Cis Element:Phage lambda ori: Difference between revisions

Latest revision as of 08:40, 27 May 2013

Cis element summary table

Standard Name	Lambda ori
Synonyms
Function	Initiation control site for replication of the lambda genome
Location	within O gene
SO terms
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Notes

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: 39034..39137	Gbrowse (Bacteriophage lambda)	FASTA Dump
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Notes

The lambda ori has 4 repeated segments (commonly referred to as 'iterons') located at the following coordinates^[1]:

- ori1 - nt 39034 - 39051
- ori2 - nt 39054 - 39071
- ori3 - nt 39078 - 39095
- ori4 - nt 39101 - 39118

Below is the location of each of the ori iteron (underlined) in the lambda genomic sequence ^[1] :

Lambda  nt39034  ATCCCTCAAA ACGAGGGAAA ATCCCCTAAAA CGAGGGATAA AACATCCCTC AAATTGGGGG ATTGCT  39100
Lambda  nt39101  ATCCCTCAAA ACAGGGGGAC ACAAAAGACA CTATTACAAA AGAAAAAAGA AAA   39153

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
Protein	Phage lambda O protein		PMID:6264392^[2]	Purified O protein protects lambda DNA in the ori region from ExoIII nuclease digestion (FIgure 2) and DNase cleavage (Figure 4).
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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.

↑ ^1.0 ^1.1 Moore, DD et al. () Sequence organization of the origins of DNA replication in lambdoid coliphages. Gene 14 91-101 PubMed
↑ Tsurimoto, T & Matsubara, K (1981) Purified bacteriophage lambda O protein binds to four repeating sequences at the lambda replication origin. Nucleic Acids Res. 9 1789-99 PubMed

Cis Element:Phage lambda ori: 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

Categories

Navigation menu

@@ Line 1: / Line 1: @@
 __NOTOC__
 ==Cis element summary table==
-<newTableEdit>Template:Cis_element_summary_table</newTableEdit>
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.164822.J4a3fc721aea64-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->
+{|   id="J4a3fc721aea64"  class=" tableEdit Cis_element_summary_table"
+|-
+!align=left {{table_heading_style}} |Standard Name
+||
+''Lambda ori''
+|-
+!align=left {{table_heading_style}} |Synonyms
+||
+|-
+!align=left {{table_heading_style}} |Function
+||
+Initiation control site for replication of the lambda genome
+|-
+!align=left {{table_heading_style}} |Location
+||
+within ''O'' gene
+|-
+!align=left {{table_heading_style}} |SO terms
+||
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164822.J4a3fc721aea64&page=164822&pagename={{FULLPAGENAMEE}}&type=1&template=Cis_element_summary_table edit table]</span> ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.164822.J4a3fc721aea64--></protect>
 ===Notes===
 == Location and Sequence ==
 {{BacktoTop}}
-<newTableEdit>Template:Gene_location_table</newTableEdit>
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.164822.V4a3fc721c15f2-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->{{Gene_location_help}}
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V4a3fc721c15f2"  class=" tableEdit Gene_location_table"
+|- {{table_heading_style}}
+!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
+|-
+|
+Phage Lambda (NC_001416)
+|
+|
+NC_001416: 39034..39137<br />{{GBrowseFigureByCoord|39024|39147|bacteriophage_lambda|NC_001416}}
+|
+{{GBrowseLink|bacteriophage_lambda|NC_001416|39034|39137|Gbrowse (Bacteriophage lambda)}}
+|
+{{GBrowseFastaLink|bacteriophage_lambda|NC_001416|39034|39137|FASTA Dump}}
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164822.V4a3fc721c15f2&page=164822&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.164822.V4a3fc721c15f2--></protect>
 ===Notes===
+* The lambda ''ori'' has 4 repeated segments (commonly referred to as 'iterons') located at the following coordinates<ref name='PMID:6455332'/>:
+#* ori1 - nt 39034 - 39051
+#* ori2 - nt 39054 - 39071
+#* ori3 - nt 39078 - 39095
+#* ori4 - nt 39101 - 39118
+Below is the location of each of the ''ori'' iteron (underlined) in the lambda genomic sequence <ref name='PMID:6455332'/> :
+ <span style="font-size:larger;"><b>Lambda  nt39034  <u>ATCCCTCAAA ACGAGGGA</u>AA <u>ATCCCCTAAAA CGAGGGAT</u>AA AAC<u>ATCCCTC AAATTGGGGG ATTGCT</u>  39100
+ Lambda  nt39101  <u>ATCCCTCAAA ACAGGGGG</u>AC ACAAAAGACA CTATTACAAA AGAAAAAAGA AAA   39153 </b></span>
 == Interactions==
 {{BacktoTop}}
-<newTableEdit>Template:Product_interactions_table</newTableEdit>
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.164822.L4a3fc721c2884-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->{{Product_interactions_help}}
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L4a3fc721c2884"  class=" tableEdit Product_interactions_table dataTable"
+|- {{table heading style}}
+!|Partner Type!!Partner!!Notes!!References!!Evidence
+|-
+|
+Protein
+|
+Phage lambda O protein
+|
+|
+PMID:6264392
+|
+Purified O protein protects lambda DNA in the ''ori'' region from ExoIII nuclease digestion (FIgure 2) and DNase cleavage (Figure 4).
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164822.L4a3fc721c2884&page=164822&pagename={{FULLPAGENAMEE}}&type=0&template=Product_interactions_table edit table]</span> || || || ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.164822.L4a3fc721c2884--></protect>
 ===Notes===
@@ Line 18: / Line 111: @@
 == Mutant alleles and phenotypes ==
 {{BacktoTop}}
-<newTableEdit>Template:Cis_Element_allele_table</newTableEdit>
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.164822.D4a3fc721c8fb1-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D4a3fc721c8fb1"  class=" tableEdit Cis_Element_allele_table"
+|- {{table_heading_style}}
+!|Allele!!Nt change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164822.D4a3fc721c8fb1&page=164822&pagename={{FULLPAGENAMEE}}&type=0&template=Cis_Element_allele_table edit table]</span> || || || || || ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.164822.D4a3fc721c8fb1--></protect>
 ===Notes===
@@ Line 24: / Line 131: @@
 == Genetic Resources ==
 {{BacktoTop}}
-<newTableEdit>Template:Gene resource table </newTableEdit>
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.164822.N4a3fc721ca1fa-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->{{Gene_resources_help}}
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N4a3fc721ca1fa"  class=" tableEdit Gene_resource_table"
+|- {{table_heading_style}}
+!|Resource!!Resource Type!!Source!!Notes/Reference
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164822.N4a3fc721ca1fa&page=164822&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_resource_table edit table]</span> || || ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.164822.N4a3fc721ca1fa--></protect>
 ===Notes===
 == Accessions ==
 {{BacktoTop}}
-<newTableEdit>Template:Gene accessions table</newTableEdit>
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.164822.Q4a3fc721cb3b7-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->{{Gene_accessions_help}}
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q4a3fc721cb3b7"  class=" tableEdit Gene_accessions_table"
+|- {{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]]
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164822.Q4a3fc721cb3b7&page=164822&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.164822.Q4a3fc721cb3b7--></protect>
 ===Notes===
@@ Line 36: / Line 206: @@
 {{BacktoTop}}
 {{RefHelp}}
-<references/>
+<references />
 ===Categories===
+[[Category:Phage lambda:Cis_Element]]

Cis Element:Phage lambda ori: 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

Categories

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