arnA: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="A46a9d9b47bac0" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''arnA''  
''arnA''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
ara4N (4-amino-4-deoxy-L-arabinose)
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''yfbG, ECK2248, b2255, JW2249, pmrI, SAF''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''yfbG, ECK2248, b2255, JW2249, pmrI, SAF''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, pbgP3, SAF''


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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="B46a9d9b50533f"  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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51 minutes&nbsp;
51 minutes&nbsp;
|
|
MG1655: 2366061..2368043<br />{{GBrowseFigureByCoord|2365061|2369043|ecoli|MG1655}}
MG1655: 2366061..2368043<br /><gbrowseImage>
name=NC_000913:2366061..2368043
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7168 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7168 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2365061|2369043|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2365061|2369043|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2366061|2368043|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2366061|2368043|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7168 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7168 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 2314552..2316534<br /><gbrowseImage>
name=NC_012967:2314552..2316534
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|2314552|2316534|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2314552|2316534|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 2251866..2253848<br /><gbrowseImage>
name=NC_012759:2251866..2253848
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2251866|2253848|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2251866|2253848|FASTA Dump}}
|-  
|-  
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&nbsp;
&nbsp;
|
|
W3110: 2372709..2374691<br />{{GBrowseFigureByCoord|2371709|2375691|ecoli_W3110|W3110}}
W3110: 2372709..2374691<br /><gbrowseImage>
name=NC_007779:2372709..2374691
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2371709|2375691|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2371709|2375691|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2372709|2374691|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2372709|2374691|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 2457049..2459031<br /><gbrowseImage>
name=NC_010473:2457049..2459031
source=DH10B
preset=GeneLocation
</gbrowseImage>


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{{GBrowseLink|DH10B|NC_010473|2453085|2462995|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2453085|2462995|FASTA Dump}}
 
|- class="tableEdit_footer"
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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="C46a9d9b5afd06"  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]]
|
2366061
|
Edman degradation
|
PMID:11248028<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="S46a9d9b6008dc"  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
|-
|
arnAR619M
|
|
R619M
|
|
400-fold lower activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAR619E,Y
|
|
R619E,Y
|
|
No activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAE434Q
|
|
E434Q
|
|
No activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAS433T
|
|
S433T
|
|
No activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAE434A
|
|
E434A
|
|
100-fold lower specific activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAD140A,N
|
|
D140A,N
|
|
Less than 1% residual activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAS433A
|
|
S433A
|
|
40-fold lower specific activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAH104K
|
|
H104K
|
|
Less than 1% residual activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAN102A
|
|
N102A
|
|
No activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-
|
arnAH104A
|
|
H104A
|
|
25-fold lower activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P77398 UniProt:P77398]
|-  
|-  
|
|
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|
|


|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
|
|
[[cgscmutation:106130|CGSC:106130]]
[[cgscmutation:106130|CGSC:106130]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15071.F4e04b79f8c6b4-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F4e04b79f8c6b4"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.15071.F4e04b79f8c6b4&page=15071&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15071.F4e04b79f8c6b4--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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*  
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****************************************************************************************** -->{{Gene_resources_help}}
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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:
Status:
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Primer 2:  
Primer 2:  
|-
|
[[:Category:Kohara_Phage:4B4|4B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=379 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5H12|5H12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=380 Genobase]
|
PMID:3038334


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*  
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****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_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="Y46a9d9b74bb95"  class=" tableEdit Gene_accessions_table"   
|- {{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=G7168 EcoCyc:G7168]
EcoCyc:G7168
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3844 EchoBASE:EB3844]
|
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2255 EcoliGenExpDB:b2255]
EcoGene:EG14091
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2797 ECOL199310CYC:C2797]
RegulonDB:ECK120003744
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14091 EcoGene:EG14091]
[http://www.ncbi.nlm.nih.gov/gene?term=947683 GeneID:947683]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z3513 ECOO157CYC:Z3513]
EchoBASE:EB3844
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007460&formSubmitReturn=1 ASAP:ABE-0007460]
ASAP:ABE-0007460
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


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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 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:arn genes]]
[[Category:arn genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 19 September 2013

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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

arnA

Mnemonic

ara4N (4-amino-4-deoxy-L-arabinose)

Synonyms

yfbG, ECK2248, b2255, JW2249, pmrI, SAF[1][2], pbgP3, SAF

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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

51 minutes 

MG1655: 2366061..2368043
<gbrowseImage> name=NC_000913:2366061..2368043 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2314552..2316534
<gbrowseImage> name=NC_012967:2314552..2316534 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2251866..2253848
<gbrowseImage> name=NC_012759:2251866..2253848 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2372709..2374691
<gbrowseImage> name=NC_007779:2372709..2374691 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2457049..2459031
<gbrowseImage> name=NC_010473:2457049..2459031 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

2366061

Edman degradation

PMID:11248028[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

arnAR619M

R619M

400-fold lower activity

seeded from UniProt:P77398

arnAR619E,Y

R619E,Y

No activity

seeded from UniProt:P77398

arnAE434Q

E434Q

No activity

seeded from UniProt:P77398

arnAS433T

S433T

No activity

seeded from UniProt:P77398

arnAE434A

E434A

100-fold lower specific activity

seeded from UniProt:P77398

arnAD140A,N

D140A,N

Less than 1% residual activity

seeded from UniProt:P77398

arnAS433A

S433A

40-fold lower specific activity

seeded from UniProt:P77398

arnAH104K

H104K

Less than 1% residual activity

seeded from UniProt:P77398

arnAN102A

N102A

No activity

seeded from UniProt:P77398

arnAH104A

H104A

25-fold lower activity

seeded from UniProt:P77398

ΔarnA736::kan

PMID:16738554[4]

CGSC:106130


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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[5]

Status:

Primer 1:

Primer 2:

4B4

Kohara Phage

Genobase

PMID:3038334[6]

5H12

Kohara Phage

Genobase

PMID:3038334[6]

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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:G7168

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14091

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003744

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947683

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3844

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007460

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Karzai, AW & Sauer, RT (2001) Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex. Proc. Natl. Acad. Sci. U.S.A. 98 3040-4 PubMed
  4. ↑ 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. ↑ 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

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