cspE: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

cspE

Gene Synonym(s)

ECK0616, b0623, JW0618, gicA, msmC[1], msmC

Product Desc.

cold shock protein CspE[2]; transcription antiterminator and regulator of RNA stability[3]

Binds and melts RNA, involved in cold acclimation; binds ssDNA; high copy protects the chromosome from decondensation by camphor and increases DNA supercoiling; dimeric[4]

Product Synonyms(s)

DNA-binding transcriptional repressor[1], B0623[2][1], MsmC[2][1], GicA[2][1], CspE[2][1] , ECK0616, gicA, JW0618, msmC, b0623

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): cspE[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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The cspABEG deletion BX04 is cold-sensitive and forms filaments at 15C (Xia, 2001). CspE is a cold shock protein homolog, but is constitutively expressed at 37C. CspE has transcription antitermination activity. CspE affects rpoS and uspA expression. CspE is a negative regulator of cspA transcription. CspE binds ssDNA containing six or more contiguous dT residues with high affinity (Johnston, 2006).[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

cspE

Mnemonic

Cold shock protein

Synonyms

ECK0616, b0623, JW0618, gicA, msmC[1], msmC

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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

14.15 minutes 

MG1655: 656515..656724
<gbrowseImage> name=NC_000913:656515..656724 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 639873..640082
<gbrowseImage> name=NC_012967:639873..640082 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 559275..559484
<gbrowseImage> name=NC_012759:559275..559484 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 657714..657923
<gbrowseImage> name=NC_007779:657714..657923 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 595847..596056
<gbrowseImage> name=NC_010473:595847..596056 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 709107..709316
<gbrowseImage> name=NC_010473:709107..709316 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

656518

Edman degradation

PMID:9735283


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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

ΔcspE (Keio:JW0618)

deletion

deletion

PMID:16738554

Shigen


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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

JW0618

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTAAGATTAAAGGTAACGT

Primer 2:CCCAGAGCGATTACGTTTGCAGC

1G6

Kohara Phage

Genobase

PMID:3038334

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[5]

est. P1 cotransduction: 93% [6]
Synonyms:zbe-280::Tn10

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[5]

est. P1 cotransduction: 14% [6]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

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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:EG12179

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12179

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002072

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947024

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2096

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002142

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

CspE

Synonyms

DNA-binding transcriptional repressor[1], B0623[2][1], MsmC[2][1], GicA[2][1], CspE[2][1] , ECK0616, gicA, JW0618, msmC, b0623

Product description

cold shock protein CspE[2]; transcription antiterminator and regulator of RNA stability[3]

Binds and melts RNA, involved in cold acclimation; binds ssDNA; high copy protects the chromosome from decondensation by camphor and increases DNA supercoiling; dimeric[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:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002059

P

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

PMID:10476034

IDA: Inferred from Direct Assay

F

Figure 2

complete

GO:0003697

single-stranded DNA binding

PMID:17088256

IDA: Inferred from Direct Assay

F

Figure 1

complete

GO:0001072

RNA binding transcription antitermination factor activity

PMID:10884409

IDA: Inferred from Direct Assay

F

Figure 1, data not shown to determine RNA interaction (HPLC size-exclusion chromatography, native PAGE, and Ni2+-nitrilotriacetic acid agarose coimmobilization assays)

