asnS: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="H46a9bbe744804" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''asnS''  
''asnS''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Asparagine
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0921, b0930, JW0913, lcs, tss''<ref name='LIB:Riley_2006'/>
''ECK0921, b0930, JW0913, lcs, tss''<ref name='LIB:Riley_2006'/>, tss''


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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="T46a9bbe7bcf20"  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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21.27 minutes&nbsp;
21.27 minutes&nbsp;
|
|
MG1655: 988208..986808<br />{{GBrowseFigureByCoord|985808|989208|ecoli|MG1655}}
MG1655: 988208..986808<br /><gbrowseImage>
name=NC_000913:986808..988208
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10094 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10094 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|985808|989208|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|985808|989208|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|986808|988208|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|986808|988208|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10094 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10094 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 1006076..1004676<br /><gbrowseImage>
name=NC_012967:1004676..1006076
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|1004676|1006076|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1004676|1006076|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 889776..891176<br /><gbrowseImage>
name=NC_012759:889776..891176
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|889776|891176|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|889776|891176|FASTA Dump}}
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
W3110: 989407..988007<br />{{GBrowseFigureByCoord|987007|990407|ecoli_W3110|W3110}}
W3110: 989407..988007<br /><gbrowseImage>
name=NC_007779:988007..989407
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|987007|990407|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|987007|990407|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|988007|989407|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|988007|989407|FASTA Dump}}  
|-  
|-  
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|
|
DH10B: 1042136..1040736<br />{{GBrowseFigureByCoord|1037936|1044936|ecoli_DH10B|DH10B}}
DH10B: 1042136..1040736<br /><gbrowseImage>
name=NC_010473:1040736..1042136
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1037936|1044936|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1037936|1044936|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1037936|1044936|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1037936|1044936|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="H46a9bbe86723b"  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]]
|
986811
|
Edman degradation
|
PMID:2693216<br />PMID:9298646<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="N46a9bbe8a7c4c"  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
|-
|
asnSP231L
|
|
P231L
|
Auxotrophies
|
(in temperature-sensitive mutant HO202)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P0A8M0 UniProt:P0A8M0]
|-
|
asnSY426F
|
|
Y426F
|
Auxotrophies
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A8M0 UniProt:P0A8M0]
|-
|
asnSY426S
|
|
Y426S
|
Auxotrophies
|
15-fold increase in Km for ATP
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A8M0 UniProt:P0A8M0]
|-  
|-  
|
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|
|
 
Auxotrophies
|
|
temperature sensitive
temperature sensitive
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12419.A4e04b7daee577-->
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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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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Primer 2:CCGAAGCTGGCGTTACGCGGAGT  
Primer 2:CCGAAGCTGGCGTTACGCGGAGT  
|-
|
[[:Category:Kohara_Phage:E1D1|E1D1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=218 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:11F5|11F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=219 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7F5|7F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=220 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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est. P1 cotransduction: 58% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 58% <ref name='LIB:Nichols_linked_Tn'/>  


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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;"   
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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=EG10094 EcoCyc:EG10094]
EcoCyc:EG10094
|
|
''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=EB0092 EchoBASE:EB0092]
EcoGene:EG10094
|
|
''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=b0930 EcoliGenExpDB:b0930]
RegulonDB:ECK120000090
|
|
''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=C1072 ECOL199310CYC:C1072]
[http://www.ncbi.nlm.nih.gov/gene?term=945555 GeneID:945555]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10094 EcoGene:EG10094]
EchoBASE:EB0092
|
|
''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=ASNS ECOO157CYC:ASNS]
ASAP:ABE-0003162
|
|
''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/993 CGSC:993]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0003162&formSubmitReturn=1 ASAP:ABE-0003162]
|


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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:asn genes]][[Category:Gene_List:DH10B]]
[[Category:asn genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 19 September 2013

{{#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

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

Standard name

asnS

Mnemonic

Asparagine

Synonyms

ECK0921, b0930, JW0913, lcs, tss[1], tss

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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

21.27 minutes 

MG1655: 988208..986808
<gbrowseImage> name=NC_000913:986808..988208 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1006076..1004676
<gbrowseImage> name=NC_012967:1004676..1006076 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 889776..891176
<gbrowseImage> name=NC_012759:889776..891176 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 989407..988007
<gbrowseImage> name=NC_007779:988007..989407 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1042136..1040736
<gbrowseImage> name=NC_010473:1040736..1042136 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

986811

Edman degradation

PMID:2693216[2]
PMID:9298646[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

asnSP231L

P231L

Auxotrophies

(in temperature-sensitive mutant HO202)

Strain variation; seeded from UniProt:P0A8M0

asnSY426F

Y426F

Auxotrophies

No effect

seeded from UniProt:P0A8M0

asnSY426S

Y426S

Auxotrophies

15-fold increase in Km for ATP

seeded from UniProt:P0A8M0

asnS40(ts)

Auxotrophies

temperature sensitive

CGSC:7220


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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

JW0913

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAGCGTTGTGCCTGTAGCCGA

Primer 2:CCGAAGCTGGCGTTACGCGGAGT

E1D1

Kohara Phage

Genobase

PMID:3038334[5]

11F5

Kohara Phage

Genobase

PMID:3038334[5]

7F5

Kohara Phage

Genobase

PMID:3038334[5]

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[6]

est. P1 cotransduction: 18% [7]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[6]

est. P1 cotransduction: 58% [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:EG10094

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10094

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000090

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945555

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0092

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003162

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. ↑ Anselme, J & Härtlein, M (1989) Asparaginyl-tRNA synthetase from Escherichia coli has significant sequence homologies with yeast aspartyl-tRNA synthetase. Gene 84 481-5 PubMed
  3. ↑ 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
  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 5.2 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  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).

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