cspC: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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<protect>

Standard Name

cspC

Gene Synonym(s)

ECK1821, b1823, JW1812, msmB[1], msmB

Product Desc.

stress protein, member of the CspA family[2]; stress protein, member of the CspA family; predicted DNA-binding transcriptional regulator[3]

Multicopy suppressor of mukB; cold shock protein homolog constitutively expressed at 37C; affects rpoS and uspA expression[4]

Product Synonyms(s)

stress protein, member of the CspA-family[1], B1823[2][1], MsmB[2][1], CspC[2][1] , ECK1821, JW1812, msmB, b1823

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): cspC[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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

Notes

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HT_Cmplx32_Mem: CspC+Hns+HupA.[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

cspC

Mnemonic

Cold shock protein

Synonyms

ECK1821, b1823, JW1812, msmB[1], msmB

</protect>

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

41.06 minutes, 41.06 minutes 

MG1655: 1905459..1905250
<gbrowseImage> name=NC_000913:1905250..1905459 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1886014..1885805
<gbrowseImage> name=NC_012967:1885805..1886014 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1797309..1797518
<gbrowseImage> name=NC_012759:1797309..1797518 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1909149..1908940
<gbrowseImage> name=NC_007779:1908940..1909149 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1996030..1995821
<gbrowseImage> name=NC_010473:1995821..1996030 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

1905253

Edman degradation

PMID:8740179
PMID:9298646
PMID:9868784


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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

cspC(del) (Keio:JW1812)

deletion

deletion

PMID:16738554

Shigen

CGSC9515[5]

cspC747(del)::kan

PMID:16738554

CGSC:100424

cspC747(del)::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554

Parental Strain: SMR4562

Experimental Strain: SMR12148

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

SMR4562 yiaG-yfp FRTcatFRT cspC747(del)::FRTKanFRT

deletion

Sigma S activity

Decrease in SigmaS activity

PMID:23224554

Parental Strain: SMR10582 Experimental Strain: SMR14263

See table S8 for full experimental data.

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Notes

Genetic Interactions

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<protect>

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

JW1812

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCAAAGATTAAAGGTCAGGT

Primer 2:CCGATAGCTGTTACGTTAACAGC

15D5

Kohara Phage

Genobase

PMID:3038334

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[5]

est. P1 cotransduction: 24% [6]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[5]

est. P1 cotransduction: 39% [6]

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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:EG12204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002092

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946339

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2120

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006070

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

CspC

Synonyms

stress protein, member of the CspA-family[1], B1823[2][1], MsmB[2][1], CspC[2][1] , ECK1821, JW1812, msmB, b1823

Product description

stress protein, member of the CspA family[2]; stress protein, member of the CspA family; predicted DNA-binding transcriptional regulator[3]

Multicopy suppressor of mukB; cold shock protein homolog constitutively expressed at 37C; affects rpoS and uspA expression[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:0001072

RNA binding transcription antitermination factor activity

PMID:10884409

IDA: Inferred from Direct Assay

F

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011129

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012156

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002059

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

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:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0060567

