carB: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}}
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{|   id="U46a9a6f6a3850" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''carB''  
''carB''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Carbamoyl P
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0034, b0033, JW0031, arg+ura, cap, pyrA''<ref name='LIB:Riley_2006'/>
''ECK0034, b0033, JW0031, arg+ura, cap, pyrA''<ref name='LIB:Riley_2006'/>, pyrA''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9a6f7282a8"  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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0.66 minutes&nbsp;
0.66 minutes&nbsp;
|
|
MG1655: 30817..34038<br />{{GBrowseFigureByCoord|29817|35038|ecoli|MG1655}}
MG1655: 30817..34038<br /><gbrowseImage>
name=NC_000913:30817..34038
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10135 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10135 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|29817|35038|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|29817|35038|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|30817|34038|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|30817|34038|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10135 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10135 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 34888..38109<br /><gbrowseImage>
name=NC_012967:34888..38109
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|34888|38109|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|34888|38109|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 30817..34038<br /><gbrowseImage>
name=NC_012759:30817..34038
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|30817|34038|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|30817|34038|FASTA Dump}}
|-  
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&nbsp;
&nbsp;
|
|
W3110: 30817..34038<br />{{GBrowseFigureByCoord|29817|35038|ecoli_W3110|W3110}}
W3110: 30817..34038<br /><gbrowseImage>
name=NC_007779:30817..34038
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|29817|35038|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|29817|35038|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|30817|34038|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|30817|34038|FASTA Dump}}  
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|
|
DH10B: 30817..34038<br />{{GBrowseFigureByCoord|24375|40480|ecoli_DH10B|DH10B}}
DH10B: 30817..34038<br /><gbrowseImage>
name=NC_010473:30817..34038
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|24375|40480|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|24375|40480|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|24375|40480|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|24375|40480|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;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
30820
|
Edman degradation
|
PMID:6308632<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="P46a9a6f80ff85"  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
|-  
|-  
|
|
&Delta;carB (Keio:JW0031)
''carB(del)'' (Keio:JW0031)
|
|
deletion
deletion
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PMID:16738554
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106630 CGSC8349]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106630 CGSC8349]<ref name='LIB:cgsc'/>  
|
|
   
   
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|-  
|-  
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''&#916;carB8''
''carB8(del)''
|
|


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''&#916;carB745::kan''
''carB745(del)::kan''
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10645.T4e04b8786c107-->
<!--
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTTGATCTGTGCGTGCATTTC  
Primer 2:CCTTTGATCTGTGCGTGCATTTC  
|-
|
[[:Category:Kohara_Phage:22B12|22B12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=103 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).  
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).  


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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=EG10135 EcoCyc:EG10135]
EcoCyc:EG10135
|
|
''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=EB0133 EchoBASE:EB0133]
EcoGene:EG10135
|
|
''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=b0033 EcoliGenExpDB:b0033]
RegulonDB:ECK120000131
|
|
''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=C0041 ECOL199310CYC:C0041]
[http://www.ncbi.nlm.nih.gov/gene?term=944775 GeneID:944775]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10135 EcoGene:EG10135]
EchoBASE:EB0133
|
|
''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=CARB ECOO157CYC:CARB]
|
|-
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
ASAP:ABE-0000121
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/935 CGSC:935]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000121&formSubmitReturn=1 ASAP:ABE-0000121]
|


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

Latest revision as of 20:36, 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

[back to top]


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

Standard name

carB

Mnemonic

Carbamoyl P

Synonyms

ECK0034, b0033, JW0031, arg+ura, cap, pyrA[1], pyrA

edit table


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

0.66 minutes 

MG1655: 30817..34038
<gbrowseImage> name=NC_000913:30817..34038 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 34888..38109
<gbrowseImage> name=NC_012967:34888..38109 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 30817..34038
<gbrowseImage> name=NC_012759:30817..34038 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 30817..34038
<gbrowseImage> name=NC_007779:30817..34038 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 30817..34038
<gbrowseImage> name=NC_010473:30817..34038 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


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

30820

Edman degradation

PMID:6308632[2]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

carB(del) (Keio:JW0031)

deletion

deletion

PMID:16738554[3]

Shigen

CGSC8349[4]

carB96::Tn10

Insertion at 33,963 bp in MG1655 (NC_000913)

adapted from Nichols et al.[5]

CAG12093 = CGSC7322[4]

Synonyms: car-96::Tn10

carB671

PMID:4373646[6]

CGSC:5037

carB8(del)

CGSC:6595

carB96::Tn10

CGSC:7106

carB3092::Tn10kan

CGSC:38009

carB745(del)::kan

PMID:16738554[3]

CGSC:100240


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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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Resource Resource Type Source Notes/Reference

JW0031

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCCAAAACGTACAGATATAAA

Primer 2:CCTTTGATCTGTGCGTGCATTTC

22B12

Kohara Phage

Genobase

PMID:3038334[8]

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 30% [5]
Synonyms:thr-34::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[4]

est. P1 cotransduction: 8% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:EG10135

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10135

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000131

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944775

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0133

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000121

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. ↑ Nyunoya, H & Lusty, CJ (1983) The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase. Proc. Natl. Acad. Sci. U.S.A. 80 4629-33 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 4.3 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 5.2 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).
  6. ↑ Mergeay, M et al. (1974) Physiology and genetics of carbamoylphosphate synthesis in Escherichia coli K12. Mol. Gen. Genet. 133 299-316 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. ↑ 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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