ybcJ:On One Page

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

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Standard Name

ybcJ

Gene Synonym(s)

ECK0521, b0528, JW5070[1], JW5070

Product Desc.

putative RNA-binding protein[2]; predicted RNA-binding protein[3]

Ribosome-associated protein, function unknown; putative RNA binding protein[4]

Product Synonyms(s)

predicted RNA-binding protein[1], YbcJ[2][1], B0528[2][1] , ECK0521, JW5070, b0528

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybcJ[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Ribosome-associated protein (Jiang, 2007).[4]



Gene

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Nomenclature

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

Standard name

ybcJ

Mnemonic

Systematic nomenclature

Synonyms

ECK0521, b0528, JW5070[1], JW5070

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Notes

Location(s) and DNA Sequence

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<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

11.98 minutes 

MG1655: 556096..555884
<gbrowseImage> name=NC_000913:555884..556096 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 528981..528769
<gbrowseImage> name=NC_012967:528769..528981 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 458644..458856
<gbrowseImage> name=NC_012759:458644..458856 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 556096..555884
<gbrowseImage> name=NC_007779:555884..556096 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 495428..495216
<gbrowseImage> name=NC_010473:495216..495428 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
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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

ybcJ(del) (Keio:JW5070)

deletion

deletion

PMID:16738554

Shigen

CGSC11157[5]

ybcJ739(del)::kan

PMID:16738554

CGSC:103684


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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

JW5070

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGACATTTTCTTTAGGTAA

Primer 2:CCGGCAACAACCTGTACGCTGTG

6E7

Kohara Phage

Genobase

PMID:3038334

2C4

Kohara Phage

Genobase

PMID:3038334

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[5]

est. P1 cotransduction: 88% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[5]

est. P1 cotransduction: % [6]
Synonyms:zbd-601::Tn10, zbe-601::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:EG12879

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12879

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002418

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945158

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2717

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001816

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

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

Standard name

YbcJ

Synonyms

predicted RNA-binding protein[1], YbcJ[2][1], B0528[2][1] , ECK0521, JW5070, b0528

Product description

putative RNA-binding protein[2]; predicted RNA-binding protein[3]

Ribosome-associated protein, function unknown; putative RNA binding protein[4]

EC number (for enzymes)


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Notes

Function

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<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

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002942

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

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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

