typA: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="B46aa010fa1f8c"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''typA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''typA''
Tyrosine phosphoprotein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''bipA, ECK3864, b3871, JW5571, yihK''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, yihK''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18303.B46aa010fa1f8c&page=18303&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''bipA, ECK3864, b3871, JW5571, yihK''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18303.B46aa010fa1f8c&page=18303&pagename={{FULLPAGENAMEE}} edit table]
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='148115'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46aa011030c19"  class=" tableEdit Gene_location_table" 
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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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|
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MG1655
MG1655
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87.43 minutes&nbsp;
87.43 minutes&nbsp;
|
|
MG1655: 4056430..4058253<br />{{GBrowseFigureByCoord|4055430|4059253|ecoli|MG1655}}
MG1655: 4056430..4058253<br /><gbrowseImage>
name=NC_000913:4056430..4058253
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11837 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11837 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4055430..4059253 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4055430|4059253|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4056430..4058253&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4056430|4058253|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11837 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11837 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4036665..4038488<br /><gbrowseImage>
name=NC_012967:4036665..4038488
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4036665|4038488|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4036665|4038488|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3946099..3947922<br /><gbrowseImage>
name=NC_012759:3946099..3947922
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3946099|3947922|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3946099|3947922|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3578274..3576451<br />{{GBrowseFigureByCoord|3575451|3579274|ecoli_W3110|W3110}}
W3110: 3578274..3576451<br /><gbrowseImage>
name=NC_007779:3576451..3578274
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3575451..3579274 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3575451|3579274|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3576451..3578274&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3576451|3578274|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]]
|
4056430
|
Edman degradation
|
PMID:7783627<br />PMID:9298646<br />
|
 
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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="O46aa0111413cc"  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
|-
|
typAV497A
|
|
V497A
|
|
(in strain: MAR001)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P32132 UniProt:P32132]
|-
|
typAI489T
|
|
I489T
|
|
(in strain: MAR001)
|
|
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P32132 UniProt:P32132]
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100204|CGSC:100204]]
[[cgscmutation:100204|CGSC:100204]]
|
|
   
   
|-
|
∆bipA::kan
|
|
|
Growth Phenotype
|
MG1655 ∆bipA::kan doesn't form isolated colonies on LB medium at 20°C (plates were incubated for 4 days).  In liquid LB medium, the mutant grows more slowly than the bipA+ parent strain. 
|
PMID:11683274
|
|
The growth phenotypes were complemented by a plasmid clone of ''bipA''.


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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18303.P4e04c51632380-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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:  
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[[:Category:Kohara_Phage:9H1|9H1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=545 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10F1|10F1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=546 Genobase]
|
PMID:3038334
 
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===Notes===
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|- {{table_heading_style}}
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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=EG11837 EcoCyc:EG11837] 
EcoCyc:EG11837
|
|
''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=EB1783 EchoBASE:EB1783] 
EcoGene:EG11837
|
|
''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=b3871 EcoliGenExpDB:b3871] 
RegulonDB:ECK120001768
|
|
''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=C4820 ECOL199310CYC:C4820]
[http://www.ncbi.nlm.nih.gov/gene?term=948369 GeneID:948369]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11837 EcoGene:EG11837] 
EchoBASE:EB1783
|
|
''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=YIHK ECOO157CYC:YIHK] 
ASAP:ABE-0012648
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{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:typ genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 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

[back to top]


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

Standard name

typA

Mnemonic

Tyrosine phosphoprotein

Synonyms

bipA, ECK3864, b3871, JW5571, yihK[1][2], yihK

edit table


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

87.43 minutes 

MG1655: 4056430..4058253
<gbrowseImage> name=NC_000913:4056430..4058253 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4036665..4038488
<gbrowseImage> name=NC_012967:4036665..4038488 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3946099..3947922
<gbrowseImage> name=NC_012759:3946099..3947922 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3578274..3576451
<gbrowseImage> name=NC_007779:3576451..3578274 source=W3110 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

4056430

Edman degradation

PMID:7783627[3]
PMID:9298646[4]


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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

typAV497A

V497A

(in strain: MAR001)

Strain variation; seeded from UniProt:P32132

typAI489T

I489T

(in strain: MAR001)

Strain variation; seeded from UniProt:P32132

ΔbipA733::kan

PMID:16738554[5]

CGSC:100204

∆bipA::kan

Growth Phenotype

MG1655 ∆bipA::kan doesn't form isolated colonies on LB medium at 20°C (plates were incubated for 4 days). In liquid LB medium, the mutant grows more slowly than the bipA+ parent strain.

PMID:11683274[6]

The growth phenotypes were complemented by a plasmid clone of bipA.

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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[7]

Status:

Primer 1:

Primer 2:

9H1

Kohara Phage

Genobase

PMID:3038334[8]

10F1

Kohara Phage

Genobase

PMID:3038334[8]

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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:EG11837

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11837

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001768

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948369

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1783

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012648

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. ↑ Freestone, P et al. (1995) Identification of phosphoproteins in Escherichia coli. Mol. Microbiol. 15 573-80 PubMed
  4. ↑ 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
  5. ↑ 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
  6. ↑ Pfennig, PL & Flower, AM (2001) BipA is required for growth of Escherichia coi K12 at low temperature. Mol. Genet. Genomics 266 313-7 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

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