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Expression|

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Standard Name	yjiY
Gene Synonym(s)	ECK4344, b4354, JW5791^[1], JW5791
Product Desc.	predicted inner membrane protein^[2]^[3] Function unknown; cstA paralog; probable oppE locus affection oligopeptide transport^[4]
Product Synonyms(s)	predicted inner membrane protein ^[1], B4354 ^[2]^[1], YjiY ^[2]^[1] , ECK4344, JW5791, b4354
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yjiY^[2]
Regulation/Activity
Quick Links
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Notes

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The prediction that yjiY is oppE is based upon genetic mapping that places oppE in this region and the peptide utilization phenotype of its paralog cstA. Both cstA and yjiY are in operons with a small protein of unknown function, ybdD and yjiX, respectively. HT_Cmplx48_Mem: SecA+YdgA+YjiY.^[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	yjiY
Mnemonic	Systematic nomenclature
Synonyms	ECK4344, b4354, JW5791^[1], JW5791
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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	98.87 minutes	MG1655: 4589302..4587152 <gbrowseImage> name=NC_000913:4587152..4589302 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4569254..4567104 <gbrowseImage> name=NC_012967:4567104..4569254 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4525636..4527786 <gbrowseImage> name=NC_012759:4525636..4527786 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4595959..4593809 <gbrowseImage> name=NC_007779:4593809..4595959 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
ΔyjiY (Keio:JW5791)	deletion	deletion	PMID:16738554	Shigen CGSC11579^[5]
ΔyjiY752::kan			PMID:16738554	CGSC:105618
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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
JW5791	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATACTAAAAAGATATTCAA Primer 2:CCGTGGTGCGAAGAGATCTTCAC
10H12	Kohara Phage	Genobase	PMID:3038334
7C1	Kohara Phage	Genobase	PMID:3038334
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[5]	est. P1 cotransduction: % ^[6] Synonyms:zjh-901::Tn10, zjg-920::Tn10
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: 81% ^[6] Synonyms:zjj-202::Tn10, zji-202::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:G7942	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12586	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004436	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948914	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2472	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014278	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	YjiY
Synonyms	predicted inner membrane protein ^[1], B4354 ^[2]^[1], YjiY ^[2]^[1] , ECK4344, JW5791, b4354
Product description	predicted inner membrane protein^[2]^[3] Function unknown; cstA paralog; probable oppE locus affection oligopeptide transport^[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:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009267	cellular response to starvation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003706	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003706	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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	rplS	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplI	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplW	PMID:19402753	LCMS(ID Probability):99.6
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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
plasma membrane	C-terminus localized in the cytoplasm with 16 predicted transmembrane domains	Daley et al. (2005) ^[7]
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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 MPGFTMDTKK IFKHIPWVIL GIIGAFCLAV VALRRGEHIS ALWIVVASVS VYLVAYRYYS LYIAQKVMKL DPTRATPAVI NNDGLNYVPT NRYVLFGHHF AAIAGAGPLV GPVLAAQMGY LPGTLWLLAG VVLAGAVQDF MVLFISSRRN GASLGEMIKE EMGPVPGTIA LFGCFLIMII ILAVLALIVV KALAESPWGV FTVCSTVPIA LFMGIYMRFI RPGRVGEVSV IGIVLLVASI YFGGVIAHDP YWGPALTFKD TTITFALIGY AFVSALLPVW LILAPRDYLA TFLKIGVIVG LALGIVVLNP ELKMPAMTQY IDGTGPLWKG ALFPFLFITI ACGAVSGFHA LISSGTTPKL LANETDARFI GYGAMLMESF VAIMALVAAS IIEPGLYFAM NTPPAGLGIT MPNLHEMGGE NAPIIMAQLK DVTAHAAATV SSWGFVISPE QILQTAKDIG EPSVLNRAGG APTLAVGIAH VFHKVLPMAD MGFWYHFGIL FEALFILTAL DAGTRSGRFM LQDLLGNFIP FLKKTDSLVA GIIGTAGCVG LWGYLLYQGV VDPLGGVKSL WPLFGISNQM LAAVALVLGT VVLIKMKRTQ YIWVTVVPAV WLLICTTWAL GLKLFSTNPQ MEGFFYMASQ YKEKIANGTD LTAQQIANMN HIVVNNYTNA GLSILFLIVV YSIIFYGFKT WLAVRNSDKR TDKETPYVPI PEGGVKISSH H
Length	721
Mol. Wt	77.859 kDa
pI	9.1 (calculated)
Extinction coefficient	121,240 - 121,990 (calc based on 26 Y, 15 W, and 6 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	34..455	PF02554 Carbon starvation protein CstA		PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=yjiY 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:90111739	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948914	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014278	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39396	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7942	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12586	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948914	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004436	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2472	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 MC4100	2.63E+02	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	134.859+/-1.441	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.21777+/-0.02055	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.005581395	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	7006	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	9	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	3525	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)
yjiY
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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_000913:4589282..4589322 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:b4354 (EcoliWiki Page)	NCBI GEO profiles for yjiY
microarray	GenExpDB:b4354 (EcoliWiki Page)	Summary of data for yjiY 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 (4588781..4589264) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ12; Well:A6^[8]
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Notes

Accessions Related to yjiY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7942	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2472	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4354
EcoGene	EcoGene:EG12586	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004436	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014278	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
Anopheles gambiae	ENSANGP00000002207 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YJIY	From SHIGELLACYC
E. coli O157	YJIY	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)	PF02554 Carbon starvation protein CstA
EcoCyc	EcoCyc:G7942	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12586	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004436	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2472	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014278	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 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 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
↑ ^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.
↑ ^5.0 ^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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yjiY: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 yjiY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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