Protein

pnp

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

pssA

PMID:15690043

Experiment(s):EBI-878757

Protein

rhlB

PMID:15690043

Experiment(s):EBI-878757

Protein

rplA

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

rplC

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

rplI

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

rpoA

PMID:15690043

Experiment(s):EBI-878757

Protein

rpoC

PMID:15690043

Experiment(s):EBI-878757

Protein

rpsA

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

rpsB

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

rpsC

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

srmB

PMID:15690043

Experiment(s):EBI-878757

Protein

yajQ

PMID:15690043

Experiment(s):EBI-878757

Protein

ycbY

PMID:15690043

Experiment(s):EBI-878757

Protein

rluC

PMID:15690043

Experiment(s):EBI-878757, EBI-890236

Protein

rluB

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

yfiF

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

ygiF

PMID:15690043

Experiment(s):EBI-878757

Protein

yhiR

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

aceF

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

deaD

PMID:15690043

Experiment(s):EBI-878757

Protein

dnaJ

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

lpdA

PMID:15690043

Experiment(s):EBI-878757

Protein

aidB

PMID:15690043

Experiment(s):EBI-878757

Protein

rnr

PMID:15690043

Experiment(s):EBI-878757, EBI-881754

Protein

eno

PMID:15690043

Experiment(s):EBI-881754

Protein

hupA

PMID:15690043

Experiment(s):EBI-881754

Protein

hupB

PMID:15690043

Experiment(s):EBI-881754

Protein

rne

PMID:15690043

Experiment(s):EBI-881754

Protein

rplD

PMID:15690043

Experiment(s):EBI-881754

Protein

rplF

PMID:15690043

Experiment(s):EBI-881754

Protein

rplK

PMID:15690043

Experiment(s):EBI-881754

Protein

rplL

PMID:15690043

Experiment(s):EBI-881754

Protein

rplM

PMID:15690043

Experiment(s):EBI-881754

Protein

rplQ

PMID:15690043

Experiment(s):EBI-881754

Protein

rplR

PMID:15690043

Experiment(s):EBI-881754

Protein

rplS

PMID:15690043

Experiment(s):EBI-881754

Protein

rplT

PMID:15690043

Experiment(s):EBI-881754

Protein

rplU

PMID:15690043

Experiment(s):EBI-881754

Protein

rplV

PMID:15690043

Experiment(s):EBI-881754

Protein

rplX

PMID:15690043

Experiment(s):EBI-881754

Protein

rpmG

PMID:15690043

Experiment(s):EBI-881754

Protein

rpsE

PMID:15690043

Experiment(s):EBI-881754

Protein

rpsF

PMID:15690043

Experiment(s):EBI-881754

Protein

rpsI

PMID:15690043

Experiment(s):EBI-881754

Protein

yibL

PMID:15690043

Experiment(s):EBI-881754, EBI-887431

Protein

yihI

PMID:15690043

Experiment(s):EBI-881754

Protein

adhE

PMID:19402753

MALDI(Z-score):20.164404

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplK

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.474606

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.4

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.270072

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.385625

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

hybC

PMID:19402753

MALDI(Z-score):27.785239

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.146331

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

ihfA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.3 MALDI(Z-score):28.004333

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):15.842353

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):20.914227

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.2

Protein

rpoA

PMID:19402753

MALDI(Z-score):35.894115

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):33.954940

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):32.533390

Protein

prs

PMID:19402753

MALDI(Z-score):26.749891

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):8.510244

Protein

yihI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rlmL

PMID:19402753

MALDI(Z-score):27.059128

Protein

srmB

PMID:19402753

MALDI(Z-score):26.839928

Protein

aidB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.246624

Protein

ygiF

PMID:19402753

MALDI(Z-score):38.881696

Protein

hrpA

PMID:19402753

MALDI(Z-score):18.662063

Protein

pnp

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.259636

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.162485

Protein

yfiF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):36.415270

Protein

yhiR

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.708365

Protein

rne

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.497979

Protein

yibL

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.923336

Protein

pssA

PMID:19402753

MALDI(Z-score):25.268877

Protein

rhlB

PMID:19402753

MALDI(Z-score):37.343590

Protein

pcnB

PMID:19402753

MALDI(Z-score):29.263305

Protein

deaD

PMID:19402753

LCMS(ID Probability):81.3 MALDI(Z-score):27.822436

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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MIHRMSNMAT FSLGKHPHVE LCDLLKLEGW SESGAQAKIA IAEGQVKVDG AVETRKRCKI
VAGQTVSFAG HSVQVVA
Length

77

Mol. Wt

8.258 kDa

pI

8.7 (calculated)

Extinction coefficient

5,500 - 5,750 (calc based on 0 Y, 1 W, and 2 C residues)

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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
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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type Source Notes/Reference
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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

NCBI (Protein) (EcoliWiki Page)

GI:90111146

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945158

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001816

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AAS7

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12879

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12879

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945158

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002418

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2717

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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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

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See Help:Cellular levels

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

Protein

E. coli K-12 MC4100

6.13E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

3974

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1294

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1948

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

ybcJ

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Figure courtesy of RegulonDB

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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

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<protect><gbrowseImage> name=NC_000913:556076..556116 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0528 (EcoliWiki Page)

NCBI GEO profiles for ybcJ

microarray

GenExpDB:b0528 (EcoliWiki Page)

Summary of data for ybcJ from multiple microarray studies

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

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to ybcJ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12879

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2717

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0528

EcoGene

EcoGene:EG12879

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002418

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001816

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000000604 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YBCJ

From SHIGELLACYC

E. coli O157

YBCJ

From ECOO157CYC

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Notes

Families

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

Database Accession Notes
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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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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