negative regulation of transcription termination

PMID:10884409

IDA: Inferred from Direct Assay

P

complete

GO:0003723

RNA binding

PMID:10476034

IDA: Inferred from Direct Assay

F

Figure 2

complete

GO:0003697

single-stranded DNA binding

PMID:10476034

IDA: Inferred from Direct Assay

F

Figure 4

complete

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

accA

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

aidB

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

deaD

PMID:15690043

Experiment(s):EBI-879643, EBI-881486, EBI-883980

Protein

hrpA

PMID:15690043

Experiment(s):EBI-879643

Protein

pnp

PMID:15690043

Experiment(s):EBI-879643

Protein

rho

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rplA

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rplB

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rplC

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rplE

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rplM

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rpsA

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rpsB

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rpsD

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rpsE

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rpsM

PMID:15690043

Experiment(s):EBI-879643

Protein

rnr

PMID:15690043

Experiment(s):EBI-879643

Protein

ycbY

PMID:15690043

Experiment(s):EBI-879643

Protein

rluC

PMID:15690043

Experiment(s):EBI-879643

Protein

rluB

PMID:15690043

Experiment(s):EBI-879643

Protein

yfiF

PMID:15690043

Experiment(s):EBI-879643

Protein

yhiR

PMID:15690043

Experiment(s):EBI-879643, EBI-883980

Protein

rplD

PMID:15690043

Experiment(s):EBI-883980

Protein

rplI

PMID:15690043

Experiment(s):EBI-883980

Protein

rplR

PMID:15690043

Experiment(s):EBI-883980

Protein

rplS

PMID:15690043

Experiment(s):EBI-883980

Protein

rplU

PMID:15690043

Experiment(s):EBI-883980

Protein

rplV

PMID:15690043

Experiment(s):EBI-883980

Protein

rplW

PMID:15690043

Experiment(s):EBI-883980

Protein

rplX

PMID:15690043

Experiment(s):EBI-883980

Protein

rpsC

PMID:15690043

Experiment(s):EBI-883980

Protein

rpsF

PMID:15690043

Experiment(s):EBI-883980

Protein

rpsI

PMID:15690043

Experiment(s):EBI-883980

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-883980

Protein

rpsN

PMID:15690043

Experiment(s):EBI-883980

Protein

rpsT

PMID:15690043

Experiment(s):EBI-883980

Protein

rsmB

PMID:15690043

Experiment(s):EBI-883980

Protein

gmr

PMID:15690043

Experiment(s):EBI-883980

Protein

ydaY

PMID:15690043

Experiment(s):EBI-883980

Protein

yhbY

PMID:15690043

Experiment(s):EBI-883980

Protein

yhiP

PMID:15690043

Experiment(s):EBI-883980

Protein

yjdB

PMID:15690043

Experiment(s):EBI-883980

Protein

rluE

PMID:15690043

Experiment(s):EBI-883980

Protein

accD

PMID:15690043

Experiment(s):EBI-883980

Protein

yeeJ

PMID:15690043

Experiment(s):EBI-883980

Protein

creC

PMID:15690043

Experiment(s):EBI-883980

Protein

cspE

PMID:15690043

Experiment(s):EBI-883980

Protein

dnaJ

PMID:15690043

Experiment(s):EBI-883980

Protein

entB

PMID:15690043

Experiment(s):EBI-883980

Protein

glpK

PMID:15690043

Experiment(s):EBI-883980

Protein

hupA

PMID:15690043

Experiment(s):EBI-883980

Protein

hupB

PMID:15690043

Experiment(s):EBI-883980

Protein

metR

PMID:15690043

Experiment(s):EBI-883980

Protein

prpD

PMID:15690043

Experiment(s):EBI-883980

Protein

putA

PMID:15690043

Experiment(s):EBI-883980

Protein

rcsB

PMID:15690043

Experiment(s):EBI-883980

Protein

recN

PMID:15690043

Experiment(s):EBI-883980

Protein

rfaJ

PMID:15690043

Experiment(s):EBI-883980

Protein

rhlE

PMID:15690043

Experiment(s):EBI-883980

Protein

topA

PMID:16606699

Experiment(s):EBI-1140933

Protein

uspG

PMID:16606699

Experiment(s):EBI-1140933

Protein

rpsG

PMID:16606699

Experiment(s):EBI-1140933

Protein

rpsM

PMID:16606699

Experiment(s):EBI-1140933

Protein

rplA

PMID:16606699

Experiment(s):EBI-1140933

Protein

rplB

PMID:16606699

Experiment(s):EBI-1140933

Protein

cpxR

PMID:16606699

Experiment(s):EBI-1140933

Protein

rplD

PMID:16606699

Experiment(s):EBI-1140933

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1140933

Protein

nadE

PMID:16606699

Experiment(s):EBI-1140933

Protein

ycgE

PMID:16606699

Experiment(s):EBI-1140933

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1140933

Protein

accD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):3.000505

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):10.363976

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.290188

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):4.815931

Protein

rho

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):39.189659

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):8.825591

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753

LCMS(ID Probability):80.0 MALDI(Z-score):18.672179

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.294551

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.999468

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):24.294405

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):36.483049

Protein

clpA

PMID:19402753

MALDI(Z-score):18.860804

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):31.855298

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):8.291252

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

accA

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):31.439125

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):31.854353

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):4.275541

Protein

rlmL

PMID:19402753

MALDI(Z-score):26.179233

Protein

yfiF

PMID:19402753

MALDI(Z-score):36.427608

Protein

aidB

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):24.911783

Protein

rnr

PMID:19402753

MALDI(Z-score):24.701159

Protein

recN

PMID:19402753

LCMS(ID Probability):99.4

Protein

rluB

PMID:19402753

LCMS(ID Probability):90.0 MALDI(Z-score):37.004990

Protein

pnp

PMID:19402753

MALDI(Z-score):23.617200

Protein

hfq

PMID:19402753

LCMS(ID Probability):99.6

Protein

yhiR

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):38.827197

Protein

hrpA

PMID:19402753

MALDI(Z-score):18.552100

Protein

rluC

PMID:19402753

LCMS(ID Probability):90.0 MALDI(Z-score):34.129450

Protein

cspE

PMID:19402753

LCMS(ID Probability):99.0

Protein

ybjX

PMID:19402753

MALDI(Z-score):21.166940

Protein

rhlE

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):9.883347

</protect>

Notes

selective RNA binding sequence

AGGGAGGGA

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

MAKIKGQVKW FNESKGFGFI TPADGSKDVF VHFSAIQGNG FKTLAEGQNV EFEIQDGQKG
PAAVNVTAI
Length

69

Mol. Wt

7.401 kDa

pI

7.3 (calculated)

Extinction coefficient

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


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:P0A9Y6

Domain

3..69

PF00313 'Cold-shock' DNA-binding domain

PMID:19920124

<motif_map/>

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

Structures

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

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

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

<protect></protect>

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:16129777

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946339

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006070

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9Y6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12204

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946339

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002092

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2120

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

5.85E+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

7890.539+/-69.415

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

6.578947368

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 EMG2

8300

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M39

PMID: 9298646

Protein

E. coli K-12 MG1655

106172

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

50154

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

80903

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

cspC

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_000913:1905439..1905479 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


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

Type Reference Notes

microarray

GEO Profiles:b1823 (EcoliWiki Page)

NCBI GEO profiles for cspC

microarray

GenExpDB:b1823 (EcoliWiki Page)

Summary of data for cspC 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

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Notes

Accessions Related to cspC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12204

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2120

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1823

EcoGene

EcoGene:EG12204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002092

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006070

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

CSPC

From SHIGELLACYC

E. coli O157

CSPC

From ECOO157CYC


Do-It-Yourself Web Tools

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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:EG12204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002092

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2120

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006070

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. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 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 2.7 2.8 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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