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Gene |

Product(s) |

Expression|

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Standard Name	rhsA
Gene Synonym(s)	ECK3582, b3593, JW3566^[1], JW3566
Product Desc.	RhsA protein in rhs element^[2]^[3] Role in polysaccharide synthesis/export; encoded within RhsA repeat; hotspot for chromosomal duplication formation^[4]
Product Synonyms(s)	rhsA element core protein RshA^[1], B3593^[2]^[1], RhsA^[2]^[1] , ECK3582, JW3566, b3593
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rhsA^[2]
Regulation/Activity
Quick Links
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Notes

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Transcription of rhsA was detected. RhsA coud be cross-linked to Kps proteins in K5+ K-12 strain. rhsA mutant has reduced K5 polysaccharide biosynthesis in K-12 K5+ strain. Swiss-Prot prediction of 26 aa signal peptide is a probable false positve.^[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	rhsA
Mnemonic	Recombination hotsot
Synonyms	ECK3582, b3593, JW3566^[1], JW3566
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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	81.04 minutes, 81.04 minutes	MG1655: 3760206..3764339 <gbrowseImage> name=NC_000913:3760206..3764339 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3696877..3701010 <gbrowseImage> name=NC_012967:3696877..3701010 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3648532..3652665 <gbrowseImage> name=NC_012759:3648532..3652665 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3878232..3874099 <gbrowseImage> name=NC_007779:3874099..3878232 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
ΔrhsA (Keio:JW3566)	deletion	deletion	PMID:16738554	Shigen CGSC10629^[5]
ΔrhsA777::kan			PMID:16738554	CGSC:102696
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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
JW3566	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGGAAAACCGGCAGCGCG Primer 2:CCTCTTTTTTTATCGTTTGACTG
17G2	Kohara Phage	Genobase	PMID:3038334
2C10	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: 2% ^[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:EG10846	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10846	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000837	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948120	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0839	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011742	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	RhsA
Synonyms	rhsA element core protein RshA^[1], B3593^[2]^[1], RhsA^[2]^[1] , ECK3582, JW3566, b3593
Product description	RhsA protein in rhs element^[2]^[3] Role in polysaccharide synthesis/export; encoded within RhsA repeat; hotspot for chromosomal duplication formation^[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
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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
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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 MSGKPAARQG DMTQYGGSIV QGSAGVRIGA PTGVACSVCP GGVTSGHPVN PLLGAKVLPG ETDIALPGPL PFILSRTYSS YRTKTPAPVG SLGPGWKMPA DIRLQLRDNT LILSDNGGRS LYFEHLFPGE DGYSRSESLW LVRGGVAKLD EGHRLAALWQ ALPEELRLSP HRYLATNSPQ GPWWLLGWCE RVPEADEVLP APLPPYRVLT GLVDRFGRTQ TFHREAAGEF SGEITGVTDG AWRHFRLVLT TQAQRAEEAR QQAISGGTEP SAFPDTLPGY TEYGRDNGIR LSAVWLTHDP EYPENLPAAP LVRYGWTPRG ELAVVYDRSG KQVRSFTYDD KYRGRMVAHR HTGRPEIRYR YDSDGRVTEQ LNPAGLSYTY QYEKDRITIT DSLDRREVLH TQGEAGLKRV VKKEHADGSV TQSQFDAVGR LRAQTDAAGR TTEYSPDVVT GLITRITTPD GRASAFYYNH HNQLTSATGP DGLELRREYD ELGRLIQETA PDGDITRYRY DNPHSDLPCA TEDATGSRKT MTWSRYGQLL SFTDCSGYVT RYDHDRFGQM TAVHREEGLS QYRAYDSRGQ LIAVKDTQGH ETRYEYNIAG DLTAVIAPDG SRNGTQYDAW GKAVRTTQGG LTRSMEYDAA GRVIRLTSEN GSHTTFRYDV LDRLIQETGF DGRTQRYHHD LTGKLIRSED EGLVTHWHYD EADRLTHRTV KGETAERWQY DERGWLTDIS HISEGHRVAV HYRYDEKGRL TGERQTVHHP QTEALLWQHE TRHAYNAQGL ANRCIPDSLP AVEWLTYGSG YLAGMKLGDT PLVEYTRDRL HRETLRSFGR YELTTAYTPA GQLQSQHLNS LLSDRDYTWN DNGELIRISS PRQTRSYSYS TTGRLTGVHT TAANLDIRIP YATDPAGNRL PDPELHPDST LSMWPDNRIA RDAHYLYRYD RHGRLTEKTD LIPEGVIRTD DERTHRYHYD SQHRLVHYTR TQYEEPLVES RYLYDPLGRR VAKRVWRRER DLTGWMSLSR KPQVTWYGWD GDRLTTIQND RTRIQTIYQP GSFTPLIRVE TATGELAKTQ RRSLADALQQ SGGEDGGSVV FPPVLVQMLD RLESEILADR VSEESRRWLA SCGLTVEQMQ NQMDPVYTPA RKIHLYHCDH RGLPLALISK EGTTEWCAEY DEWGNLLNEE NPHQLQQLIR LPGQQYDEES GLYYNRHRYY DPLQGRYITQ DPIGLKGGWN FYQYPLNPVT NTDPLGLEVF PRPFPLPIPW PKSPAQQQAD DNAAKALTKW WNDTASQRIF DSLILNNPGL ALDITMIASR GNVADTGITD RVNDIINDRF WSDGKKPDRC DVLQELIDCG DISAKDAKST QKAWNCRHSR QSNDKKR
Length	1,377
Mol. Wt	156.323 kDa
pI	6.8 (calculated)
Extinction coefficient	277,780 - 279,280 (calc based on 72 Y, 31 W, and 12 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	1143..1183	PF03527 RHS protein	PMID:19920124
Domain	425..463	PF05593 RHS Repeat	PMID:19920124
Domain	468..505	PF05593 RHS Repeat	PMID:19920124
Domain	489..515	PF05593 RHS Repeat	PMID:19920124
Domain	533..570	PF05593 RHS Repeat	PMID:19920124
Domain	575..612	PF05593 RHS Repeat	PMID:19920124
Domain	617..652	PF05593 RHS Repeat	PMID:19920124
Domain	637..674	PF05593 RHS Repeat	PMID:19920124
Domain	699..738	PF05593 RHS Repeat	PMID:19920124
Domain	939..985	PF05593 RHS Repeat	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=rhsA 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:16131464	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948120	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011742	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P16916	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10846	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10846	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948120	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000837	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0839	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	0^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^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)
rhsA
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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_000913:3760186..3760226 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:b3593 (EcoliWiki Page)	NCBI GEO profiles for rhsA
microarray	GenExpDB:b3593 (EcoliWiki Page)	Summary of data for rhsA 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 (3759292..3759622) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:D8^[7]
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Notes

