serC: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="R46a9bb60df0a1"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''serC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''serC''
Serine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0898, b0907, JW0890, pdxC, pdxF''<ref name='LIB:Riley_2006'/>, pdxF''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12373.R46a9bb60df0a1&page=12373&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0898, b0907, JW0890, pdxC, pdxF''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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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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MG1655
MG1655
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20.62 minutes&nbsp;
20.62 minutes&nbsp;
|
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MG1655: 956876..957964<br />{{GBrowseFigureByCoord|955876|958964|ecoli|MG1655}}
MG1655: 956876..957964<br /><gbrowseImage>
name=NC_000913:956876..957964
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10946 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10946 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:955876..958964 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|955876|958964|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:956876..957964&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|956876|957964|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10946 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10946 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 974745..975833<br /><gbrowseImage>
name=NC_012967:974745..975833
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|974745|975833|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|974745|975833|FASTA Dump}}
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[[BW2952]]
|
 
|
NC_012759: 859844..860932<br /><gbrowseImage>
name=NC_012759:859844..860932
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|859844|860932|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|859844|860932|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 958075..959163<br />{{GBrowseFigureByCoord|957075|960163|ecoli_W3110|W3110}}
W3110: 958075..959163<br /><gbrowseImage>
name=NC_007779:958075..959163
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:957075..960163 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|957075|960163|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:958075..959163&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|958075|959163|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 1010804..1011892<br /><gbrowseImage>
name=NC_010473:1010804..1011892
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1008628|1014068|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1008628|1014068|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
956879
|
Edman degradation
|
PMID:9298646<br />PMID:9740056<br />
|
 
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<protect><!--Sequence_notes--></protect>
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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="Z46a9bb624e319"  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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|
|
[[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=107194 CGSC8913]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107194 CGSC8913]<ref name='LIB:cgsc'/>  
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''serC13''
|
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[[cgscmutation:10177|CGSC:10177]]
|
|-
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''serC903''
|


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|
 
|
 
|
 
|
[[cgscmutation:23663|CGSC:23663]]
|
|-
|
''&#916;serC731::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102918|CGSC:102918]]
|
|-
|
pdxF5
|
 
|
 
|
Auxotrophies
|
Mutation in allele causes production of pyridoxine to halt and can be restored when supplemented with L-serine, Figure 1.
|
PMID:4321330
|
[http://cgsc.biology.yale.edu/Site.php?ID=171 pdxF]
|
Strain History: WG1
|-
|
SerC57
|
 
|
 
|
Auxotrophies
|
Mutation causes double requirement for pyridoxine and serine due to lack of 3-phosphoserine-2-oxoglutarate aminotransferase (POA), Figure 6.
|
PMID:4321330
|
 
|
Strain History: WG1145
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0890
JW0890
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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:CCACCGTGACGGCGTTCGAACTC  
Primer 2:CCACCGTGACGGCGTTCGAACTC  
|-
|-
|
[[:Category:Kohara_Phage:13E3|13E3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=216 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6D12|6D12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=217 Genobase]
|
PMID:3038334
|-  
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zca-1230::Tn10
zca-1230::Tn10
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CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 70% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 70% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zbj-1230::Tn10  
Synonyms:zbj-1230::Tn10  
|-
|-  
|
|
[[ycbS:Gene|zcb-3059::Tn10]]
[[ycbS:Gene|zcb-3059::Tn10]]
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|
|
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10946 EcoCyc:EG10946] 
EcoCyc:EG10946
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|
''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=EB0939 EchoBASE:EB0939] 
EcoGene:EG10946
|
|
''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=b0907 EcoliGenExpDB:b0907] 
RegulonDB:ECK120000935
|
|
''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=C1045 ECOL199310CYC:C1045]
[http://www.ncbi.nlm.nih.gov/gene?term=945527 GeneID:945527]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10946 EcoGene:EG10946] 
EchoBASE:EB0939
|
|
''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=SERC ECOO157CYC:SERC] 
ASAP:ABE-0003093
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12373.M46a9bb6382465&page=12373&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/171 CGSC:171] 
|
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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:ser genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

serC

Mnemonic

Serine

Synonyms

ECK0898, b0907, JW0890, pdxC, pdxF[1], pdxF

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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

20.62 minutes 

MG1655: 956876..957964
<gbrowseImage> name=NC_000913:956876..957964 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 974745..975833
<gbrowseImage> name=NC_012967:974745..975833 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 859844..860932
<gbrowseImage> name=NC_012759:859844..860932 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 958075..959163
<gbrowseImage> name=NC_007779:958075..959163 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1010804..1011892
<gbrowseImage> name=NC_010473:1010804..1011892 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

956879

Edman degradation

PMID:9298646[2]
PMID:9740056[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

ΔserC (Keio:JW0890)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC8913[5]

serC53

CGSC:9696

serC13

CGSC:10177

serC903

CGSC:23663

ΔserC731::kan

PMID:16738554[4]

CGSC:102918

pdxF5

Auxotrophies

Mutation in allele causes production of pyridoxine to halt and can be restored when supplemented with L-serine, Figure 1.

PMID:4321330[6]

pdxF

Strain History: WG1

SerC57

Auxotrophies

Mutation causes double requirement for pyridoxine and serine due to lack of 3-phosphoserine-2-oxoglutarate aminotransferase (POA), Figure 6.

PMID:4321330[6]

Strain History: WG1145

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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

JW0890

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGCTCAAATCTTCAATTTTAG

Primer 2:CCACCGTGACGGCGTTCGAACTC

13E3

Kohara Phage

Genobase

PMID:3038334[8]

6D12

Kohara Phage

Genobase

PMID:3038334[8]

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 70% [9]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 13% [9]

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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:EG10946

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10946

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000935

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945527

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0939

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003093

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. ↑ 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. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 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. ↑ 6.0 6.1 Dempsey, WB & Ito, H (1970) Characterization of pyridoxine auxotrophs of Escherichia coli: serine and pdxF mutants. J. Bacteriol. 104 658-67 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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