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casD:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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See Help:Quickview for help with entering information in the Quickview table.

Standard Name

casD

Gene Synonym(s)

ECK2752, b2757, JW5844, ygcI[1]

Product Desc.

predicted protein[2][3]

Function unknown[4]

Product Synonyms(s)

predicted protein[1], B2757[2][1], YgcI[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ygbF[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(ygcI)    Textpresso(ygcI)

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Notes

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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

casD

Mnemonic

CRISPR associated CRISP-associated

Synonyms

ECK2752, b2757, JW5844, ygcI[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

62.04 minutes 

MG1655: 2879070..2878396
gbrowse_img.php?coord=2878396..2879070&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 2879704..2879030
gbrowse_img.php?coord=2879030..2879704&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2971612..2970938
gbrowse_img.php?coord=2970938..2971612&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 2764208..2764882
gbrowse_img.php?coord=2764208..2764882&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔygcI (Keio:JW5844)

deletion

deletion

PMID:16738554

Shigen


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW5844

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGATCTTATTTGATCTTGCG

Primer 2:CCtTGAGATACATCCATACCTCC

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 8% [6]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[5]

est. P1 cotransduction: 78% [6]
Synonyms:cysC95::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7427

EchoBASE (EcoliWiki Page)

EchoBASE:EB2917

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2757

EcoGene (EcoliWiki Page)

EcoGene:EG13116

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z4066

ASAP (EcoliWikiPage)

ASAP:ABE-0009044


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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

CasD

Synonyms

predicted protein[1], B2757[2][1], YgcI[2][1]

Product description

predicted protein[2][3]

Function unknown[4]

EC number (for enzymes)


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Notes

Function

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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus
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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 TypePartnerNotesReferencesEvidence
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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MNMRSYLILR LAGPMQAWGQ PTFEGTRPTG RFPTRSGLLG LLGACLGIQR DDTSSLQALS
ESVQFAVRCD ELILDDRRVS VTGLRDYHTV LGAREDYRGL KSHETIQTWR EYLCDASFTV
ALWLTPHATM VISELEKAVL KPRYTPYLGR RSCPLTHPLF LGTCQASDPQ KALLNYEPVG
GDIYSEESVT GHHLKFTARD EPMITLPRQF ASREWYVIKG GMDVSQ
Length

226

Mol. Wt

25.454 kDa

pI

7.5 (calculated)

Extinction coefficient

35,410 - 36,035 (calc based on 9 Y, 4 W, and 5 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.

TypeResiduesDescriptionNotesReferences

motif

1-17

UniProt Manual:Signal Peptides

UniProt:Q46898


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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7427-MONOMER

UniProt (EcoliWiki Page)

UniProt:Q46898

RefSeq (EcoliWiki Page)

RefSeq:NP_417237


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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)

ygbF

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=2879050..2879090&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b2757 (EcoliWiki Page)

NCBI GEO profiles for ygcI

microarray

GenExpDB:b2757 (EcoliWiki Page)

Summary of data for ygcI 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to casD Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7427

EchoBASE (EcoliWiki Page)

EchoBASE:EB2917

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2757

EcoGene (EcoliWiki Page)

EcoGene:EG13116


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Notes

Links

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Evolution

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Homologs in Other Organisms

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Do-It-Yourself Web Tools

Notes

Families

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

OrganismHomologs (Statistics)Comments

E. coli O157

Z4066

From ECOO157CYC

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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 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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