tyrA: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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{|{{Prettytable}}
{|   id="T46a9e1e105c55"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''tyrA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''tyrA''
Tyrosine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2597, b2600, JW2581''<ref name='LIB:Riley_2006'/>, JW2581''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15769.T46a9e1e105c55&page=15769&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2597, b2600, JW2581''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='140503'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9e1e184380"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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58.99 minutes, 58.99 minutes&nbsp;
58.99 minutes, 58.99 minutes&nbsp;
|
|
MG1655: 2738091..2736970<br />{{GBrowseFigureByCoord|2735970|2739091|ecoli|MG1655}}
MG1655: 2738091..2736970<br /><gbrowseImage>
name=NC_000913:2736970..2738091
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11039 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11039 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2735970..2739091 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2735970|2739091|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2736970..2738091&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2736970|2738091|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11039 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11039 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2661476..2660355<br /><gbrowseImage>
name=NC_012967:2660355..2661476
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2660355|2661476|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2660355|2661476|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2622782..2623903<br /><gbrowseImage>
name=NC_012759:2622782..2623903
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2622782|2623903|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2622782|2623903|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2738725..2737604<br />{{GBrowseFigureByCoord|2736604|2739725|ecoli_W3110|W3110}}  
W3110: 2738725..2737604<br /><gbrowseImage>
name=NC_007779:2737604..2738725
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2736604|2739725|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2737604|2738725|FASTA Dump}}  
|-
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[[DH10B]]
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|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2736604..2739725 GBrowse(W3110)]
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2737604..2738725&plugin_action=Go FASTA Dump]
DH10B: 2829856..2828735<br /><gbrowseImage>
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name=NC_010473:2828735..2829856
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2826493|2832098|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2826493|2832098|FASTA Dump}}
 
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9e1e284eb9"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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&Delta;tyrA (Keio:JW2581)
''tyrA(del)'' (Keio:JW2581)
|
|
deletion
deletion
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108330 CGSC10049]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108330 CGSC10049]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008547 tyrA::Tn5KAN-I-SceI] (FB20865)
|
Insertion at nt 491 in Plus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20865]
|
contains [[pKD46]]
|-  
|-  
|
|
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|
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amber (UAG) mutation  
amber (UAG) mutation  
|-
|
''tyrA16::Tn10''
|
|
|
|
|
|
[[cgscmutation:8868|CGSC:8868]]
|
|-
|
''tyrA6''
|
|
|
|
|
|
[[cgscmutation:8934|CGSC:8934]]
|
|-
|
''tyrA1::Mu''
|
|
|
|
|
|
[[cgscmutation:23654|CGSC:23654]]
|
|-
|
''tyrA117::Mu cts''
|
|
|
|
|
|
[[cgscmutation:73503|CGSC:73503]]
|
|-
|
''tyrA763(del)''::kan
|
|


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|
 
|
PMID:16738554
|
[[cgscmutation:103260|CGSC:103260]]
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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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JW2581
JW2581
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCtTGGCGATTGTCATTCGCCTG  
Primer 2:CCtTGGCGATTGTCATTCGCCTG  
|-
|-
|
[[:Category:Kohara_Phage:E8F2|E8F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=438 Genobase]
|
PMID:3038334
|-  
|
|
[[nadB:Gene|nadB51::Tn10]]
[[nadB:Gene|nadB51::Tn10]]
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|
|
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[pheA:Gene|pheA18::Tn10]]
[[pheA:Gene|pheA18::Tn10]]
Line 273: Line 470:
|
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est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11039 EcoCyc:EG11039] 
EcoCyc:EG11039
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1032 EchoBASE:EB1032] 
EcoGene:EG11039
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2600 EcoliGenExpDB:b2600] 
RegulonDB:ECK120001028
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3121 ECOL199310CYC:C3121]
[http://www.ncbi.nlm.nih.gov/gene?term=947115 GeneID:947115]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11039 EcoGene:EG11039] 
EchoBASE:EB1032
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=TYRA ECOO157CYC:TYRA] 
ASAP:ABE-0008547
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15769.W46a9e1e3d57ef&page=15769&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/58 CGSC:58] 
|
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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:tyr genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 19 September 2013

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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

tyrA

Mnemonic

Tyrosine

Synonyms

ECK2597, b2600, JW2581[1], JW2581

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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

58.99 minutes, 58.99 minutes 

MG1655: 2738091..2736970
<gbrowseImage> name=NC_000913:2736970..2738091 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2661476..2660355
<gbrowseImage> name=NC_012967:2660355..2661476 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2622782..2623903
<gbrowseImage> name=NC_012759:2622782..2623903 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2738725..2737604
<gbrowseImage> name=NC_007779:2737604..2738725 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2829856..2828735
<gbrowseImage> name=NC_010473:2828735..2829856 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

tyrA(del) (Keio:JW2581)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10049[3]

tyrA::Tn5KAN-I-SceI (FB20865)

Insertion at nt 491 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20865

contains pKD46

tyrA4

CGSC:4851

tyrA2

CGSC:5299

tyrA14

CGSC:7359

tyrA15(Am)

CGSC:8790

amber (UAG) mutation

tyrA16::Tn10

CGSC:8868

tyrA6

CGSC:8934

tyrA1::Mu

CGSC:23654

tyrA117::Mu cts

CGSC:73503

tyrA763(del)::kan

PMID:16738554[2]

CGSC:103260


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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

JW2581

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGTTGCTGAATTGACCGCATT

Primer 2:CCtTGGCGATTGTCATTCGCCTG

E8F2

Kohara Phage

Genobase

PMID:3038334[6]

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[3]

est. P1 cotransduction: 35% [7]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[3]

est. P1 cotransduction: 99% [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

EcoCyc:EG11039

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11039

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001028

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947115

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1032

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008547

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ 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
  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).

Categories

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