thrA:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|thrA}}{{Tab On|Gene|thrA}}{{Tab|Gene Product(s)|thrA}}{{Tab|Expression|thrA}}{{Tab|Evolution|thrA}}{{Tab|On One Page|thrA}}{{TabsBottom}}
{{Tab|Quickview|thrA}}{{Tab On|Gene|thrA}}{{Tab|Gene Product(s)|thrA}}{{Tab|Expression|thrA}}{{Tab|Evolution|thrA}}{{Tab|On One Page|thrA}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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{|   id="K46a9a62c8ab90"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''thrA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''thrA''
Threonine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0002, b0002, JW0001, Hs, thrA1, thrA2, thrD''<ref name='LIB:Riley_2006'/>, thrD''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.1758.K46a9a62c8ab90&page=1758&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0002, b0002, JW0001, Hs, thrA1, thrA2, thrD''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9a62d0f09b"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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0.01 minutes&nbsp;
0.01 minutes&nbsp;
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|
MG1655: 337..2799<br />{{GBrowseFigureByCoord|0|3799|ecoli|MG1655}}
MG1655: 337..2799<br /><gbrowseImage>
name=NC_000913:337..2799
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10998 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10998 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:0..3799 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|0|3799|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:337..2799&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|337|2799|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10998 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10998 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 336..2798<br /><gbrowseImage>
name=NC_012967:336..2798
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|336|2798|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|336|2798|FASTA Dump}}
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[[BW2952]]
|
 
|
NC_012759: 337..2799<br /><gbrowseImage>
name=NC_012759:337..2799
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|NC_012759|337|2799|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|337|2799|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 337..2799<br />{{GBrowseFigureByCoord|0|3799|ecoli_W3110|W3110}}  
W3110: 337..2799<br /><gbrowseImage>
name=NC_007779:337..2799
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|W3110|NC_007779|0|3799|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|337|2799|FASTA Dump}}  
|-
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[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:0..3799 GBrowse(W3110)]
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:337..2799&plugin_action=Go FASTA Dump]
DH10B: 337..2799<br /><gbrowseImage>
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name=NC_010473:337..2799
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|0|7723|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|0|7723|FASTA Dump}}
 
|- class="tableEdit_footer"
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<!--Location_notes--></protect>
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===Notes===
===Notes===




===Sequence Features===
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9a62daa902"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
337
|
Edman degradation
|
PMID:354697<br />PMID:4562989<br />
|
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9a62dea9c8"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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''thrA(del)'' (Keio:JW0001)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|-
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thrA34::Tn10
|
Insertion at 425 bp in [[MG1655]] (NC_000913)
|
 
|
 
|
 
|
adapted from Nichols ''et al.''
|
 
|
|-
|
''thrA34::Tn10''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:4834|CGSC:4834]]
|
|-
|
''thrA1101''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:5343|CGSC:5343]]
|
|-
|
''thrA1015''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:5352|CGSC:5352]]
|
|-
|
''thrA1100''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:5879|CGSC:5879]]
|
|-
|
''thrA3092::Tn10kan''
|
 
|
 
|
 
|
 
|
PMID:2540407 PMID:9829956
|
[[cgscmutation:38986|CGSC:38986]]
|
|-
|
''thrA1016''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:73731|CGSC:73731]]
|
 
|- class="tableEdit_footer"
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04c49bc8b50"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0001
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCCGAGTGTTGAAGTTCGGCGG
 
Primer 2:CCGACTCCTAACTTCCATGAGAG
|-
|
[[:Category:Kohara_Phage:9E4|9E4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=101 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:15A5|15A5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=676 Genobase]
|
PMID:3038334
|-
|
[[carB:Gene|carB96::Tn10]]
|
Linked marker
|
CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:car-96::Tn10
|-
|
[[mdoB:Gene|mdoB202::Tn10]]
|
Linked marker
|
CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zjj-202::Tn10, zji-202::Tn10
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10998 EcoCyc:EG10998] 
EcoCyc:EG10998
|
|
''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=EB0991 EchoBASE:EB0991] 
EcoGene:EG10998
|
|
''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=b0002 EcoliGenExpDB:b0002] 
RegulonDB:ECK120000987
|
|
''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=C0003 ECOL199310CYC:C0003]
[http://www.ncbi.nlm.nih.gov/gene?term=945803 GeneID:945803]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10998 EcoGene:EG10998] 
EchoBASE:EB0991
|
|
''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=THRA ECOO157CYC:THRA] 
ASAP:ABE-0000008
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.1758.U46a9a62f25c4d&page=1758&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/111 CGSC:111] 
|
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:thr genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:19, 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

thrA

Mnemonic

Threonine

Synonyms

ECK0002, b0002, JW0001, Hs, thrA1, thrA2, thrD[1], thrD

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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

0.01 minutes 

MG1655: 337..2799
<gbrowseImage> name=NC_000913:337..2799 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 336..2798
<gbrowseImage> name=NC_012967:336..2798 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 337..2799
<gbrowseImage> name=NC_012759:337..2799 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 337..2799
<gbrowseImage> name=NC_007779:337..2799 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 337..2799
<gbrowseImage> name=NC_010473:337..2799 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

Coding Start (SO:0000323)

MG1655

337

Edman degradation

PMID:354697[2]
PMID:4562989[3]


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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

thrA(del) (Keio:JW0001)

deletion

deletion

PMID:16738554[4]

Shigen

thrA34::Tn10

Insertion at 425 bp in MG1655 (NC_000913)

adapted from Nichols et al.

thrA34::Tn10

CGSC:4834

thrA1101

CGSC:5343

thrA1015

CGSC:5352

thrA1100

CGSC:5879

thrA3092::Tn10kan

PMID:2540407[5] PMID:9829956[6]

CGSC:38986

thrA1016

CGSC:73731


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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

JW0001

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCGAGTGTTGAAGTTCGGCGG

Primer 2:CCGACTCCTAACTTCCATGAGAG

9E4

Kohara Phage

Genobase

PMID:3038334[8]

15A5

Kohara Phage

Genobase

PMID:3038334[8]

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[9]

est. P1 cotransduction: 28% [10]
Synonyms:car-96::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[9]

est. P1 cotransduction: 12% [10]
Synonyms:zjj-202::Tn10, zji-202::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:EG10998

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10998

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000987

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945803

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0991

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000008

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. ↑ Cossart-Gheerbrant, P et al. (1978) The primary structure of Escherichia coli K12 aspartokinase I-homoserine dehydrogenase I-Isolation and characterisation of the peptides produced by cyanogen bromide. Biochim. Biophys. Acta 535 206-15 PubMed
  3. ↑ Falcoz-Kelly, F et al. (1972) Revised structure of aspartokinase I-homoserine dehydrogenase I of Escherichia coli K12. Evidence for four identical subunits. Eur. J. Biochem. 28 507-19 PubMed
  4. ↑ 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. ↑ Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
  6. ↑ Nichols, BP et al. (1998) Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction. J. Bacteriol. 180 6408-11 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 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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