dsrA:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1952, b1954, JWR0036, IS095''<ref name='LIB:Riley_2006'/>
''ECK1952, b1954, JWR0036, IS095''<ref name='LIB:Riley_2006'/>, IS095''


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{|   id="U46a9d2d2b673b"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9d2d2b673b"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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43.61 minutes&nbsp;
43.61 minutes&nbsp;
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MG1655: 2023337..2023251<br />{{GBrowseFigureByCoord|2023251|2023337|ecoli|MG1655}}
MG1655: 2023337..2023251<br /><gbrowseImage>
name=NC_000913:2023251..2023337
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7047 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7047 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2022251|2024337|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2022251|2024337|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|2023251|2023337|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2023251|2023337|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7047 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7047 EcoCyc Sequence Dump]  
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W3110
[[BW2952]]
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W3110: 2027450..2027364<br />{{GBrowseFigureByCoord|2027364|2027450|ecoli_W3110|W3110}}
NC_012759: 1915734..1915820<br /><gbrowseImage>
name=NC_012759:1915734..1915820
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|2026364|2028450|GBrowse(W3110)}}  
{{GBrowseLink|BW2952|NC_012759|1915734|1915820|GBrowse (BW2952)}}
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2027364|2027450|FASTA Dump}}  
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[[DH10B]]
W3110
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W3110: 2027450..2027364<br /><gbrowseImage>
name=NC_007779:2027364..2027450
source=W3110
preset=GeneLocation
</gbrowseImage>


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DH10B: 2114345..2114259<br />{{GBrowseFigureByCoord|2114259|2114345|ecoli_DH10B|DH10B}}
{{GBrowseLink|W3110|NC_007779|2026364|2028450|GBrowse(W3110)}}  
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{{GBrowseLink|ecoli_DH10B|NC_010473|2114087|2114517|GBrowse(DH10B)}}
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[[BW2952]]
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NC_012759: 1915734..1915820<br />{{GBrowseFigureByCoord|1915734|1915820|BW2952|NC_012759}}
DH10B: 2114345..2114259<br /><gbrowseImage>
name=NC_010473:2114259..2114345
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|1915734|NC_1915820|GBrowse (BW2952)}}
{{GBrowseLink|DH10B|NC_010473|2114087|2114517|GBrowse(DH10B)}}
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{{GBrowseFastaLink|BW2952|012759|1915734|NC_1915820|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2114087|2114517|FASTA Dump}}  


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{|   id="I46a9d2d36af4e"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9d2d36af4e"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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{| {{Prettytable}} id="V46a9d2d3af16b"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="V46a9d2d3af16b"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14479.P4e04ba21ecbb7-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="R46a9d2d46348a"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9d2d46348a"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:25D8|25D8]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=344 Genobase]
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PMID:3038334
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{|   id="F46a9d2d500d91"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9d2d500d91"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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EcoCyc:G7047
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[EcoGene]]
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EcoGene:EG31118
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7047 EcoCyc:G7047]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[RegulonDB]]
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RegulonDB:ECK120003633
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4281 EchoBASE:EB4281]
[http://www.ncbi.nlm.nih.gov/gene?term=946470 GeneID:946470]
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Escherichia coli str. K-12 substr. MG1655
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1954 EcoliGenExpDB:b1954]
EchoBASE:EB4281
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[ASAP]]
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[http://ecogene.org/geneinfo.php?eg_id=EG31118 EcoGene:EG31118]
ASAP:ABE-0006490
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:39, 19 September 2013

{{#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 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

dsrA

Mnemonic

Down-stream region

Synonyms

ECK1952, b1954, JWR0036, IS095[1], IS095

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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

43.61 minutes 

MG1655: 2023337..2023251
<gbrowseImage> name=NC_000913:2023251..2023337 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1915734..1915820
<gbrowseImage> name=NC_012759:1915734..1915820 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2027450..2027364
<gbrowseImage> name=NC_007779:2027364..2027450 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2114345..2114259
<gbrowseImage> name=NC_010473:2114259..2114345 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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

ΔdsrA5

CGSC:90663

dsrA1::cat

PMID:7534408[2]

CGSC:90670


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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

Plasmid clone

Shigen

PMID:16769691[3]

Status:

Primer 1:

Primer 2:

25D8

Kohara Phage

Genobase

PMID:3038334[4]

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[5]

est. P1 cotransduction: 27% [6]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[5]

est. P1 cotransduction: 62% [6]

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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

EcoCyc:G7047

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG31118

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003633

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946470

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4281

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006490

Escherichia coli str. K-12 substr. MG1655

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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. ↑ Sledjeski, D & Gottesman, S (1995) A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 92 2003-7 PubMed
  3. ↑ 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
  4. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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