dinB:Gene: Difference between revisions

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Primer 2:CCTAATCCCAGCACCAGTTGTCT  
Primer 2:CCTAATCCCAGCACCAGTTGTCT  
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[[:Category:Kohara_Phage:8F9|8F9]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=127 Genobase]
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PMID:3038334
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est. P1 cotransduction: 74% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 74% <ref name='LIB:Nichols_linked_Tn'/>  
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[[:Category:Kohara_Phage:8F9|8F9]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=127 Genobase]
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PMID:3038334


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6115 EcoCyc:G6115]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2935 EchoBASE:EB2935]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0231 EcoliGenExpDB:b0231]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C0379 ECOL199310CYC:C0379]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG13141 EcoGene:EG13141]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=DINP ECOO157CYC:DINP]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000789&formSubmitReturn=1 ASAP:ABE-0000789]
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Revision as of 19:53, 21 September 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

dinB

Mnemonic

damage inducible Damage inducible

Synonyms

ECK0232, b0231, JW0221, dinP[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

5.41 minutes 

MG1655: 250898..251953
<gbrowseImage> name=NC_000913:250898..251953 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 255461..256516
<gbrowseImage> name=NC_012967:255461..256516 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 250897..251952
<gbrowseImage> name=NC_012759:250897..251952 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 250898..251953
<gbrowseImage> name=AC_000091:250898..251953 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 225002..226057
<gbrowseImage> name=NC_010473:225002..226057 source=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
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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

ΔdinB (Keio:JW0221)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8456[3]

dinP::Tn5KAN-I-SceI (FB20062)

Insertion at nt 89 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20062

does not contain pKD46

dinP::Tn5KAN-I-SceI (FB20063)

Insertion at nt 89 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20063

contains pKD46

dinBA310S

A310S

(in strain: ECOR 57B2, ECOR 59B2, ECOR 60B2 and ECOR 62B2)

Strain variation; seeded from UniProt:Q47155

dinBD321N

D321N

(in strain: ECOR 35D)

Strain variation; seeded from UniProt:Q47155

dinBD8A,H

D8A,H

Loss of function

seeded from UniProt:Q47155

dinBR49A,F

R49A,F

Loss of function

seeded from UniProt:Q47155

dinBD103A,N

D103A,N

Loss of function

seeded from UniProt:Q47155

dinBE104A

E104A

Loss of function

seeded from UniProt:Q47155

dinBM210I

M210I

(in strain: ECOR 37UG, ECOR 45B1, ECOR 51B2, ECOR 52B2, ECOR 58B1 and ECOR 70B1)

Strain variation; seeded from UniProt:Q47155

dinBM210T

M210T

(in strain: ECOR 35D, ECOR 46D, ECOR 49D, ECOR 50D, ECOR 57B2, ECOR 59B2, ECOR 60B2 and ECOR 62B2)

Strain variation; seeded from UniProt:Q47155

dinBR225C

R225C

(in strain: ECOR 59B2 and ECOR 60B2)

Strain variation; seeded from UniProt:Q47155

dinBERR36ARG

ERR36ARG

(in strain: ECOR 45B1)

Strain variation; seeded from UniProt:Q47155

dinBQ124K

Q124K

(in strain: ECOR 35D)

Strain variation; seeded from UniProt:Q47155

dinBN132S

N132S

(in strain: ECOR 34B1 and ECOR 37UG)

Strain variation; seeded from UniProt:Q47155

dinBQ135H

Q135H

(in strain: ECOR 70B1)

Strain variation; seeded from UniProt:Q47155

dinBP170S

P170S

(in strain: ECOR 37UG)

Strain variation; seeded from UniProt:Q47155

dinBA171T

A171T

(in strain: ECOR 45B1, ECOR 46D, ECOR 49D and ECOR 50D)

Strain variation; seeded from UniProt:Q47155

dinBL176F

L176F

(in strain: ECOR 37UG)

Strain variation; seeded from UniProt:Q47155

dinBG201S

G201S

(in strain: ECOR 59B2)

Strain variation; seeded from UniProt:Q47155

dinB10

xx

PMID:| SMR

we like this mutation a lot

F172A

PMID:18158902[5]

defective in UMuD interaction

ΔdinB749::kan

PMID:16738554[2]

CGSC:100600


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Notes

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

JW0221

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCGTAAAATCATTCATGTGGA

Primer 2:CCTAATCCCAGCACCAGTTGTCT

8F9

Kohara Phage

Genobase

PMID:3038334[7]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 50% [8]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[3]

est. P1 cotransduction: 74% [8]

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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
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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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Godoy, VG et al. (2007) UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB. Mol. Cell 28 1058-70 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

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