hcaD: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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{|   id="P46a9e07cc19d9" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''hcaD''  
''hcaD''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Hydrocinnamic acid
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2539, b2542, JW2526, hcaA4, yfhY, phdA''<ref name='LIB:Riley_2006'/>
''ECK2539, b2542, JW2526, hcaA4, yfhY, phdA''<ref name='LIB:Riley_2006'/>, phdA''


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*  
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9e07d4c4cc"  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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57.55 minutes&nbsp;
57.55 minutes&nbsp;
|
|
MG1655: 2670069..2671271<br />{{GBrowseFigureByCoord|2670069|2671271|ecoli|MG1655}}
MG1655: 2670069..2671271<br /><gbrowseImage>
name=NC_000913:2670069..2671271
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7336 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7336 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2669069|2672271|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2669069|2672271|GBrowse(MG1655)}}
   
   
|
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{{GBrowseFastaLink|ecoli|NC_000913|2670069|2671271|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2670069|2671271|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7336 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7336 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 2592746..2593948<br /><gbrowseImage>
name=NC_012967:2592746..2593948
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|2592746|2593948|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2592746|2593948|FASTA Dump}}
|-
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[[BW2952]]
|
|
NC_012759: 2555874..2557076<br /><gbrowseImage>
name=NC_012759:2555874..2557076
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2555874|2557076|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2555874|2557076|FASTA Dump}}
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&nbsp;
&nbsp;
|
|
W3110: 2670703..2671905<br />{{GBrowseFigureByCoord|2670703|2671905|ecoli_W3110|W3110}}
W3110: 2670703..2671905<br /><gbrowseImage>
name=NC_007779:2670703..2671905
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2669703|2672905|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2669703|2672905|GBrowse(W3110)}}  
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2670703|2671905|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2670703|2671905|FASTA Dump}}  
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|
|
DH10B: 2761834..2763036<br />{{GBrowseFigureByCoord|2761834|2763036|ecoli_DH10B|DH10B}}
DH10B: 2761834..2763036<br /><gbrowseImage>
name=NC_010473:2761834..2763036
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|2759430|2765440|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|2759430|2765440|GBrowse(DH10B)}}
|
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2759430|2765440|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|2759430|2765440|FASTA Dump}}  


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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}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!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}}
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|- {{table_heading_style}}
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!|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
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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Primer 2:CCaAGTGATTTAAGCGCGATGTT  
Primer 2:CCaAGTGATTTAAGCGCGATGTT  
|-
|
[[:Category:Kohara_Phage:6F10|6F10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=431 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:8E12|8E12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=432 Genobase]
|
PMID:3038334
|-  
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est. P1 cotransduction: 19% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 19% <ref name='LIB:Nichols_linked_Tn'/>  


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|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7336 EcoCyc:G7336]
EcoCyc:G7336
|
|
''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=EB3233 EchoBASE:EB3233]
EcoGene:EG13460
|
|
''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=b2542 EcoliGenExpDB:b2542]
RegulonDB:ECK120003906
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[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=EG13460 EcoGene:EG13460]
[http://www.ncbi.nlm.nih.gov/gene?term=945427 GeneID:945427]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=HCAD ECOO157CYC:HCAD]
EchoBASE:EB3233
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0008363&formSubmitReturn=1 ASAP:ABE-0008363]
ASAP:ABE-0008363
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:hca genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:hca genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

hcaD

Mnemonic

Hydrocinnamic acid

Synonyms

ECK2539, b2542, JW2526, hcaA4, yfhY, phdA[1], phdA

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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

57.55 minutes 

MG1655: 2670069..2671271
<gbrowseImage> name=NC_000913:2670069..2671271 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2592746..2593948
<gbrowseImage> name=NC_012967:2592746..2593948 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2555874..2557076
<gbrowseImage> name=NC_012759:2555874..2557076 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2670703..2671905
<gbrowseImage> name=NC_007779:2670703..2671905 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2761834..2763036
<gbrowseImage> name=NC_010473:2761834..2763036 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
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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

ΔhcaD (Keio:JW2526)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10012[3]

ΔhcaD787::kan

PMID:16738554[2]

CGSC:101310


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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

JW2526

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAGAAAAAACGATCATTAT

Primer 2:CCaAGTGATTTAAGCGCGATGTT

6F10

Kohara Phage

Genobase

PMID:3038334[5]

8E12

Kohara Phage

Genobase

PMID:3038334[5]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[3]

est. P1 cotransduction: 79% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[3]

est. P1 cotransduction: 19% [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:G7336

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13460

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003906

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945427

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3233

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008363

Escherichia coli str. K-12 substr. MG1655

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  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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 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 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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