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Gene |

Product(s) |

Expression|

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Standard Name	xylA
Gene Synonym(s)	ECK3554, b3565, JW3537^[1], JW3537
Product Desc.	XylA^[2]^[3]; Component of xylose isomerase^[2]^[3] D-Xylose isomerase^[4]
Product Synonyms(s)	D-xylose isomerase^[1], B3565^[2]^[1], XylA^[2]^[1] , ECK3554, JW3537, b3565
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): xylAB^[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	xylA
Mnemonic	Xylose
Synonyms	ECK3554, b3565, JW3537^[1], JW3537
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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	80.34 minutes, 80.34 minutes	MG1655: 3728788..3727466 <gbrowseImage> name=NC_000913:3727466..3728788 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3661223..3659901 <gbrowseImage> name=NC_012967:3659901..3661223 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3615792..3617114 <gbrowseImage> name=NC_012759:3615792..3617114 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3909650..3910972 <gbrowseImage> name=NC_007779:3909650..3910972 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3826365..3825043 <gbrowseImage> name=NC_010473:3825043..3826365 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)	AA change(s)	Reference	Availability	Comments
ΔxylA (Keio:JW3537)	deletion	deletion	PMID:16738554	Shigen CGSC10610^[5]
xylA::Tn5KAN-I-SceI (FB21288)	Insertion at nt 1064 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21288	does not contain pKD46
xylA::Tn5KAN-I-SceI (FB21289)	Insertion at nt 1064 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21289	contains pKD46
xylA5				CGSC:9158
xylA13				CGSC:11511
ΔxylA748::kan			PMID:16738554	CGSC:103422
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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
JW3537	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAGCCTATTTTGACCAGCT Primer 2:CCTTTGTCGAACAGATAATGGTT
10C8	Kohara Phage	Genobase	PMID:3038334
6F2	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: % ^[6] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[5]	est. P1 cotransduction: % ^[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:EG11074	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11074	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001063	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948141	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1067	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011639	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	XylA
Synonyms	D-xylose isomerase^[1], B3565^[2]^[1], XylA^[2]^[1] , ECK3554, JW3537, b3565
Product description	XylA^[2]^[3]; Component of xylose isomerase^[2]^[3] D-Xylose isomerase^[4]
EC number (for enzymes)	5.3.1.5^[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:0000287	magnesium ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00455	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00455	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:0006098	pentose-phosphate shunt	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00455	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006098	pentose-phosphate shunt	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0570	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009045	xylose isomerase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00455	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009045	xylose isomerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001998	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009045	xylose isomerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013452	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009045	xylose isomerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.3.1.5	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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 xylose isomerase	could be indirect
Protein	mfd		PMID:16606699	Experiment(s):EBI-1146146
Protein	phnN		PMID:16606699	Experiment(s):EBI-1146146
Protein	yjeS		PMID:16606699	Experiment(s):EBI-1146146
Protein	ynfE		PMID:16606699	Experiment(s):EBI-1146146
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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
cytoplasm			From EcoCyc^[3]
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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 MQAYFDQLDR VRYEGSKSSN PLAFRHYNPD ELVLGKRMEE HLRFAACYWH TFCWNGADMF GVGAFNRPWQ QPGEALALAK RKADVAFEFF HKLHVPFYCF HDVDVSPEGA SLKEYINNFA QMVDVLAGKQ EESGVKLLWG TANCFTNPRY GAGAATNPDP EVFSWAATQV VTAMEATHKL GGENYVLWGG REGYETLLNT DLRQEREQLG RFMQMVVEHK HKIGFQGTLL IEPKPQEPTK HQYDYDAATV YGFLKQFGLE KEIKLNIEAN HATLAGHSFH HEIATAIALG LFGSVDANRG DAQLGWDTDQ FPNSVEENAL VMYEILKAGG FTTGGLNFDA KVRRQSTDKY DLFYGHIGAM DTMALALKIA ARMIEDGELD KRIAQRYSGW NSELGQQILK GQMSLADLAK YAQEHHLSPV HQSGRQEQLE NLVNHYLFDK
Length	440
Mol. Wt	49.742 kDa
pI	5.7 (calculated)
Extinction coefficient	70,820 - 71,320 (calc based on 18 Y, 8 W, and 4 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
Domain	83..314	PF01261 Xylose isomerase-like TIM barrel		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=xylA 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:16131436	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948141	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011639	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P00944	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11074	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11074	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948141	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001063	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1067	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	Notes	Reference(s)
Protein	E. coli K-12 MG1655	20	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	13	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	3^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
xylAB
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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_000913:3728768..3728808 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
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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:b3565 (EcoliWiki Page)	NCBI GEO profiles for xylA
microarray	GenExpDB:b3565 (EcoliWiki Page)	Summary of data for xylA 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 xylA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11074	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1067	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3565
EcoGene	EcoGene:EG11074	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001063	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011639	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
Arabidopsis thaliana	AT5G57655 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000019094 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q40082 (score: 1.000; bootstrap: 100%) Q8H3Q7 (score: 0.847)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000131957 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00009517001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	XYLA	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)	PF01261 Xylose isomerase-like TIM barrel
Superfamily (EcoliWiki Page)	SUPERFAMILY:51658
EcoCyc	EcoCyc:EG11074	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11074	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001063	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1067	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011639	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 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).

xylA:On One Page

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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 xylA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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