aspV:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

aspV

Gene Synonym(s)

ECK0216, b0216, JWR0007[1], JWR0007

Product Desc.


Product Synonyms(s)

tRNA-Asp(GUC) (Aspartate tRNA1)[1]

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): aspV[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png pubmed.jpg   textpresso.jpg  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

Standard name

aspV

Mnemonic

Aspartate

Synonyms

ECK0216, b0216, JWR0007[1], JWR0007

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<protect> 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

5.11 minutes 

MG1655: 236931..237007
<gbrowseImage> name=NC_000913:236931..237007 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 239855..239931
<gbrowseImage> name=NC_012967:239855..239931 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 236930..237006
<gbrowseImage> name=NC_012759:236930..237006 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 236931..237007
<gbrowseImage> name=NC_007779:236931..237007 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 211035..211111
<gbrowseImage> name=NC_010473:211035..211111 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

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

<protect></protect>

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

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</protect>

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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

7D5

Kohara Phage

Genobase

PMID:3038334

4A11

Kohara Phage

Genobase

PMID:3038334

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 85% [4]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[3]

est. P1 cotransduction: 43% [4]

<protect></protect>

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:EG30025

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002468

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947541

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4188

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000724

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

tRNA-Asp(GUC) (Aspartate tRNA1)

Synonyms

tRNA-Asp(GUC) (Aspartate tRNA1)[1]

Product description


EC number (for enzymes)


<protect></protect>

Notes

Function

[back to top]


<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

Interactions 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

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties

Type

tRNA

Sequence
GGAGCGGUAG UUCAGUCGGU UAGAAUACCU GCCUGUCACG CAGGGGGUCG CGGGUUCGAG
UCCCGUCCGU UCCGCCA
Mol. Wt

25019.83


Domains/Motifs/Modification Sites See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

<motif_map />

Image couresy of Rfam


Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=aspV taxon=562,83333 </beststructure>

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

<protect></protect>

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:EG30025

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002468

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4188

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000724

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

aspV

Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]


<protect><gbrowseImage> name=NC_000913:236911..236951 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0216 (EcoliWiki Page)

NCBI GEO profiles for aspV

microarray

GenExpDB:b0216 (EcoliWiki Page)

Summary of data for aspV from multiple microarray studies


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

<protect></protect>

Notes

Accessions Related to aspV Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG30025

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4188

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0216

EcoGene

EcoGene:EG30025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002468

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000724

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

</protect>


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


Database Accession Notes

PFAM (EcoliWiki Page)

PFAM:PF00929

edit table

<protect></protect>

Notes

Families

[back to top]


<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

</protect> <protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. 1.0 1.1 1.2 1.3 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. 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. 4.0 4.1 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

[back to top]