preT:Gene: Difference between revisions

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Move help links into the <above> tag inside templates.
m 127.0.0.1 moved page preB:Gene to preT:Gene: Correct bad gene renaming from 2011
 
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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|yeiT}}{{Tab On|Gene|yeiT}}{{Tab|Gene Product(s)|yeiT}}{{Tab|Expression|yeiT}}{{Tab|Evolution|yeiT}}{{Tab|On One Page|yeiT}}{{TabsBottom}}
{{Tab|Quickview|preT}}{{Tab On|Gene|preT}}{{Tab|Gene Product(s)|preT}}{{Tab|Expression|preT}}{{Tab|Evolution|preT}}{{Tab|On One Page|preT}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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="D46a9d716f1e4b" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''yeiT''  
''preT''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Systematic nomenclature
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2139, b2146, JW2133''<ref name='LIB:Riley_2006'/>
''ECK2139, b2146, JW2133, yeiT, dpdA, preB''


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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="U46a9d7177a910"  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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48.11 minutes&nbsp;
48.11 minutes&nbsp;
|
|
MG1655: 2232055..2233293<br />{{GBrowseFigureByCoord|2231055|2234293|ecoli|MG1655}}
MG1655: 2232055..2233293<br /><gbrowseImage>
name=NC_000913:2232055..2233293
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7145 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7145 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2231055|2234293|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2231055|2234293|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2232055|2233293|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2232055|2233293|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7145 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7145 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 2185271..2186509<br /><gbrowseImage>
name=NC_012967:2185271..2186509
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|2185271|2186509|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2185271|2186509|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 2124538..2125776<br /><gbrowseImage>
name=NC_012759:2124538..2125776
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2124538|2125776|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2124538|2125776|FASTA Dump}}
|-  
|-  
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&nbsp;
&nbsp;
|
|
W3110: 2237367..2238605<br />{{GBrowseFigureByCoord|2236367|2239605|ecoli_W3110|W3110}}  
W3110: 2237367..2238605<br /><gbrowseImage>
name=NC_007779:2237367..2238605
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2236367|2239605|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2237367|2238605|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 2323063..2324301<br /><gbrowseImage>
name=NC_010473:2323063..2324301
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2236367|2239605|GBrowse(W3110)}}  
{{GBrowseLink|DH10B|NC_010473|2320587|2326777|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2237367|2238605|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2320587|2326777|FASTA Dump}}  


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*  
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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="D46a9d7183007f"  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]]
|
2232055
|
Edman degradation
|
PMID:18482579<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="D46a9d71874afa"  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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|
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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=108010 CGSC9729]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108010 CGSC9729]<ref name='LIB:cgsc'/>  
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|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
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[[cgscmutation:104590|CGSC:104590]]
[[cgscmutation:104590|CGSC:104590]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14853.Y4e04c8c0ea056-->
<!--
******************************************************************************************
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y4e04c8c0ea056"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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Synonyms:zeg-722, zei-722::Tn10  
Synonyms:zeg-722, zei-722::Tn10  


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*  
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9d719bd9b8"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7145 EcoCyc:G7145]
[http://www.ncbi.nlm.nih.gov/gene?term=949049 GeneID:949049]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3827 EchoBASE:EB3827]
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2146 EcoliGenExpDB:b2146]
EchoBASE:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2679 ECOL199310CYC:C2679]
ASAP:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG14074 EcoGene:EG14074]
|
|-  
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=Z3401 ECOO157CYC:Z3401]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007096&formSubmitReturn=1 ASAP:ABE-0007096]
|


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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:yei genes]]
[[Category:yei genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:10, 13 July 2015

{{#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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

preT

Mnemonic

Systematic nomenclature

Synonyms

ECK2139, b2146, JW2133, yeiT, dpdA, preB

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

48.11 minutes 

MG1655: 2232055..2233293
<gbrowseImage> name=NC_000913:2232055..2233293 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2185271..2186509
<gbrowseImage> name=NC_012967:2185271..2186509 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2124538..2125776
<gbrowseImage> name=NC_012759:2124538..2125776 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2237367..2238605
<gbrowseImage> name=NC_007779:2237367..2238605 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2323063..2324301
<gbrowseImage> name=NC_010473:2323063..2324301 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

2232055

Edman degradation

PMID:18482579[1]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔyeiT (Keio:JW2133)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9729[3]

ΔyeiT773::kan

PMID:16738554[2]

CGSC:104590


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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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Resource Resource Type Source Notes/Reference

JW2133

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCCGCAACAAAATTATCTGGA

Primer 2:CCACATGAGCAAGCTCCCTCTAA

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[3]

est. P1 cotransduction: 6% [5]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[3]

est. P1 cotransduction: 2% [5]
Synonyms:zeg-722, zei-722::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

NCBI (EcoliWiki Page)

GeneID:949049

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ Mihara, H et al. (2008) The iscS gene deficiency affects the expression of pyrimidine metabolism genes. Biochem. Biophys. Res. Commun. 372 407-11 PubMed
  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. ↑ 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
  5. ↑ 5.0 5.1 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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