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 | |
Quickview
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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 | |
| Regulation/Activity | |
| Quick Links | |
| edit table |
See Help:Quickview for help with entering information in the Quickview table.
Notes
Ribosome-associated protein (Jiang, 2007).[4]
Gene
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Nomenclature
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 |
| edit table |
Notes
Location(s) and DNA Sequence
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 |
||
|
NC_012967: 528981..528769 |
||||
|
NC_012759: 458644..458856 |
||||
|
W3110 |
|
W3110: 556096..555884 |
||
|
DH10B: 495428..495216 |
||||
| edit table |
Notes
Sequence Features
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
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 |
||||
|
ybcJ739(del)::kan |
PMID:16738554 |
| |||||
| edit table |
Notes
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW5070 |
Plasmid clone |
PMID:16769691 Status:Clone OK Primer 1:GCCGCGACATTTTCTTTAGGTAA Primer 2:CCGGCAACAACCTGTACGCTGTG | |
|
Kohara Phage |
PMID:3038334 | ||
|
Kohara Phage |
PMID:3038334 | ||
|
Linked marker |
est. P1 cotransduction: 88% [6] | ||
|
Linked marker |
est. P1 cotransduction: % [6] | ||
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG12879 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG12879 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120002418 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EchoBASE:EB2717 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0001816 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
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) |
|
| edit table |
Notes
Function
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 |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| edit table |
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 |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
pssA |
Experiment(s):EBI-878757 | ||
|
Protein |
rhlB |
Experiment(s):EBI-878757 | ||
|
Protein |
rplA |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
rplC |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
rplI |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
rpoA |
Experiment(s):EBI-878757 | ||
|
Protein |
rpoC |
Experiment(s):EBI-878757 | ||
|
Protein |
rpsA |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
rpsB |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
rpsC |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
srmB |
Experiment(s):EBI-878757 | ||
|
Protein |
yajQ |
Experiment(s):EBI-878757 | ||
|
Protein |
ycbY |
Experiment(s):EBI-878757 | ||
|
Protein |
rluC |
Experiment(s):EBI-878757, EBI-890236 | ||
|
Protein |
rluB |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
yfiF |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
ygiF |
Experiment(s):EBI-878757 | ||
|
Protein |
yhiR |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
aceF |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
deaD |
Experiment(s):EBI-878757 | ||
|
Protein |
dnaJ |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
lpdA |
Experiment(s):EBI-878757 | ||
|
Protein |
aidB |
Experiment(s):EBI-878757 | ||
|
Protein |
rnr |
Experiment(s):EBI-878757, EBI-881754 | ||
|
Protein |
eno |
Experiment(s):EBI-881754 | ||
|
Protein |
hupA |
Experiment(s):EBI-881754 | ||
|
Protein |
hupB |
Experiment(s):EBI-881754 | ||
|
Protein |
rne |
Experiment(s):EBI-881754 | ||
|
Protein |
rplD |
Experiment(s):EBI-881754 | ||
|
Protein |
rplF |
Experiment(s):EBI-881754 | ||
|
Protein |
rplK |
Experiment(s):EBI-881754 | ||
|
Protein |
rplL |
Experiment(s):EBI-881754 | ||
|
Protein |
rplM |
Experiment(s):EBI-881754 | ||
|
Protein |
rplQ |
Experiment(s):EBI-881754 | ||
|
Protein |
rplR |
Experiment(s):EBI-881754 | ||
|
Protein |
rplS |
Experiment(s):EBI-881754 | ||
|
Protein |
rplT |
Experiment(s):EBI-881754 | ||
|
Protein |
rplU |
Experiment(s):EBI-881754 | ||
|
Protein |
rplV |
Experiment(s):EBI-881754 | ||
|
Protein |
rplX |
Experiment(s):EBI-881754 | ||
|
Protein |
rpmG |
Experiment(s):EBI-881754 | ||
|
Protein |
rpsE |
Experiment(s):EBI-881754 | ||
|
Protein |
rpsF |
Experiment(s):EBI-881754 | ||
|
Protein |
rpsI |
Experiment(s):EBI-881754 | ||
|
Protein |
yibL |
Experiment(s):EBI-881754, EBI-887431 | ||
|
Protein |
yihI |
Experiment(s):EBI-881754 | ||
|
Protein |
adhE |
MALDI(Z-score):20.164404 | ||
|
Protein |
rpmG |
LCMS(ID Probability):99.6 | ||
|
Protein |
eno |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplK |
LCMS(ID Probability):99.6 | ||
|
Protein |
dnaJ |
LCMS(ID Probability):99.6 MALDI(Z-score):28.474606 | ||
|
Protein |
hupB |
LCMS(ID Probability):99.4 | ||
|
Protein |
rpsA |
LCMS(ID Probability):99.6 MALDI(Z-score):28.270072 | ||
|
Protein |
rplP |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsF |
LCMS(ID Probability):99.6 | ||
|
Protein |
hupA |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsN |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplT |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpmB |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsT |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplI |
LCMS(ID Probability):99.6 MALDI(Z-score):30.385625 | ||
|
Protein |
rplR |
LCMS(ID Probability):99.6 | ||
|
Protein |
hybC |
MALDI(Z-score):27.785239 | ||
|
Protein |
rplS |
LCMS(ID Probability):99.6 MALDI(Z-score):2.146331 | ||
|
Protein |
rplU |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplX |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplM |
LCMS(ID Probability):99.6 | ||
|
Protein |
ihfA |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsD |
LCMS(ID Probability):99.3 MALDI(Z-score):28.004333 | ||
|
Protein |
rplF |
