asd:Gene: Difference between revisions

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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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{|{{Prettytable}}
{|  id="C46a9f5cda8c12"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''asd''  
''asd''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Aspartate semialdehyde deHase
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3419, b3433, JW3396, dap, hom, dap+hom''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3419, b3433, JW3396, dap, hom, dap+hom''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='145443'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9f5ce36321"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
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MG1655
MG1655
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76.98 minutes&nbsp;
76.98 minutes&nbsp;
|
|
MG1655: 3572901..3571798<br />{{GBrowseFigureByCoord|3570798|3573901|ecoli|MG1655}}
MG1655: 3572901..3571798<br /><gbrowseImage>
name=NC_000913:3571798..3572901
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10088 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10088 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3570798|3573901|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3570798|3573901|GBrowse(MG1655)}}
   
   
|
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{{GBrowseFastaLink|ecoli|NC_000913|3571798|3572901|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3571798|3572901|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10088 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10088 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 3506332..3505229<br /><gbrowseImage>
name=NC_012967:3505229..3506332
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3505229|3506332|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3505229|3506332|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3460292..3461395<br /><gbrowseImage>
name=NC_012759:3460292..3461395
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3460292|3461395|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3460292|3461395|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 4065537..4066640<br />{{GBrowseFigureByCoord|4064537|4067640|ecoli_W3110|W3110}}
W3110: 4065537..4066640<br /><gbrowseImage>
name=NC_007779:4065537..4066640
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|4064537|4067640|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4064537|4067640|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|4065537|4066640|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|4065537|4066640|FASTA Dump}}  
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[[DH10B]]
|
 
|
DH10B: 3670646..3669543<br /><gbrowseImage>
name=NC_010473:3669543..3670646
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3667337|3672852|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3667337|3672852|FASTA Dump}}
 
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
3571798
|
Edman degradation
|
PMID:9298646<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q46a9f5cf4079a"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!|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
|-
|
asdC135S
|
|
C135S
|
|
99.7% loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A9Q9 UniProt:P0A9Q9]
|-
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asdC135A
|
|
C135A
|
|
Complete loss of activity
|
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|
seeded from [http://www.uniprot.org/uniprot/P0A9Q9 UniProt:P0A9Q9]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17413.I4e04b7ce68542-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I4e04b7ce68542"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW3396
JW3396
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCgGCCAGTTGACGAAGCATCCG  
Primer 2:CCgGCCAGTTGACGAAGCATCCG  
|-
|-
|
[[:Category:Kohara_Phage:10F5|10F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=615 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:16A5|16A5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=616 Genobase]
|
PMID:3038334
|-  
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[[glgP:Gene|glgP721::Tn10]]
[[glgP:Gene|glgP721::Tn10]]
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CAG18638 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40317 CGSC7451]<ref name='LIB:cgsc'/>
CAG18638 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40317 CGSC7451]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 75% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 75% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zhg-3086::Tn10, zhh-21::Tn10  
Synonyms:zhg-3086::Tn10, zhh-21::Tn10  
|-
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zhg-50::Tn10
zhg-50::Tn10
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CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhf-50::Tn10, zhf-5::Tn10


Synonyms:zhf-50::Tn10, zhf-5::Tn10
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===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10088 EcoCyc:EG10088]
EcoCyc:EG10088
|
|
''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=EB0086 EchoBASE:EB0086]
EcoGene:EG10088
|
|
''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=b3433 EcoliGenExpDB:b3433]
RegulonDB:ECK120000084
|
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''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=C4220 ECOL199310CYC:C4220]
[http://www.ncbi.nlm.nih.gov/gene?term=947939 GeneID:947939]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10088 EcoGene:EG10088]
EchoBASE:EB0086
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=ASD ECOO157CYC:ASD]
|
|-
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/996 CGSC:996]
|
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011211&formSubmitReturn=1 ASAP:ABE-0011211] 
ASAP:ABE-0011211
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:asd genes]]
[[Category:asd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:47, 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

asd

Mnemonic

Aspartate semialdehyde deHase

Synonyms

ECK3419, b3433, JW3396, dap, hom, dap+hom[1][2]

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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

76.98 minutes 

MG1655: 3572901..3571798
<gbrowseImage> name=NC_000913:3571798..3572901 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3506332..3505229
<gbrowseImage> name=NC_012967:3505229..3506332 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3460292..3461395
<gbrowseImage> name=NC_012759:3460292..3461395 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4065537..4066640
<gbrowseImage> name=NC_007779:4065537..4066640 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3670646..3669543
<gbrowseImage> name=NC_010473:3669543..3670646 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

3571798

Edman degradation

PMID:9298646[3]


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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

asdC135S

C135S

99.7% loss of activity

seeded from UniProt:P0A9Q9

asdC135A

C135A

Complete loss of activity

seeded from UniProt:P0A9Q9

asd-1

CGSC:5115


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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

JW3396

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAAATGTTGGTTTTATCGG

Primer 2:CCgGCCAGTTGACGAAGCATCCG

10F5

Kohara Phage

Genobase

PMID:3038334[5]

16A5

Kohara Phage

Genobase

PMID:3038334[5]

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[6]

est. P1 cotransduction: 75% [7]
Synonyms:zhg-3086::Tn10, zhh-21::Tn10

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[6]

est. P1 cotransduction: 50% [7]
Synonyms:zhf-50::Tn10, zhf-5::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:EG10088

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10088

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000084

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947939

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0086

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011211

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. ↑ 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
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  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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