Cis Element:Phage lambda attR: Difference between revisions

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
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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 (Bacteriophage lambda)	FASTA Dump
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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.

↑ 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===

[LIB:Lambda_II-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)

[1]

@@ Line 8: / Line 8: @@
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+{|   id="W4a4256cf8f6b1"  class=" tableEdit Cis_element_summary_table"
 |-
 !align=left {{table_heading_style}} |Standard Name
+||
+''lambda attR''
 |-
 !align=left {{table_heading_style}} |Synonyms
+||
 |-
 !align=left {{table_heading_style}} |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).
 |-
 !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
+||
-|-class='sortbottom'
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164844.W4a4256cf8f6b1&page=164844&pagename={{FULLPAGENAMEE}}&type=1&template=Cis_element_summary_table edit table]
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164844.W4a4256cf8f6b1&page=164844&pagename={{FULLPAGENAMEE}}&type=1&template=Cis_element_summary_table edit table]</span> ||
 |}
 <!--box uid=63ce1649aab8b3180235b0af7618f667.164844.W4a4256cf8f6b1--></protect>
 ===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 ==
@@ Line 36: / Line 49: @@
 *
 ****************************************************************************************** -->{{Gene_location_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}}
 !|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
+|-
+|
+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}}
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164844.J4a4256cfeaf7a&page=164844&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164844.J4a4256cfeaf7a&page=164844&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
 |}
 <!--box uid=63ce1649aab8b3180235b0af7618f667.164844.J4a4256cfeaf7a--></protect>
 ===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==
@@ Line 56: / Line 83: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
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 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
-|-class='sortbottom'
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 |- {{table_heading_style}}
 !|Allele!!Nt change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
-|-class='sortbottom'
+|- class="tableEdit_footer"
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 |- {{table_heading_style}}
 !|Resource!!Resource Type!!Source!!Notes/Reference
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 |}
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 ****************************************************************************************** -->{{Gene_accessions_help}}
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 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[RegulonDB]]
+|
+RegulonDB:
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EchoBASE]]
+|
+EchoBASE:
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[ASAP]]
+|
+ASAP:
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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+|- class="tableEdit_footer"
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 |}
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 {{BacktoTop}}
 {{RefHelp}}
-<references/>
+<references />
 ===Categories===[[Category:Phage lambda:Cis_Element]]

Cis Element:Phage lambda attR: Difference between revisions

Latest revision as of 08:40, 27 May 2013

Cis element summary table

Notes

Location and Sequence

Notes

Interactions

Notes

Mutant alleles and phenotypes

Notes

Genetic Resources

Notes

Accessions

Notes

References

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