yciM:Gene: Difference between revisions

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Automated update of mnemonics from EcoGene.
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!align=left |Standard name
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''yciM''  
''yciM''
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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Systematic nomenclature
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1275, b1280, JW1272''<ref name='LIB:Riley_2006'/>
''ECK1275, b1280, JW1272''<ref name='LIB:Riley_2006'/>
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{|  id="C46a9c3b378936"  class=" tableEdit Gene_location_table"   
{|  id="C46a9c3b378936"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature type!!Location!!Description
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Database!!Accession!!Notes
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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yci genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:yci genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]

Revision as of 21:59, 25 February 2010

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

yciM

Mnemonic

Systematic nomenclature

Synonyms

ECK1275, b1280, JW1272[1]

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Notes

Location(s) and DNA Sequence

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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

28.85 minutes 

MG1655: 1338582..1339751
gbrowse_img.php?coord=1338582..1339751&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 1338930..1340099
gbrowse_img.php?coord=1338930..1340099&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 1342272..1343441
gbrowse_img.php?coord=1342272..1343441&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 1427978..1429147
gbrowse_img.php?coord=1427978..1429147&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature type Location Description
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Notes

Alleles and Phenotypes

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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

ΔyciM (Keio:JW1272)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9144[3]

ΔyciM788::kan

PMID:16738554[2]

CGSC:104066


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1272

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCTGGAGTTGTTGTTTCTGCT

Primer 2:CCaAGGCCATCAAGACCGCGAAT

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[3]

est. P1 cotransduction: 46% [5]
Synonyms:trpB83::Tn10

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[3]

est. P1 cotransduction: 31% [5]
Synonyms:zci-233::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12691

EchoBASE (EcoliWiki Page)

EchoBASE:EB2554

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1280

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1749

EcoGene (EcoliWiki Page)

EcoGene:EG12691

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YCIM

ASAP (EcoliWikiPage)

ASAP:ABE-0004300


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Notes

Links

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References

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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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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. ↑ 5.0 5.1 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

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