseImage> name=AC_000091:2238599..2239834 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2324295..2325530
<gbrowseImage> name=NC_010473:2324295..2325530 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

2233287

Edman degradation

PMID:18482579[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

ΔyeiA (Keio:JW2134)

deletion

deletion

PMID:16738554[4]

Shigen


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

JW2134

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTAACGAAAGATCTTTCGAT

Primer 2:CCtAACGTTACCGGGTGTTCTTT

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[6]

est. P1 cotransduction: 6% [7]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[6]

est. P1 cotransduction: 2% [7]
Synonyms:zeg-722, zei-722::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 (EcoliWiki Page)

EcoCyc:EG11289

EchoBASE (EcoliWiki Page)

EchoBASE:EB1266

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2147

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2680

EcoGene (EcoliWiki Page)

EcoGene:EG11289

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YEIA

ASAP (EcoliWikiPage)

ASAP:ABE-0007098


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. ↑ Mihara, H et al. (2008) The iscS gene deficiency affects the expression of pyrimidine metabolism genes. Biochem. Biophys. Res. Commun. 372 407-11 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. ↑ 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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=preA:Gene&oldid=1312016"