asnV: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''asnV''  
''asnV''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Asparagine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1984, b1989, JWR0041''<ref name='LIB:Riley_2006'/>, JWR0041''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14543.B46a9d38f3d550&page=14543&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1984, b1989, JWR0041''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<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="H46a9d38fb9708"  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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44.41 minutes&nbsp;
44.41 minutes&nbsp;
|
|
MG1655: 2060284..2060359<br />{{GBrowseFigureByCoord|2059284|2061359|ecoli|MG1655}}
MG1655: 2060284..2060359<br /><gbrowseImage>
name=NC_000913:2060284..2060359
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30022 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30022 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2059284..2061359 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2059284|2061359|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2060284..2060359&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2060284|2060359|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG30022 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG30022 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2000260..2000335<br /><gbrowseImage>
name=NC_012967:2000260..2000335
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2000260|2000335|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2000260|2000335|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1952767..1952842<br /><gbrowseImage>
name=NC_012759:1952767..1952842
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1952767|1952842|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1952767|1952842|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2064397..2064472<br />{{GBrowseFigureByCoord|2063397|2065472|ecoli_W3110|W3110}}  
W3110: 2064397..2064472<br /><gbrowseImage>
name=NC_007779:2064397..2064472
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2063397|2065472|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2063397..2065472 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|2064397|2064472|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2064397..2064472&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 2151292..2151367<br /><gbrowseImage>
name=NC_010473:2151292..2151367
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2151142|2151517|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2151142|2151517|FASTA Dump}}
 
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9d3906df31"  class=" tableEdit Gene_sequence_features_table" 
|- {{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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<protect><!--Sequence_notes--></protect>
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====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9d390b24d3"  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!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
&Delta;asnV (Keio:)
|
deletion
|
deletion
|
 
|


|
|- class="tableEdit_footer"
[[PMID:16738554]]<ref name=PMID:16738554/>
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14543.H46a9d390b24d3&page=14543&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14543.K4e04b7debe81a-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K4e04b7debe81a"  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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9d391665e3"  class=" tableEdit Gene_resource_table" 
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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:
Status:
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Primer 2:  
Primer 2:  
|-
|-
|
[[:Category:Kohara_Phage:7D4|7D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=346 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9B2|9B2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=347 Genobase]
|
PMID:3038334
|-  
|
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[[yedZ:Gene|zed-3069::Tn10]]
[[yedZ:Gene|zed-3069::Tn10]]
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|
|
est. P1 cotransduction: 42% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 42% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
|
zef-3129::Tn10
zef-3129::Tn10
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CAG12099 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39996 CGSC7397]<ref name='LIB:cgsc'/>
CAG12099 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39996 CGSC7397]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 43% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 43% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zee-3129::Tn10


Synonyms:zee-3129::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
|
EcoCyc:EG30022
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG30022 EcoCyc:EG30022] 
EcoGene:EG30022
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4185 EchoBASE:EB4185] 
RegulonDB:ECK120002465
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1989 EcoliGenExpDB:b1989]
[http://www.ncbi.nlm.nih.gov/gene?term=946509 GeneID:946509]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG30022 EcoGene:EG30022] 
EchoBASE:EB4185
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17743 CGSC:17743] 
ASAP:ABE-0006605
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:asn genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:40, 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

asnV

Mnemonic

Asparagine

Synonyms

ECK1984, b1989, JWR0041[1], JWR0041

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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

44.41 minutes 

MG1655: 2060284..2060359
<gbrowseImage> name=NC_000913:2060284..2060359 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2000260..2000335
<gbrowseImage> name=NC_012967:2000260..2000335 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1952767..1952842
<gbrowseImage> name=NC_012759:1952767..1952842 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2064397..2064472
<gbrowseImage> name=NC_007779:2064397..2064472 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2151292..2151367
<gbrowseImage> name=NC_010473:2151292..2151367 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
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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
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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

Plasmid clone

Shigen

PMID:16769691[2]

Status:

Primer 1:

Primer 2:

7D4

Kohara Phage

Genobase

PMID:3038334[3]

9B2

Kohara Phage

Genobase

PMID:3038334[3]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[4]

est. P1 cotransduction: 42% [5]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: 43% [5]
Synonyms:zee-3129::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:EG30022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30022

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002465

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946509

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4185

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006605

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. ↑ 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
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  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).

Categories

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