panD: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="Y46a9a9207231e"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''panD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''panD''
Pantothenate
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0130, b0131, JW0127''<ref name='LIB:Riley_2006'/>, JW0127''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10837.Y46a9a9207231e&page=10837&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0130, b0131, JW0127''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125709'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9a920eaddc"  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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3.15 minutes&nbsp;
3.15 minutes&nbsp;
|
|
MG1655: 146694..146314<br />{{GBrowseFigureByCoord|145314|147694|ecoli|MG1655}}
MG1655: 146694..146314<br /><gbrowseImage>
name=NC_000913:146314..146694
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11747 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11747 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:145314..147694 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|145314|147694|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:146314..146694&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|146314|146694|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11747 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11747 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 149497..149117<br /><gbrowseImage>
name=NC_012967:149117..149497
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|149117|149497|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|149117|149497|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 146313..146693<br /><gbrowseImage>
name=NC_012759:146313..146693
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|146313|146693|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|146313|146693|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 146694..146314<br />{{GBrowseFigureByCoord|145314|147694|ecoli_W3110|W3110}}
W3110: 146694..146314<br /><gbrowseImage>
name=NC_007779:146314..146694
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:145314..147694 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|145314|147694|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:146314..146694&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|146314|146694|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 120798..120418<br /><gbrowseImage>
name=NC_010473:120418..120798
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|119658|121558|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|119658|121558|FASTA Dump}}
 
|- class="tableEdit_footer"
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<!--Location_notes--></protect>
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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
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
146314
|
Edman degradation
|
PMID:9169598<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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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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&Delta;panD (Keio:JW0127)
''panD(del)'' (Keio:JW0127)
|
|
deletion
deletion
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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]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106685 CGSC8404]<ref name='LIB:cgsc'/>  
|
|-
|
''panD1''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:6017|CGSC:6017]]
|
|-
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''panD2''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:6021|CGSC:6021]]
|
|-
|
''panD3''
|
 
|
 
|
 
|
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
|
[[cgscmutation:6023|CGSC:6023]]
|
|
   
   
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''panD748(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102250|CGSC:102250]]
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10837.M4e04c0bd9854a-->
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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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JW0127
JW0127
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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:CCAGCAACCTGTACCGGAATCGC  
Primer 2:CCAGCAACCTGTACCGGAATCGC  
|-
|-
|
[[:Category:Kohara_Phage:17C11|17C11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=114 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:11C5|11C5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=115 Genobase]
|
PMID:3038334
|-  
|
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leuO3051::Tn10
leuO3051::Tn10
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CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
CAG12095 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37901 CGSC7324]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).  
Synonyms:zab-3051::Tn10  
|-  
 
 
The start of leuO was reannotated by Riley et al. (2006).  
|-
|
|
[[yadC:Gene|zad-220::Tn10]]
[[yadC:Gene|zad-220::Tn10]]
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|
|
est. P1 cotransduction: 93% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 93% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===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=EG11747 EcoCyc:EG11747] 
EcoCyc:EG11747
|
|
''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=EB1697 EchoBASE:EB1697] 
EcoGene:EG11747
|
|
''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=b0131 EcoliGenExpDB:b0131] 
RegulonDB:ECK120001685
|
|
''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=C0160 ECOL199310CYC:C0160]
[http://www.ncbi.nlm.nih.gov/gene?term=945686 GeneID:945686]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11747 EcoGene:EG11747] 
EchoBASE:EB1697
|
|
''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=PAND ECOO157CYC:PAND] 
ASAP:ABE-0000459
|
|
''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=421aa90e079fa326b6494f812ad13e79.10837.U46a9a92312615&page=10837&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/425 CGSC:425]
|
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===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:pan genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:37, 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

panD

Mnemonic

Pantothenate

Synonyms

ECK0130, b0131, JW0127[1], JW0127

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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

3.15 minutes 

MG1655: 146694..146314
<gbrowseImage> name=NC_000913:146314..146694 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 149497..149117
<gbrowseImage> name=NC_012967:149117..149497 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 146313..146693
<gbrowseImage> name=NC_012759:146313..146693 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 146694..146314
<gbrowseImage> name=NC_007779:146314..146694 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 120798..120418
<gbrowseImage> name=NC_010473:120418..120798 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

146314

Edman degradation

PMID:9169598[2]


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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

panD(del) (Keio:JW0127)

deletion

deletion

PMID:16738554[3]

Shigen

CGSC8404[4]

panD1

CGSC:6017

panD2

CGSC:6021

panD3

CGSC:6023

panD748(del)::kan

PMID:16738554[3]

CGSC:102250


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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

JW0127

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCATTCGCACGATGCTGCAGGG

Primer 2:CCAGCAACCTGTACCGGAATCGC

17C11

Kohara Phage

Genobase

PMID:3038334[6]

11C5

Kohara Phage

Genobase

PMID:3038334[6]

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 3% [7]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[4]

est. P1 cotransduction: 93% [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:EG11747

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11747

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001685

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945686

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1697

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000459

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. ↑ Ramjee, MK et al. (1997) Escherichia coli L-aspartate-alpha-decarboxylase: preprotein processing and observation of reaction intermediates by electrospray mass spectrometry. Biochem. J. 323 ( Pt 3) 661-9 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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. ↑ 6.0 6.1 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
  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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