hupA:Gene: Difference between revisions

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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="A46aa046793cce"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46aa046793cce"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
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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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10466 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10466 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4197304|4199576|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4197304|4199576|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|4198304|4198576|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4198304|4198576|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10466 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10466 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|4087984|NC_4088256|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|4087984|NC_4088256|FASTA Dump}}  
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W3110: 3436400..3436128<br /><gbrowseImage>
W3110: 3436400..3436128<br /><gbrowseImage>
name=AC_000091:3436128..3436400
name=NC_007779:3436128..3436400
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3435128|3437400|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3435128|3437400|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3436128|3436400|FASTA Dump}}  
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DH10B: 4298000..4298272<br /><gbrowseImage>
DH10B: 4298000..4298272<br /><gbrowseImage>
name=NC_010473:4298000..4298272
name=NC_010473:4298000..4298272
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|4297456|4298816|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4297456|4298816|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4297456|4298816|FASTA Dump}}  
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{|   id="D46aa04685a772"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46aa04685a772"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="E46aa0468a5644"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="E46aa0468a5644"  class=" tableEdit Gene_allele_table dataTable"   
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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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{|   id="J4e04bd5020656"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04bd5020656"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="G46aa04696ec90"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa04696ec90"  class=" tableEdit Gene_resource_table"   
|- {{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:CCtTTAACTGCGTCTTTCAGTGC  
Primer 2:CCtTTAACTGCGTCTTTCAGTGC  
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[[:Category:Kohara_Phage:7B7|7B7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=533 Genobase]
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PMID:3038334
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{|   id="Z46aa046a1c400"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aa046a1c400"  class=" tableEdit Gene_accessions_table"   
|- {{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]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10466 EcoCyc:EG10466]
EcoCyc:EG10466
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0461 EchoBASE:EB0461]
EcoGene:EG10466
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b4000 EcoliGenExpDB:b4000]
RegulonDB:ECK120000459
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C4957 ECOL199310CYC:C4957]
[http://www.ncbi.nlm.nih.gov/gene?term=948499 GeneID:948499]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10466 EcoGene:EG10466]
EchoBASE:EB0461
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=HUPA ECOO157CYC:HUPA]
ASAP:ABE-0013077
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/34243 CGSC:34243]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013077&formSubmitReturn=1 ASAP:ABE-0013077]
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{|   id="W46a71dcc1be68"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a71dcc1be68"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
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Latest revision as of 20:50, 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

hupA

Mnemonic

HU protein

Synonyms

ECK3992, b4000, JW3964, G119, hydL[1][2]

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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

90.49 minutes 

MG1655: 4198304..4198576
<gbrowseImage> name=NC_000913:4198304..4198576 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4179893..4180165
<gbrowseImage> name=NC_012967:4179893..4180165 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4087984..4088256
<gbrowseImage> name=NC_012759:4087984..4088256 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3436400..3436128
<gbrowseImage> name=NC_007779:3436128..3436400 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4298000..4298272
<gbrowseImage> name=NC_010473:4298000..4298272 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

4198304

Edman degradation

PMID:350619[3]
PMID:6987059[4]
PMID:9298646[5]


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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

ΔhupA (Keio:JW3964)

deletion

deletion

PMID:16738554[6]

Shigen
CGSC10851[7]

ΔhupA771::kan

PMID:16738554[6]

CGSC:101440


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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

JW3964

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAACAAGACTCAACTGATTGA

Primer 2:CCtTTAACTGCGTCTTTCAGTGC

7B7

Kohara Phage

Genobase

PMID:3038334[9]

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[7]

est. P1 cotransduction: 88% [10]
Synonyms:thi-39::Tn10

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[7]

est. P1 cotransduction: 16% [10]

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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:EG10466

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10466

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000459

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948499

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0461

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013077

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ Laine, B et al. (1978) The amino- and carboxy-terminal amino acid sequences of protein HU from Escherichia coli. FEBS Lett. 89 116-20 PubMed
  4. ↑ Laine, B et al. (1980) Complete amino-acid sequences of DNA-binding proteins HU-1 and HU-2 from Escherichia coli. Eur. J. Biochem. 103 447-61 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 7.2 CGSC: The Coli Genetics Stock Center
  8. ↑ 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
  9. ↑ 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
  10. ↑ 10.0 10.1 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).

Categories

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