Cis Element:Phage lambda attR: Difference between revisions

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__NOTOC__
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==Cis element summary table==
==Cis element summary table==
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|-
!align=left {{table_heading_style}} |Standard Name
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''lambda attR''
|-
!align=left {{table_heading_style}} |Synonyms
||
 
|-
!align=left {{table_heading_style}} |Function
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Right prophage ''att'' site; DNA sequence at right end of integrated prophage lambda genome that mediate synapsis and strand exchange along with ''attL'' site (left end of lambda genome).
|-
!align=left {{table_heading_style}} |Location
||
In the <b>linear</b> sequence of the lambda genome (NC_001416), the sequence position is: nt 27,571 - 27,742
 
The position in the ''E. coli'' genome: 
|-
!align=left {{table_heading_style}} |SO terms
||
 
 
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===Notes===
===Notes===
In the free phage, the ''att'' site is referred to as ''attP'' (<u>p</u>hage <u>att</u>achment site) while the corresponding site in a host genome is called ''attB'' (<u>b</u>acterial <u>att</u>achment site).  After integration occurs to create a prophage, these sites are then known as ''attL'' (<u>l</u>eft end of prophage) and ''attR'' (<u>r</u>ight end of prophage).  Reviewed in <u>Lambda II.</u><ref name=LIB:Lambda_II/>


== Location and Sequence ==
== Location and Sequence ==
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
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Phage lambda (NC_001416)
|
 
|
NC_001416: 27571..27742<br />{{GBrowseFigureByCoord|27521|27792|bacteriophage_lambda|NC_001416}}
 
|
{{GBrowseLink|bacteriophage_lambda|NC_001416|27571|27742|Gbrowse (Bacteriophage lambda)}}
|
{{GBrowseFastaLink|bacteriophage_lambda|NC_001416|27571|27742|FASTA Dump}}
 
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===Notes===
===Notes===
The sequence of [http://www.ncbi.nlm.nih.gov/nuccore/215191?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum attR] is:
<span style="font-size:larger;"><b>1 GCGCTAATGC TCTGTTACAG GTCACTAATA CCATCTAAGT AGTTGATTCA TAGTGACTGC ATATGTTGTG <br\>  TTTTACAGTA TTATGTAGTC TGTTTTTTAT GCAAAATCTA ATTTAATATA TTGATATTTA TATCATTTTA <br\>  CGTTTCTCGT TCAGCTTTTT TATACTAACT TG 172 </b></span>


== Interactions==
== Interactions==
{{BacktoTop}}
{{BacktoTop}}
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!|Partner Type!!Partner!!Notes!!References!!Evidence
 
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===Notes===
===Notes===
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== Mutant alleles and phenotypes ==
== Mutant alleles and phenotypes ==
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!|Allele!!Nt change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
 
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===Notes===
===Notes===
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== Genetic Resources ==
== Genetic Resources ==
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<newTableEdit>Template:Gene resource table </newTableEdit>  
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!|Resource!!Resource Type!!Source!!Notes/Reference
 
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===Notes===
===Notes===


== Accessions ==
== Accessions ==
{{BacktoTop}}
{{BacktoTop}}
<newTableEdit>Template:Gene accessions table</newTableEdit>
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!|Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
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EcoGene:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[RegulonDB]]
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RegulonDB:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[EchoBASE]]
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EchoBASE:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[ASAP]]
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ASAP:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 
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===Notes===
===Notes===
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{{RefHelp}}
{{RefHelp}}
<references/>
<references />


===Categories===
===Categories===[[Category:Phage lambda:Cis_Element]]

Latest revision as of 08:40, 27 May 2013

Cis element summary table

Standard Name

lambda attR

Synonyms
Function

Right prophage att site; DNA sequence at right end of integrated prophage lambda genome that mediate synapsis and strand exchange along with attL site (left end of lambda genome).

Location

In the linear sequence of the lambda genome (NC_001416), the sequence position is: nt 27,571 - 27,742

The position in the E. coli genome:

SO terms


edit table

Notes

In the free phage, the att site is referred to as attP (phage attachment site) while the corresponding site in a host genome is called attB (bacterial attachment site). After integration occurs to create a prophage, these sites are then known as attL (left end of prophage) and attR (right end of prophage). Reviewed in Lambda II.[1]

Location and 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

Phage lambda (NC_001416)

NC_001416: 27571..27742
gbrowse_img.php?coord=27521..27792&genome=bacteriophage_lambda&name=NC_001416&trackset=0&width=300&.png

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Notes

The sequence of attR is: 

1 GCGCTAATGC TCTGTTACAG GTCACTAATA CCATCTAAGT AGTTGATTCA TAGTGACTGC ATATGTTGTG <br\>  TTTTACAGTA TTATGTAGTC TGTTTTTTAT GCAAAATCTA ATTTAATATA TTGATATTTA TATCATTTTA <br\>  CGTTTCTCGT TCAGCTTTTT TATACTAACT TG 172

Interactions

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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence
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Notes

Mutant alleles and phenotypes

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Allele Nt change(s) Phenotype: Type Phenotype: Description Reference Availability Comments
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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
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Notes

Accessions

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

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Notes

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Edited by Roger W. Hendrix, Jeffrey W. Roberts, Franklin W. Stahl and Robert A. Weisberg (1983) Lambda II (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY)

===Categories===

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