complete

GO:0060567

negative regulation of transcription termination

PMID:10884409

IDA: Inferred from Direct Assay

P

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

dnaN

PMID:15690043

Experiment(s):EBI-879589

Protein

gabT

PMID:15690043

Experiment(s):EBI-879589

Protein

hflB

PMID:15690043

Experiment(s):EBI-879589

Protein

hrpA

PMID:15690043

Experiment(s):EBI-879589

Protein

pnp

PMID:15690043

Experiment(s):EBI-879589

Protein

rho

PMID:15690043

Experiment(s):EBI-879589

Protein

rplA

PMID:15690043

Experiment(s):EBI-879589, EBI-883848

Protein

rplB

PMID:15690043

Experiment(s):EBI-879589

Protein

rplC

PMID:15690043

Experiment(s):EBI-879589, EBI-883848

Protein

rpsA

PMID:15690043

Experiment(s):EBI-879589

Protein

rpsD

PMID:15690043

Experiment(s):EBI-879589

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879589, EBI-883848

Protein

secA

PMID:15690043

Experiment(s):EBI-879589

Protein

rnr

PMID:15690043

Experiment(s):EBI-879589

Protein

ycbY

PMID:15690043

Experiment(s):EBI-879589

Protein

rluB

PMID:15690043

Experiment(s):EBI-879589

Protein

dcuR

PMID:15690043

Experiment(s):EBI-879589

Protein

cspI

PMID:15690043

Experiment(s):EBI-883848

Protein

glmU

PMID:15690043

Experiment(s):EBI-883848

Protein

hfq

PMID:15690043

Experiment(s):EBI-883848

Protein

hupA

PMID:15690043

Experiment(s):EBI-883848

Protein

hyfG

PMID:15690043

Experiment(s):EBI-883848

Protein

rplD

PMID:15690043

Experiment(s):EBI-883848

Protein

rplS

PMID:15690043

Experiment(s):EBI-883848

Protein

rplX

PMID:15690043

Experiment(s):EBI-883848

Protein

rpsE

PMID:15690043

Experiment(s):EBI-883848

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-883848

Protein

rpsP

PMID:15690043

Experiment(s):EBI-883848

Protein

serS

PMID:15690043

Experiment(s):EBI-883848

Protein

rplB

PMID:16606699

Experiment(s):EBI-1137461

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1137461

Protein

rpoC

PMID:16606699

Experiment(s):EBI-1137461

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1137461

Protein

ogrK

PMID:16606699

Experiment(s):EBI-1137461

Protein

rplO

PMID:16606699

Experiment(s):EBI-1137461

Protein

rplD

PMID:16606699

Experiment(s):EBI-1137461

Protein

ygbA

PMID:16606699

Experiment(s):EBI-1137461

Protein

yafO

PMID:16606699

Experiment(s):EBI-1137461

Protein

rpoB

PMID:16606699

Experiment(s):EBI-1137461

Protein

hchA

PMID:16606699

Experiment(s):EBI-1137461

Protein

rplA

PMID:16606699

Experiment(s):EBI-1137461

Protein

uspG

PMID:16606699

Experiment(s):EBI-1137461

Protein

torA

PMID:16606699

Experiment(s):EBI-1137461

Protein

prs

PMID:16606699

Experiment(s):EBI-1137461

Protein

rplU

PMID:16606699

Experiment(s):EBI-1137461

Protein

ulaF

PMID:16606699

Experiment(s):EBI-1137461

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1137461

Protein

nrdI

PMID:16606699

Experiment(s):EBI-1137461

Protein

dnaN

PMID:19402753

MALDI(Z-score):38.397986

Protein

rho

PMID:19402753

MALDI(Z-score):38.327248

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):3.633502

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

clpA

PMID:19402753

MALDI(Z-score):21.714935

Protein

rpsA

PMID:19402753

MALDI(Z-score):26.544566

Protein

rplB

PMID:19402753

MALDI(Z-score):21.191895

Protein

rpsD

PMID:19402753

MALDI(Z-score):35.999379

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):24.553794

Protein

pnp

PMID:19402753

MALDI(Z-score):26.191468

Protein

hrpA

PMID:19402753

MALDI(Z-score):18.161567

Protein

glmU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rnr

PMID:19402753

MALDI(Z-score):25.704700

Protein

dcuR

PMID:19402753

MALDI(Z-score):17.053160

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):4.393096

Protein

cspI

PMID:19402753

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753

MALDI(Z-score):27.600158

Protein

hfq

PMID:19402753

LCMS(ID Probability):99.6

Protein

rluB

PMID:19402753

LCMS(ID Probability):90.0 MALDI(Z-score):33.056271

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Notes

selective RNA binding sequence

AAAUUU

PMID: 10476034

Figure 1

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 

MSKIKGNVKW FNESKGFGFI TPEDGSKDVF VHFSAIQTNG FKTLAEGQRV EFEITNGAKG
PSAANVIAL
Length

69

Mol. Wt

7.463 kDa

pI

9.6 (calculated)

Extinction coefficient

5,500 (calc based on 0 Y, 1 W, and 0 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

Initiator Methionine

1

Removed

UniProt:P0A972

Domain

3..69

PF00313 'Cold-shock' DNA-binding domain

PMID:19920124

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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=cspE 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:16128606

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002142

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A972

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12179

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12179

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947024

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002072

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2096

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 strain JC7623

30 uM

uM

  • Medium: M9 glucose
  • Temperature (°C): 37°C
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

Estimated from 2D-PAGE, data not shown.

PMID:10200963

Protein

E. coli K-12 MC4100

8.19E+03

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

Ecoli K-12

3057.05+/-24.364

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

1.8759+/-0.19292

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

5.224880383

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

186416

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

29309

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

56258

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)

cspE

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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_000913:656495..656535 source=MG1655 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:b0623 (EcoliWiki Page)

NCBI GEO profiles for cspE

microarray

GenExpDB:b0623 (EcoliWiki Page)

Summary of data for cspE 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 cspE Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12179

