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Expression|

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Standard Name	ygdG
Gene Synonym(s)	exo, ECK2793, b2798, JW5446, ygdG, xni^[1]^[2], xni
Product Desc.	exonuclease IX, 3'-5' exonuclease^[2]^[3]
Product Synonyms(s)	exonuclease IX (5'-3' exonuclease)^[1], B2798^[2]^[1], YgdG^[2]^[1], Xni^[2]^[1], Exo^[2]^[1] , ECK2793, exo, JW5446, xni, b2798
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links
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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	ygdG
Mnemonic	Systematic nomenclature
Synonyms	exo, ECK2793, b2798, JW5446, ygdG, xni^[1]^[2], xni
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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	63.13 minutes	MG1655: 2928987..2929832 <gbrowseImage> name=NC_000913:2928987..2929832 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2819894..2820739 <gbrowseImage> name=NC_012967:2819894..2820739 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2816135..2816980 <gbrowseImage> name=NC_012759:2816135..2816980 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2929621..2930466 <gbrowseImage> name=NC_007779:2929621..2930466 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3022865..3023710 <gbrowseImage> name=NC_010473:3022865..3023710 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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)	Reference	Availability	Comments
exo::Tn5KAN-I-SceI (FB20783)	Insertion at nt 62 in Plus orientation	PMID:15262929	E. coli Genome Project:FB20933	contains pKD46
exo::Tn5KAN-I-SceI (FB20783)	Insertion at nt 62 in Plus orientation	PMID:15262929	E. coli Genome Project:FB20934	does not contain pKD46
Δxni-725::kan		PMID:16738554	CGSC:106382
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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

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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:EG12372	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12372	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002240	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947256	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2275	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009174	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	Exo
Synonyms	exonuclease IX (5'-3' exonuclease)^[1], B2798^[2]^[1], YgdG^[2]^[1], Xni^[2]^[1], Exo^[2]^[1] , ECK2793, exo, JW5446, xni, b2798
Product description	exonuclease IX, 3'-5' exonuclease^[2]^[3]
EC number (for enzymes)	3.1.11.-^[1]
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See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki. <protect></protect>

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. 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				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008918	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020045	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020046	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020047	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008918	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020045	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004518	nuclease activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0540	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004527	exonuclease activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0269	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008409	5'-3' exonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002421	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008409	5'-3' exonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020046	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008409	5'-3' exonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020047	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	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	References	Evidence
Protein	dnaK	PMID:15690043	Experiment(s):EBI-894844
Protein	rpsB	PMID:15690043	Experiment(s):EBI-894844
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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki. </protect>

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 MRGLFPISHP AVACSGIECY PYRLIFKGVI VAVHLLIVDA LNLIRRIHAV QGSPCVETCQ HALDQLIMHS QPTHAVAVFD DENRSSGWRH QRLPDYKAGR PPMPEELHDE MPALRAAFEQ RGVPCWSTSG NEADDLAATL AVKVTQAGHQ ATIVSTDKGY CQLLSPTLRI RDYFQKRWLD APFIDKEFGV QPQQLPDYWG LAGISSSKVP GVAGIGPKSA TQLLVEFQSL EGIYENLDAV AEKWRKKLET HKEMAFLCRD IARLQTDLHI DGNLQQLRLV R
Length	281
Mol. Wt	31.454 kDa
pI	7.1 (calculated)
Extinction coefficient	37,930 - 38,805 (calc based on 7 Y, 5 W, and 7 C residues)
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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Domains/Motifs/Modification Sites

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

Type	Residues	Description	References
Domain	35..188	PF02739 5'-3' exonuclease, N-terminal resolvase-like domain	PMID:19920124
Domain	190..281	PF01367 5'-3' exonuclease, C-terminal SAM fold	PMID:19920124
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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

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

Structures

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

Models

View models at:

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

</protect>

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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki. <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:226524743	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947256	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009174	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P38506	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12372	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12372	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947256	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002240	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2275	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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	Ecoli K-12	4.156+/-0.039	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.010650888	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	160	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	58	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	194	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
exo
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Figure courtesy of RegulonDB

</protect>

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_000913:2928967..2929007 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

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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:b2798 (EcoliWiki Page)	NCBI GEO profiles for xni
microarray	GenExpDB:b2798 (EcoliWiki Page)	Summary of data for xni 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 ygdG Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12372	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2275	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2798
EcoGene	EcoGene:EG12372	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002240	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009174	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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
Shigella flexneri	EXO	From SHIGELLACYC
E. coli O157	EXO	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF02739 5'-3' exonuclease, N-terminal resolvase-like domain
Pfam (EcoliWiki Page)	PF01367 5'-3' exonuclease, C-terminal SAM fold
Superfamily (EcoliWiki Page)	SUPERFAMILY:47807
Superfamily (EcoliWiki Page)	SUPERFAMILY:88723
EcoCyc	EcoCyc:EG12372	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12372	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002240	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2275	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009174	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 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

ygdG:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ygdG Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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