cspD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|cspD}}{{Tab On|Gene|cspD}}{{Tab|Gene Product(s)|cspD}}{{Tab|Expression|cspD}}{{Tab|Evolution|cspD}}{{Tab|On One Page|cspD}}{{TabsBottom}}
{{Tab|Quickview|cspD}}{{Tab On|Gene|cspD}}{{Tab|Gene Product(s)|cspD}}{{Tab|Expression|cspD}}{{Tab|Evolution|cspD}}{{Tab|On One Page|cspD}}{{TabsBottom}}
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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="B46a9bac61f9e0"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''cspD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''cspD''
Cold shock protein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0871, b0880, JW0864, ybjA''<ref name='LIB:Riley_2006'/>, cspH, ybjA''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12319.B46a9bac61f9e0&page=12319&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0871, b0880, JW0864, cspH, ybjA''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9bac6981b3"  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
|-
|-  
|
|
MG1655
MG1655
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19.86 minutes&nbsp;
19.86 minutes&nbsp;
|
|
MG1655: 921813..921589<br />{{GBrowseFigureByCoord|920589|922813|ecoli|MG1655}}
MG1655: 921813..921589<br /><gbrowseImage>
name=NC_000913:921589..921813
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11111 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11111 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:920589..922813 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|920589|922813|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:921589..921813&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|921589|921813|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11111 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11111 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 939296..939072<br /><gbrowseImage>
name=NC_012967:939072..939296
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|939072|939296|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|939072|939296|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 824557..824781<br /><gbrowseImage>
name=NC_012759:824557..824781
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|824557|824781|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|824557|824781|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 923012..922788<br />{{GBrowseFigureByCoord|921788|924012|ecoli_W3110|W3110}}  
W3110: 923012..922788<br /><gbrowseImage>
name=NC_007779:922788..923012
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|921788|924012|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|922788|923012|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:921788..924012 GBrowse(W3110)]
DH10B: 975741..975517<br /><gbrowseImage>
name=NC_010473:975517..975741
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:922788..923012&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|975069|976189|GBrowse(DH10B)}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a9bac74236b"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
921589
|
Edman degradation
|
PMID:9868784<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9bac782a93"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;cspD (Keio:JW0864)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107177 CGSC8896]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;cspD781::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100426|CGSC:100426]]
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12319.Y4e04b923031c1-->
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9bac82c491"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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|
 
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:1E5|1E5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=212 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1H1|1H1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=213 Genobase]
|
PMID:3038334
|-
|
zbh-29::Tn10
|
Linked marker
|
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10
|-
|
zca-1230::Tn10
|
Linked marker
|
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 39% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbj-1230::Tn10
 
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<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{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=EG11111 EcoCyc:EG11111] 
EcoCyc:EG11111
|
|
''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=EB1102 EchoBASE:EB1102] 
EcoGene:EG11111
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0880 EcoliGenExpDB:b0880] 
RegulonDB:ECK120001097
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1017 ECOL199310CYC:C1017]
[http://www.ncbi.nlm.nih.gov/gene?term=945669 GeneID:945669]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11111 EcoGene:EG11111]
[[EchoBASE]]
|
|
EchoBASE:EB1102
|-
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://BioCyc.org/ECOO157/new-image?object=CSPD ECOO157CYC:CSPD]
[[ASAP]]
|
|
ASAP:ABE-0002991
|-
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
 
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/31688 CGSC:31688] 
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{{Gene_accessions_help}}
 
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===Notes===
===Notes===
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==Links==
==Links==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:csp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 19 September 2013

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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

cspD

Mnemonic

Cold shock protein

Synonyms

ECK0871, b0880, JW0864, ybjA[1], cspH, ybjA

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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

19.86 minutes 

MG1655: 921813..921589
<gbrowseImage> name=NC_000913:921589..921813 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 939296..939072
<gbrowseImage> name=NC_012967:939072..939296 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 824557..824781
<gbrowseImage> name=NC_012759:824557..824781 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 923012..922788
<gbrowseImage> name=NC_007779:922788..923012 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 975741..975517
<gbrowseImage> name=NC_010473:975517..975741 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

921589

Edman degradation

PMID:9868784[2]


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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

ΔcspD (Keio:JW0864)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8896[4]

ΔcspD781::kan

PMID:16738554[3]

CGSC:100426


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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

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

1E5

Kohara Phage

Genobase

PMID:3038334[6]

1H1

Kohara Phage

Genobase

PMID:3038334[6]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[4]

est. P1 cotransduction: % [7]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: 39% [7]
Synonyms:zbj-1230::Tn10

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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:EG11111

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11111

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001097

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945669

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1102

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002991

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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. ↑ Wasinger, VC & Humphery-Smith, I (1998) Small genes/gene-products in Escherichia coli K-12. FEMS Microbiol. Lett. 169 375-82 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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