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2096

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0623

EcoGene

EcoGene:EG12179

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002072

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002142

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

  • ENSANGP00000011455 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000035713 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G36020 (score: 1.000; bootstrap: 100%)
  • AT4G38680 (score: 1.000; bootstrap: 100%)
  • AT2G21060 (score: 1.000; bootstrap: 100%)
  • AT2G17870 (score: 0.545)
  • AT5G46730 (score: 0.091)
  • AT2G30560 (score: 0.091)
  • AT4G01985 (score: 0.067)
  • AT2G05440 (score: 0.062)
  • AT2G21660 (score: 0.051)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000023094 (score: 1.000; bootstrap: 80%)
  • ENSBTAP00000012733 (score: 1.000; bootstrap: 80%)
  • ENSBTAP00000023101 (score: 0.327)
  • ENSBTAP00000032304 (score: 0.166)
  • ENSBTAP00000005429 (score: 0.145)
  • ENSBTAP00000016451 (score: 0.071)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00025935 (score: 1.000; bootstrap: 100%)
  • WBGene00032931 (score: 1.000; bootstrap: 100%)
  • WBGene00033626 (score: 1.000; bootstrap: 100%)
  • WBGene00035267 (score: 1.000; bootstrap: 100%)
  • WBGene00025320 (score: 1.000; bootstrap: 100%)
  • WBGene00037745 (score: 0.203)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00000474 (score: 1.000; bootstrap: 100%)
  • WBGene00000472 (score: 1.000; bootstrap: 100%)
  • WBGene00003014 (score: 1.000; bootstrap: 100%)
  • WBGene00000473 (score: 0.667)
  • WBGene00000475 (score: 0.165)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000014863 (score: 1.000; bootstrap: 78%)
  • ENSCAFP00000025464 (score: 1.000; bootstrap: 78%)
  • ENSCAFP00000019752 (score: 1.000; bootstrap: 79%)
  • ENSCAFP00000003704 (score: 1.000; bootstrap: 81%)
  • ENSCAFP00000001245 (score: 1.000; bootstrap: 78%)
  • ENSCAFP00000023761 (score: 0.321)
  • ENSCAFP00000024297 (score: 0.241)
  • ENSCAFP00000024295 (score: 0.237)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000012813 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-000629-3 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-592 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040516-5 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0035626 (score: 1.000; bootstrap: 63%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA14466-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000007728 (score: 1.000; bootstrap: 78%)
  • ENSGALP00000023766 (score: 0.148)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000350456 (score: 0.892)
  • ENSP00000228251 (score: 1.000; bootstrap: 77%)
  • ENSP00000163282 (score: 1.000; bootstrap: 78%)
  • ENSP00000347863 (score: 0.769)
  • ENSP00000331292 (score: 0.426)
  • ENSP00000007699 (score: 0.272)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000022751 (score: 0.705)
  • ENSMMUP00000029562 (score: 1.000; bootstrap: 78%)
  • ENSMMUP00000017257 (score: 1.000; bootstrap: 79%)
  • ENSMMUP00000029908 (score: 0.233)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000022758 (score: 0.366)
  • ENSMODP00000021480 (score: 1.000; bootstrap: 77%)
  • ENSMODP00000021948 (score: 0.294)

From Inparanoid:20070104

Mus musculus

  • MGI:2137670 (score: 1.000; bootstrap: 100%)
  • MGI:99146 (score: 1.000; bootstrap: 100%)
  • MGI:1096372 (score: 0.292)
  • MGI:1925802 (score: 0.289)

From Inparanoid:20070104

Oryza gramene

  • Q6YUR8 (score: 1.000; bootstrap: 94%)
  • Q75QN8 (score: 1.000; bootstrap: 84%)
  • Q8LPA7 (score: 0.904)
  • Q75QN9 (score: 0.694)
  • Q84UR8 (score: 0.521)
  • Q69UP6 (score: 0.121)
  • Q69T79 (score: 0.068)
  • Q6ZL79 (score: 0.057)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000044294 (score: 0.815)
  • ENSPTRP00000010950 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000008009 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000001059 (score: 1.000; bootstrap: 100%)
  • ENSPTRP00000014791 (score: 0.276)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000044956 (score: 0.853)
  • ENSRNOP00000048698 (score: 1.000; bootstrap: 78%)
  • ENSRNOP00000007427 (score: 1.000; bootstrap: 79%)
  • ENSRNOP00000045908 (score: 1.000; bootstrap: 81%)
  • ENSRNOP00000047897 (score: 0.664)
  • ENSRNOP00000023003 (score: 0.293)
  • ENSRNOP00000050512 (score: 0.283)
  • ENSRNOP00000047157 (score: 0.164)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000146056 (score: 1.000; bootstrap: 75%)
  • NEWSINFRUP00000158886 (score: 0.194)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022541001 (score: 1.000; bootstrap: 100%)
  • GSTENP00023133001 (score: 1.000; bootstrap: 100%)
  • GSTENP00018633001 (score: 0.211)
  • GSTENP00019221001 (score: 0.185)
  • GSTENP00038594001 (score: 0.095)
  • GSTENP00009564001 (score: 0.063)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000029443 (score: 1.000; bootstrap: 79%)
  • ENSXETP00000035457 (score: 0.276)

From Inparanoid:20070104

Shigella flexneri

CSPE

From SHIGELLACYC

E. coli O157

CSPE

From ECOO157CYC

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00313 'Cold-shock' DNA-binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:50249

EcoCyc

EcoCyc:EG12179

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12179

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002072

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2096

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002142

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 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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