trg:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Fixing Gbrowse links (bug #119)
touch
 
(5 intermediate revisions by 2 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1415, b1421, JW1417''<ref name='LIB:Riley_2006'/>
''ECK1415, b1421, JW1417''<ref name='LIB:Riley_2006'/>, JW1417''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="I46a9c6a43061e"  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="I46a9c6a43061e"  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
Line 128: Line 128:
|
|
W3110: 1494184..1495824<br /><gbrowseImage>
W3110: 1494184..1495824<br /><gbrowseImage>
name=AC_000091:1494184..1495824
name=NC_007779:1494184..1495824
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
Line 134: Line 134:


|
|
{{GBrowseLink|W3110|AC_000091|1493184|1496824|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1493184|1496824|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|W3110|AC_000091|1494184|1495824|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1494184|1495824|FASTA Dump}}  
|-  
|-  
|
|
Line 172: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="J46a9c6a4d3518"  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="J46a9c6a4d3518"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
Line 194: Line 194:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="M46a9c6a52184e"  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="M46a9c6a52184e"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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
Line 353: Line 353:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="L4e04c4df6595f"  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="L4e04c4df6595f"  class=" tableEdit Genetic_interaction_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
Line 374: Line 374:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="R46a9c6a5c43da"  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="R46a9c6a5c43da"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 392: Line 392:


Primer 2:CCaACCGTAGCGAAACTAACTGG  
Primer 2:CCaACCGTAGCGAAACTAACTGG  
|-
|
[[:Category:Kohara_Phage:24D6|24D6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=270 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1A6|1A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=271 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 430: Line 448:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="D46a9c6a65dbd0"  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="D46a9c6a65dbd0"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11018 EcoCyc:EG11018]
EcoCyc:EG11018
|
|
''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=EB1011 EchoBASE:EB1011]
EcoGene:EG11018
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1421 EcoliGenExpDB:b1421]
|
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11018 EcoGene:EG11018]
RegulonDB:ECK120001007
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=TRG ECOO157CYC:TRG]
[http://www.ncbi.nlm.nih.gov/gene?term=945995 GeneID:945995]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/85 CGSC:85]
EchoBASE:EB1011
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004744&formSubmitReturn=1 ASAP:ABE-0004744]
ASAP:ABE-0004744
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 501: Line 512:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="L46a6e4189331f"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a6e4189331f"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:29, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

trg

Mnemonic

Taxis to ribose and galactose

Synonyms

ECK1415, b1421, JW1417[1], JW1417

edit table


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

32.12 minutes 

MG1655: 1490494..1492134
<gbrowseImage> name=NC_000913:1490494..1492134 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1462579..1464219
<gbrowseImage> name=NC_012967:1462579..1464219 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1382553..1384193
<gbrowseImage> name=NC_012759:1382553..1384193 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1494184..1495824
<gbrowseImage> name=NC_007779:1494184..1495824 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1581089..1582729
<gbrowseImage> name=NC_010473:1581089..1582729 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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
edit table


Notes

Alleles and Phenotypes

[back to top]


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

Δtrg (Keio:JW1417)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9242[3]

trg::Tn5KAN-2 (FB20316)

Insertion at nt 509 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20316

contains pKD46

trg::Tn5KAN-2 (FB20317)

Insertion at nt 509 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20317

does not contain pKD46

trg-2::Tn10

Insertion at 1,491,930 bp in MG1655 (NC_000913)

adapted from Nichols et al.[5]

CAG12026 = CGSC7376[3]

Synonyms:

trg-1::Tn5

CGSC:9685

trg-2::Tn10

PMID:2540407[6]

CGSC:10754

trg-3120::Tn10kan

PMID:2540407[6]

CGSC:39820

Δtrg-782::kan

PMID:16738554[2]

CGSC:103208


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1417

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAATACAACTCCCTCACAGCG

Primer 2:CCaACCGTAGCGAAACTAACTGG

24D6

Kohara Phage

Genobase

PMID:3038334[8]

1A6

Kohara Phage

Genobase

PMID:3038334[8]

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 6% [5]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[3]

est. P1 cotransduction: 13% [5]
Synonyms:zdc-235::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11018

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11018

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001007

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945995

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1011

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004744

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ 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 3.3 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 5.0 5.1 5.2 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).
  6. ↑ 6.0 6.1 Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=trg:Gene&oldid=1476253"