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agaD:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions 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

agaD

Mnemonic

Acetylgalactosamine

Synonyms

ECK3128, b3140, JW3109, yraF[1], yraF

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

70.77 minutes 

MG1655: 3283500..3284291


REL606

NC_012967: 3220711..3221502


BW2952

NC_012759: 3170648..3171439


W3110

 

W3110: 3285333..3286124


DH10B

DH10B: 3381245..3382036


Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes

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

ΔagaD (Keio:JW3109)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10368[3]

agaD::Tn5KAN-I-SceI (FB21042)

Insertion at nt 686 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21042

contains pKD46

agaD::Tn5KAN-I-SceI (FB21043)

Insertion at nt 686 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21043

does not contain pKD46

ΔagaD754::kan

PMID:16738554[2]

CGSC:99940


Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

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

JW3109

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGGATCTGAAATCAGTAAAAA

Primer 2:CCtAAAATGCCGAATGCGGAACA

20F4

Kohara Phage

Genobase

PMID:3038334[6]

16C4

Kohara Phage

Genobase

PMID:3038334[6]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[3]

est. P1 cotransduction: 2% [7]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[3]

est. P1 cotransduction: 11% [7]
Synonyms:zgj-203::Tn10, zha-203::Tn10

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

EcoCyc:G7635

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12771

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004185

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947649

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2624

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010314

Escherichia coli str. K-12 substr. MG1655

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 EcoliWiki page
  3. 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed EcoliWiki page
  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 EcoliWiki page
  6. 6.0 6.1 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 EcoliWiki page
  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).

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