LCMS(ID Probability):99.6 MALDI(Z-score):15.842353 | ||
|
Protein |
rplB |
LCMS(ID Probability):99.6 MALDI(Z-score):20.914227 | ||
|
Protein |
rplQ |
LCMS(ID Probability):99.2 | ||
|
Protein |
rpoA |
MALDI(Z-score):35.894115 | ||
|
Protein |
rpsC |
LCMS(ID Probability):99.6 MALDI(Z-score):33.954940 | ||
|
Protein |
rplA |
LCMS(ID Probability):99.6 MALDI(Z-score):32.533390 | ||
|
Protein |
prs |
MALDI(Z-score):26.749891 | ||
|
Protein |
rplD |
LCMS(ID Probability):99.6 MALDI(Z-score):8.510244 | ||
|
Protein |
yihI |
LCMS(ID Probability):99.6 | ||
|
Protein |
rlmL |
MALDI(Z-score):27.059128 | ||
|
Protein |
srmB |
MALDI(Z-score):26.839928 | ||
|
Protein |
aidB |
LCMS(ID Probability):99.6 MALDI(Z-score):38.246624 | ||
|
Protein |
ygiF |
MALDI(Z-score):38.881696 | ||
|
Protein |
hrpA |
MALDI(Z-score):18.662063 | ||
|
Protein |
pnp |
LCMS(ID Probability):99.6 MALDI(Z-score):27.259636 | ||
|
Protein |
rnr |
LCMS(ID Probability):99.6 MALDI(Z-score):28.162485 | ||
|
Protein |
yfiF |
LCMS(ID Probability):99.6 MALDI(Z-score):36.415270 | ||
|
Protein |
yhiR |
LCMS(ID Probability):99.6 MALDI(Z-score):35.708365 | ||
|
Protein |
rne |
LCMS(ID Probability):99.6 MALDI(Z-score):13.497979 | ||
|
Protein |
yibL |
LCMS(ID Probability):99.6 MALDI(Z-score):13.923336 | ||
|
Protein |
pssA |
MALDI(Z-score):25.268877 | ||
|
Protein |
rhlB |
MALDI(Z-score):37.343590 | ||
|
Protein |
pcnB |
MALDI(Z-score):29.263305 | ||
|
Protein |
deaD |
LCMS(ID Probability):81.3 MALDI(Z-score):27.822436 | ||
| edit table |
Notes
Localization
See Help:Product_localization for how to add or edit information in this section of EcoliWiki.
| Compartment | Description | Evidence | Reference/Source | Notes |
|---|---|---|---|---|
| edit table |
Notes
Structure and Physical Properties
Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
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) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
|
Structure figures
Notes
Gene Product Resources
See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.
| Resource type | Source | Notes/Reference |
|---|---|---|
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
ASAP:ABE-0001816 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
EcoCyc:EG12879 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG12879 |
Escherichia coli str. K-12 substr. MG1655 | |
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
RegulonDB:ECK120002418 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB2717 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
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
| Molecule | Organism or Strain | Value | Units | Experimental Conditions | Assay used | Notes | Reference(s) |
|---|---|---|---|---|---|---|---|
|
Protein |
E. coli K-12 MC4100 |
6.13E+02 |
molecules/cell |
|
emPAI |
PMID:18304323 | |
|
Protein |
E. coli K-12 MG1655 |
3974 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
1294 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
|
Protein |
E. coli K-12 MG1655 |
1948 |
molecules/cell/generation |
|
Ribosome Profiling |
PMID: 24766808 | |
| edit table |
Notes
Transcription and Transcriptional Regulation
|
See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.
|
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
<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.
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
Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.
| Allele Name | Mutation | Phenotype | Reference |
|---|---|---|---|
| edit table |
Expression Studies
See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.
| Type | Reference | Notes |
|---|---|---|
|
microarray |
NCBI GEO profiles for ybcJ | |
|
microarray |
Summary of data for ybcJ from multiple microarray studies | |
| edit table |
Expression Resources
See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.
| Resource Name | Resource Type | Description | Source | Notes |
|---|---|---|---|---|
| edit table |
<protect>
Notes
Accessions Related to ybcJ Expression
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
EcoCyc:EG12879 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EchoBASE:EB2717 |
Escherichia coli str. K-12 substr. MG1655 | |
|
EcoGene:EG12879 |
Escherichia coli str. K-12 substr. MG1655 | |
|
RegulonDB:ECK120002418 |
Escherichia coli str. K-12 substr. MG1655 | |
|
ASAP:ABE-0001816 |
Escherichia coli str. K-12 substr. MG1655 | |
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
Evolution
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Homologs in Other Organisms
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.
| Organism | Homologs (Statistics) | Comments |
|---|---|---|
|
Anopheles gambiae |
|
From Inparanoid:20070104 |
|
Shigella flexneri |
YBCJ |
From SHIGELLACYC |
|
E. coli O157 |
YBCJ |
From ECOO157CYC |
| edit table |
Notes
Families
See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.
| Database | Accession | Notes |
|---|---|---|
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 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)
- ↑ 2.0 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
- ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ 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.
- ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
- ↑ 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).
- ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 7.19 7.20 7.21 7.22 7.23 7.24 7.25 7.26 7.27 7.28 7.29 7.30 7.31 7.32 7.33 7.34 7.35 7.36 7.37 7.38 7.39 7.40 7.41 7.42 7.43 7.44 7.45 7.46 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 8.29 8.30 8.31 8.32 8.33 8.34 8.35 8.36 8.37 8.38 8.39 8.40 8.41 8.42 8.43 8.44 8.45 8.46 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
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