secD:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0402, b0408, JW0398''<ref name='LIB:Riley_2006'/>
''ECK0402, b0408, JW0398''<ref name='LIB:Riley_2006'/>, JW0398''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="B46a9af7f1d9fa"  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="B46a9af7f1d9fa"  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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MG1655: 426871..428718<br /><gbrowseImage>
MG1655: 426871..428718<br /><gbrowseImage>
name=NC_000913:426871..428718
name=NC_000913:426871..428718
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10938 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10938 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|425871|429718|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|425871|429718|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|426871|428718|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|426871|428718|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10938 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10938 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|329630|NC_331477|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|329630|331477|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|329630|NC_331477|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|329630|331477|FASTA Dump}}  
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W3110: 426871..428718<br /><gbrowseImage>
W3110: 426871..428718<br /><gbrowseImage>
name=AC_000091:426871..428718
name=NC_007779:426871..428718
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|425871|429718|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|425871|429718|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|426871|428718|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|426871|428718|FASTA Dump}}  
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DH10B: 366202..368049<br /><gbrowseImage>
DH10B: 366202..368049<br /><gbrowseImage>
name=NC_010473:366202..368049
name=NC_010473:366202..368049
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|362508|371743|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|362508|371743|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|362508|371743|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|362508|371743|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="Z46a9af8009f2c"  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="Z46a9af8009f2c"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="Q46a9af807b001"  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="Q46a9af807b001"  class=" tableEdit Gene_allele_table dataTable"   
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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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****************************************************************************************** -->{{Genetic_interaction_help}}
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{|   id="J4e04c3a402aea"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04c3a402aea"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="T46a9af817a514"  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="T46a9af817a514"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGATTGACAGCTTCTTGACGCG  
Primer 2:CCGATTGACAGCTTCTTGACGCG  
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[[:Category:Kohara_Phage:4F3|4F3]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=145 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:19F6|19F6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=146 Genobase]
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PMID:3038334
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{|   id="Z46a9af8266eb8"  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="Z46a9af8266eb8"  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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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10938 EcoCyc:EG10938]
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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=EB0931 EchoBASE:EB0931]
EcoCyc:EG10938
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0408 EcoliGenExpDB:b0408]
EcoGene:EG10938
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0518 ECOL199310CYC:C0518]
RegulonDB:ECK120000927
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10938 EcoGene:EG10938]
[http://www.ncbi.nlm.nih.gov/gene?term=949133 GeneID:949133]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=SECD ECOO157CYC:SECD]
EchoBASE:EB0931
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17893 CGSC:17893]
ASAP:ABE-0001417
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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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=0001417&formSubmitReturn=1 ASAP:ABE-0001417]
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{|   id="Y46a67c59bffc2"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a67c59bffc2"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:29, 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

secD

Mnemonic

Secretory

Synonyms

ECK0402, b0408, JW0398[1], JW0398

edit table


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

9.2 minutes 

MG1655: 426871..428718
<gbrowseImage> name=NC_000913:426871..428718 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 396070..397917
<gbrowseImage> name=NC_012967:396070..397917 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 329630..331477
<gbrowseImage> name=NC_012759:329630..331477 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 426871..428718
<gbrowseImage> name=NC_007779:426871..428718 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 366202..368049
<gbrowseImage> name=NC_010473:366202..368049 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

secD1

CGSC:44985

secD29(Cs)

cold sensitive

CGSC:38549


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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

JW0398

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCTTAAACCGTTATCCTTTGTG

Primer 2:CCGATTGACAGCTTCTTGACGCG

4F3

Kohara Phage

Genobase

PMID:3038334[3]

19F6

Kohara Phage

Genobase

PMID:3038334[3]

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[4]

est. P1 cotransduction: 27% [5]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[4]

est. P1 cotransduction: 86% [5]

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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:EG10938

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10938

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000927

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949133

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0931

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001417

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. ↑ 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
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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