dinB:Gene: Difference between revisions

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!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
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''dinB''  
''dinB''
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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damage inducible
damage inducible
Damage inducible
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0232, b0231, JW0221, dinP''<ref name='LIB:Riley_2006'/>
''ECK0232, b0231, JW0221, dinP''<ref name='LIB:Riley_2006'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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D103A,N
D103A,N
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Loss of function
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seeded from [http://www.uniprot.org/uniprot/Q47155 UniProt:Q47155]
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dinBE104A
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E104A
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dinBE104A
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E104A
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Loss of function
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seeded from [http://www.uniprot.org/uniprot/Q47155 UniProt:Q47155]


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Revision as of 21:05, 25 February 2010

{{#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 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

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
gbrowse_img.php?coord=250898..251953&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 255461..256516
gbrowse_img.php?coord=255461..256516&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 250898..251953
gbrowse_img.php?coord=250898..251953&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 225002..226057
gbrowse_img.php?coord=225002..226057&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

ΔdinB (Keio:JW0221)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8456[3]

dinP::Tn5KAN

PMID:12519969[4]

ASAP

At position 89 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20062

dinP::Tn5KAN

PMID:12519969[4]

ASAP

At position 89 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20063

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

Other

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 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

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 50% [7]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[3]

est. P1 cotransduction: 74% [7]

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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:G6115

EchoBASE (EcoliWiki Page)

EchoBASE:EB2935

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0231

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0379

EcoGene (EcoliWiki Page)

EcoGene:EG13141

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DINP

ASAP (EcoliWikiPage)

ASAP:ABE-0000789


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Notes

Links

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<protect>

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 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 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. ↑ 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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