Accessions Related to rhsA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10846	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0839	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3593
EcoGene	EcoGene:EG10846	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000837	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011742	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
Bos taurus	ENSBTAP00000009783 (score: 1.000; bootstrap: 100%) ENSBTAP00000039755 (score: 0.704) ENSBTAP00000036826 (score: 0.689) ENSBTAP00000018431 (score: 0.501) ENSBTAP00000034908 (score: 0.091) YP_026224 (score: 1.000; bootstrap: 100%) YP_026234 (score: 0.073)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000017541 (score: 1.000; bootstrap: 100%) YP_026224 (score: 0.856) YP_026234 (score: 0.086)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000009228 (score: 1.000; bootstrap: 100%) ENSMODP00000005061 (score: 0.735) ENSMODP00000005751 (score: 0.678) ENSMODP00000018654 (score: 0.620) YP_026224 (score: 1.000; bootstrap: 100%) YP_026234 (score: 0.087)	From Inparanoid:20070104
Mus musculus	MGI:1345183 (score: 1.000; bootstrap: 100%) MGI:2447063 (score: 0.698) MGI:1345184 (score: 0.693) MGI:1345185 (score: 0.609) YP_026224 (score: 1.000; bootstrap: 100%) YP_026234 (score: 0.080)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000003591 (score: 1.000; bootstrap: 69%) YP_026224 (score: 0.848)	From Inparanoid:20070104
E. coli O157	RHSA	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)	PF03527 RHS protein
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
Pfam (EcoliWiki Page)	PF05593 RHS Repeat
EcoCyc	EcoCyc:EG10846	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10846	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000837	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0839	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011742	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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rhsA: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 rhsA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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