thrA: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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*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="K46a9a62c8ab90" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''thrA''  
''thrA''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Threonine
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0002, b0002, JW0001, Hs, thrA1, thrA2, thrD''<ref name='LIB:Riley_2006'/>
''ECK0002, b0002, JW0001, Hs, thrA1, thrA2, thrD''<ref name='LIB:Riley_2006'/>, thrD''


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*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| 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}}
|- {{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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0.01 minutes&nbsp;
0.01 minutes&nbsp;
|
|
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]
{{GBrowseLink|ecoli|NC_000913|0|3799|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|0|3799|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|337|2799|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}}
|-
|
[[BW2952]]
|
|
NC_012759: 337..2799<br /><gbrowseImage>
name=NC_012759:337..2799
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|337|2799|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|337|2799|FASTA Dump}}
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
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>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|0|3799|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|0|3799|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|337|2799|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|337|2799|FASTA Dump}}
|-
|
[[DH10B]]
|
 
|
DH10B: 337..2799<br /><gbrowseImage>
name=NC_010473:337..2799
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|0|7723|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|0|7723|FASTA Dump}}  


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*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| 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"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
337
|
Edman degradation
|
PMID:354697<br />PMID:4562989<br />
|


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|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="I46a9a62dea9c8"  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
|-  
|-  
|
|
&Delta;thrA (Keio:JW0001)
''thrA(del)'' (Keio:JW0001)
|
|
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]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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|
|


|[[PMID:2540407]]<ref name=PMID:2540407/>[[PMID:9829956]]<ref name=PMID:9829956/>
|
PMID:2540407 PMID:9829956
|
|
[[cgscmutation:38986|CGSC:38986]]
[[cgscmutation:38986|CGSC:38986]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.1758.A4e04c49bc8b50-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| 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" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.1758.A4e04c49bc8b50&page=1758&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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****************************************************************************************** -->{{Gene_resources_help}}
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|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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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:CCGACTCCTAACTTCCATGAGAG  
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
|-  
|-  
|
|
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CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
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'/>nnSynonyms:car-96::Tn10  
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:car-96::Tn10  
|-  
|-  
|
|
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CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
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'/>nnSynonyms:zjj-202::Tn10, zji-202::Tn10  
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zjj-202::Tn10, zji-202::Tn10  


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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]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/111 CGSC:111]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000008&formSubmitReturn=1 ASAP:ABE-0000008]
|


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!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===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:thr genes]]
[[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

[back to top]


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

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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).

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