yciM:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1275, b1280, JW1272''<ref name='LIB:Riley_2006'/>
''ECK1275, b1280, JW1272''<ref name='LIB:Riley_2006'/>, JW1272''


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{|   id="C46a9c3b378936"  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="C46a9c3b378936"  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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W3110: 1342272..1343441<br /><gbrowseImage>
W3110: 1342272..1343441<br /><gbrowseImage>
name=AC_000091:1342272..1343441
name=NC_007779:1342272..1343441
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|1341272|1344441|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1341272|1344441|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|1342272|1343441|FASTA Dump}}  
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{|   id="K46a9c3b42600b"  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="K46a9c3b42600b"  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="L46a9c3b4678b1"  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="L46a9c3b4678b1"  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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yciM
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deletion
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Sensitivity to
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increases sensitivity to bicyclomycin
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PMID:21357484
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fig 2


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{|   id="G4e04c7558e29a"  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="G4e04c7558e29a"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="J46a9c3b514e8b"  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="J46a9c3b514e8b"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCaAGGCCATCAAGACCGCGAAT  
Primer 2:CCaAGGCCATCAAGACCGCGAAT  
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[[:Category:Kohara_Phage:18B6|18B6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=255 Genobase]
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PMID:3038334
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est. P1 cotransduction: 31% <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: 31% <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:zci-233::Tn10  
Synonyms:zci-233::Tn10  
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[[:Category:Kohara_Phage:18B6|18B6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=255 Genobase]
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PMID:3038334


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{|   id="F46a9c3b5a1907"  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="F46a9c3b5a1907"  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=EG12691 EcoCyc:EG12691]
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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=EB2554 EchoBASE:EB2554]
EcoCyc:EG12691
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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=b1280 EcoliGenExpDB:b1280]
EcoGene:EG12691
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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=C1749 ECOL199310CYC:C1749]
RegulonDB:ECK120002356
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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=EG12691 EcoGene:EG12691]
[http://www.ncbi.nlm.nih.gov/gene?term=944858 GeneID:944858]
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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=YCIM ECOO157CYC:YCIM]
EchoBASE:EB2554
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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]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004300&formSubmitReturn=1 ASAP:ABE-0004300]
ASAP:ABE-0004300
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:30, 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

yciM

Mnemonic

Systematic nomenclature

Synonyms

ECK1275, b1280, JW1272[1], JW1272

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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

28.85 minutes 

MG1655: 1338582..1339751
<gbrowseImage> name=NC_000913:1338582..1339751 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1338930..1340099
<gbrowseImage> name=NC_012967:1338930..1340099 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1229431..1230600
<gbrowseImage> name=NC_012759:1229431..1230600 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1342272..1343441
<gbrowseImage> name=NC_007779:1342272..1343441 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1427978..1429147
<gbrowseImage> name=NC_010473:1427978..1429147 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

ΔyciM (Keio:JW1272)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9144[3]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire DL-a-Glycerol

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire L-Alanyl-glycine

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔyciM::kan

deletion

Biolog:respiration

unable to respire L-Serine

PMID:16095938[4]

ΔyciM788::kan

PMID:16738554[2]

CGSC:104066

yciM

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[5]

fig 2

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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

JW1272

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCTGGAGTTGTTGTTTCTGCT

Primer 2:CCaAGGCCATCAAGACCGCGAAT

18B6

Kohara Phage

Genobase

PMID:3038334[7]

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[3]

est. P1 cotransduction: 46% [8]
Synonyms:trpB83::Tn10

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[3]

est. P1 cotransduction: 31% [8]
Synonyms:zci-233::Tn10

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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:EG12691

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12691

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002356

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944858

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2554

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004300

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. ↑ 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. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 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).

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