hemX:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3797, b3803, JW3775''<ref name='LIB:Riley_2006'/>
''ECK3797, b3803, JW3775''<ref name='LIB:Riley_2006'/>, JW3775''


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{|   id="X46a9ff5d655ab"  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="X46a9ff5d655ab"  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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10433 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10433 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3984908|3988089|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3984908|3988089|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3985908|3987089|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3985908|3987089|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10433 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10433 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|3875577|NC_3876758|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3875577|3876758|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3875577|NC_3876758|FASTA Dump}}  
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W3110: 3647615..3648796<br /><gbrowseImage>
W3110: 3647615..3648796<br /><gbrowseImage>
name=AC_000091:3647615..3648796
name=NC_007779:3647615..3648796
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3646615|3649796|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3646615|3649796|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3647615|3648796|FASTA Dump}}  
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{|   id="U46a9ff5e29d50"  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="U46a9ff5e29d50"  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="J46a9ff5e74275"  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="J46a9ff5e74275"  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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{|   id="D4e04bcec2a6f2"  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="D4e04bcec2a6f2"  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="A46a9ff5f38bba"  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="A46a9ff5f38bba"  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:CCTTCTCCTTGCGGCGCGGCTGC  
Primer 2:CCTTCTCCTTGCGGCGCGGCTGC  
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[[:Category:Kohara_Phage:12G1|12G1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=553 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:10F4|10F4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=554 Genobase]
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PMID:3038334
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{|   id="S46a9ff5fd85b0"  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="S46a9ff5fd85b0"  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=EG10433 EcoCyc:EG10433]
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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=EB0428 EchoBASE:EB0428]
EcoCyc:EG10433
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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=b3803 EcoliGenExpDB:b3803]
EcoGene:EG10433
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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=C4722 ECOL199310CYC:C4722]
RegulonDB:ECK120000426
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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=EG10433 EcoGene:EG10433]
[http://www.ncbi.nlm.nih.gov/gene?term=948446 GeneID:948446]
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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=HEMX ECOO157CYC:HEMX]
EchoBASE:EB0428
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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/33965 CGSC:33965]
ASAP:ABE-0012419
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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=0012419&formSubmitReturn=1 ASAP:ABE-0012419]
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!|Name!!URL!!Comments
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Latest revision as of 20:49, 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

hemX

Mnemonic

Hemin

Synonyms

ECK3797, b3803, JW3775[1], JW3775

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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

85.91 minutes 

MG1655: 3987089..3985908
<gbrowseImage> name=NC_000913:3985908..3987089 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3950896..3949691
<gbrowseImage> name=NC_012967:3949691..3950896 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3875577..3876758
<gbrowseImage> name=NC_012759:3875577..3876758 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3647615..3648796
<gbrowseImage> name=NC_007779:3647615..3648796 source=W3110 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

Coding Start (SO:0000323)

MG1655

3985908

Edman degradation

PMID:9298646[2]


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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

Strain DH10B

D318N

Nonsynonomous mutation

PMID:18245285[3]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔhemX (Keio:JW3775)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10747[5]

hemX::Tn5KAN-I-SceI (FB21463)

Insertion at nt 693 in Minus orientation

PMID:15262929[6]

E. coli Genome Project:FB21463

contains pKD46

ΔhemX750::kan

PMID:16738554[4]

CGSC:101344


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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

JW3775

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACGGAACAAGAAAAAACCTC

Primer 2:CCTTCTCCTTGCGGCGCGGCTGC

12G1

Kohara Phage

Genobase

PMID:3038334[8]

10F4

Kohara Phage

Genobase

PMID:3038334[8]

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[5]

est. P1 cotransduction: 27% [9]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[5]

est. P1 cotransduction: 43% [9]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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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:EG10433

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10433

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000426

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948446

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0428

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012419

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. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  3. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 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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