rapA:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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===Notes===
===Notes===
HepA has a plausible function and reasonable map location to be the gene affected by the [http://cgsc.biology.yale.edu/Mutation.php?ID=75078 psu-1] mutation.
HepA has a plausible function and reasonable map location to be the gene affected by the [http://cgsc.biology.yale.edu/Mutation.php?ID=75078 psu-1] mutation.
==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:57, 24 June 2011

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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

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

Standard name

rapA

Mnemonic
Synonyms

ECK0060, b0059, JW0058, rapA, yabA, hepA[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

1.3 minutes 

MG1655: 63264..60358
<gbrowseImage> name=NC_000913:60358..63264 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 66068..63162
<gbrowseImage> name=NC_012967:63162..66068 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 60358..63264
<gbrowseImage> name=NC_012759:60358..63264 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 63264..60358
<gbrowseImage> name=AC_000091:60358..63264 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 62378..60358
<gbrowseImage> name=NC_010473:60358..62378 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

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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 Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

60361

Edman degradation

PMID:9614128[2]
PMID:11751638[3]


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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

ΔhepA (Keio:JW0058)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC8366[5]

rapAK183A

K183A

Loss of function. Still interacts with RNAP

seeded from UniProt:P60240

rapADE280AA

DE280AA

Loss of function. Still interacts with RNAP

seeded from UniProt:P60240

ΔhepA769::kan

PMID:16738554[4]

CGSC:101346


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Notes

HepA has a plausible function and reasonable map location to be the gene affected by the psu-1 mutation.


Genetic Interactions

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

JW0058

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCCTTTTACACTTGGTCAACG

Primer 2:CCCTGATGCGTTACAACGATCAA

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 34% [7]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 42% [7]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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:EG11083

EchoBASE (EcoliWiki Page)

EchoBASE:EB1075

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0059

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0070

EcoGene (EcoliWiki Page)

EcoGene:EG11083

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0067

CGSC (EcoliWiki Page)

CGSC:29491

ASAP (EcoliWikiPage)

ASAP:ABE-0000198


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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. ↑ Muzzin, O et al. (1998) Disruption of Escherichia coli hepA, an RNA polymerase-associated protein, causes UV sensitivity. J. Biol. Chem. 273 15157-61 PubMed
  3. ↑ Sukhodolets, MV et al. (2001) RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription. Genes Dev. 15 3330-41 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  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. ↑ 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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