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Standard Name	xseA
Gene Synonym(s)	ECK2505, b2509, JW2493, xse^[1], xse
Product Desc.	exonuclease VII, large subunit^[2]^[3]; Component of Exonuclease VII^[2]^[3] Exonuclease VII, large subunit^[4]
Product Synonyms(s)	exonuclease VII, large subunit^[1], B2509^[2]^[1], Xse^[2]^[1], XseA^[2]^[1] , ECK2505, JW2493, xse, b2509
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): xseA^[2]
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	xseA
Mnemonic	Exonuclease VII
Synonyms	ECK2505, b2509, JW2493, xse^[1], xse
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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	56.73 minutes	MG1655: 2632254..2633624 <gbrowseImage> name=NC_000913:2632254..2633624 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2555051..2556421 <gbrowseImage> name=NC_012967:2555051..2556421 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2518059..2519429 <gbrowseImage> name=NC_012759:2518059..2519429 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2632888..2634258 <gbrowseImage> name=NC_007779:2632888..2634258 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2724019..2725389 <gbrowseImage> name=NC_010473:2724019..2725389 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
Coding Start (SO:0000323)	MG1655	2632254	Edman degradation	PMID:3021756
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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)	Reference	Availability	Comments
ΔxseA (Keio:JW2493)	deletion	deletion	PMID:16738554	Shigen CGSC9988^[5]
xseA::Tn5KAN-2 (FB20834)	Insertion at nt 1036 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20834	does not contain pKD46
xseA::Tn5KAN-2 (FB20835)	Insertion at nt 1036 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20835	contains pKD46
ΔxseA758::kan			PMID:16738554	CGSC:103416
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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
JW2493	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTACCTTCTCAATCCCCTGC Primer 2:CCATGCACCTTTTTACGCGATTT
8E3	Kohara Phage	Genobase	PMID:3038334
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 20% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 30% ^[6] Synonyms:zff-208::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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11072	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001061	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946988	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1065	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008263	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	XseA
Synonyms	exonuclease VII, large subunit^[1], B2509^[2]^[1], Xse^[2]^[1], XseA^[2]^[1] , ECK2505, JW2493, xse, b2509
Product description	exonuclease VII, large subunit^[2]^[3]; Component of Exonuclease VII^[2]^[3] Exonuclease VII, large subunit^[4]
EC number (for enzymes)	3.1.11.6^[1]
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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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004365	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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00378	C	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:0006308	DNA catabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00378	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006308	DNA catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003753	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008855	exodeoxyribonuclease VII activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008855	exodeoxyribonuclease VII activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003753	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008855	exodeoxyribonuclease VII activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.1.11.6	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009318	exodeoxyribonuclease VII complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003753	C	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	Notes	References	Evidence
Protein	Subunits of Exonuclease VII	could be indirect
Protein	intQ		PMID:15690043	Experiment(s):EBI-878690
Protein	eutE		PMID:16606699	Experiment(s):EBI-1143068
Protein	rplB		PMID:16606699	Experiment(s):EBI-1143068
Protein	rpsD		PMID:16606699	Experiment(s):EBI-1143068
Protein	rplC		PMID:16606699	Experiment(s):EBI-1143068
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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 MLPSQSPAIF TVSRLNQTVR LLLEHEMGQV WISGEISNFT QPASGHWYFT LKDDTAQVRC AMFRNSNRRV TFRPQHGQQV LVRANITLYE PRGDYQIIVE SMQPAGEGLL QQKYEQLKAK LQAEGLFDQQ YKKPLPSPAH CVGVITSKTG AALHDILHVL KRRDPSLPVI IYPAAVQGDD APGQIVRAIE LANQRNECDV LIVGRGGGSL EDLWSFNDER VARAIFTSRI PVVSAVGHET DVTIADFVAD LRAPTPSAAA EVVSRNQQEL LRQVQSTRQR LEMAMDYYLA NRTRRFTQIH HRLQQQHPQL RLARQQTMLE RLQKRMSFAL ENQLKRTGQQ QQRLTQRLNQ QNPQPKIHRA QTRIQQLEYR LAETLRAQLS ATRERFGNAV THLEAVSPLS TLARGYSVTT ATDGNVLKKV KQVKAGEMLT TRLEDGWIES EVKNIQPVKK SRKKVH
Length	456
Mol. Wt	51.831 kDa
pI	10.4 (calculated)
Extinction coefficient	36,900 - 37,275 (calc based on 10 Y, 4 W, and 3 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	References
Domain	30..105	PF01336 OB-fold nucleic acid binding domain	PMID:19920124
Domain	126..442	PF02601 Exonuclease VII, large subunit	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=xseA 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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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:16130434	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946988	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008263	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P04994	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11072	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11072	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946988	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001061	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1065	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	Reference(s)
Protein	E. coli K-12 MG1655	559	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	267	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	612	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)
xseA
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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_000913:2632234..2632274 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:b2509 (EcoliWiki Page)	NCBI GEO profiles for xseA
microarray	GenExpDB:b2509 (EcoliWiki Page)	Summary of data for xseA 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
	GFP Fusion	Intergenic region (2632015..2632289) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:G8^[7]
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Notes

Accessions Related to xseA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11072	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1065	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2509
EcoGene	EcoGene:EG11072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001061	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008263	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
Apis mellifera	ENSAPMP00000012777 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000028826 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	XSEA	From SHIGELLACYC
E. coli O157	XSEA	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)	PF02601 Exonuclease VII, large subunit
Pfam (EcoliWiki Page)	PF01336 OB-fold nucleic acid binding domain
EcoCyc	EcoCyc:EG11072	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11072	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001061	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1065	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008263	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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

xseA: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 xseA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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