Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q6R0H1 (LHY_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 87. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protein LHY
Alternative name(s):
MYB-related transcription factor LHY
Protein LATE ELONGATED HYPOCOTYL
Gene names
Name:LHY
Ordered Locus Names:At1g01060
ORF Names:T25K16.6
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length645 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Transcription factor involved in the circadian clock. Binds to the promoter region of APRR1/TOC1 and TCP21/CHE to repress their transcription. Represses both CCA1 and itself. Ref.1 Ref.7 Ref.9 Ref.10

Subunit structure

Homodimer or heterodimer with CCA1. Interacts with CCA1 (via internal domain); independently of photoperiod. Functions probably as part of a large complex. Interacts with CKB1 and CKB3. Ref.6 Ref.10 Ref.11

Subcellular location

Nucleus Ref.10.

Tissue specificity

Expressed in leaves, roots, stems, flowers and siliques. Ref.9 Ref.10

Induction

Circadian-regulation with peak levels occurring around 1 hour after dawn. Up-regulated by APRR1/TOC1 and transiently by light treatment. Down-regulated by APRR5, APRR7 and APRR9. Ref.1 Ref.8 Ref.9 Ref.10 Ref.12 Ref.13

Post-translational modification

Phosphorylated by CK2. Ref.6

Disruption phenotype

Shorter circadian oscillations. Ref.7 Ref.10

Miscellaneous

CCA1 and LHY are only partially redundant, but they bind to the same region of the promoters.

Sequence similarities

Contains 1 HTH myb-type DNA-binding domain.

Sequence caution

The sequence AAF26474.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
   Biological processBiological rhythms
Transcription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandDNA-binding
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcircadian rhythm

Inferred from genetic interaction PubMed 21471455. Source: TAIR

long-day photoperiodism, flowering

Inferred from genetic interaction PubMed 19011118. Source: TAIR

negative regulation of circadian rhythm

Inferred from mutant phenotype PubMed 21499259. Source: TAIR

negative regulation of sequence-specific DNA binding transcription factor activity

Inferred from mutant phenotype Ref.12. Source: UniProtKB

regulation of circadian rhythm

Inferred from mutant phenotype Ref.12. Source: UniProtKB

regulation of transcription, DNA-templated

Traceable author statement PubMed 11118137. Source: TAIR

response to abscisic acid

Inferred from expression pattern Ref.2. Source: TAIR

response to auxin

Inferred from expression pattern Ref.2. Source: TAIR

response to cadmium ion

Inferred from expression pattern Ref.2. Source: TAIR

response to cold

Inferred from genetic interaction PubMed 21471455. Source: TAIR

response to ethylene

Inferred from expression pattern Ref.2. Source: TAIR

response to gibberellin

Inferred from expression pattern Ref.2. Source: TAIR

response to jasmonic acid

Inferred from expression pattern Ref.2. Source: TAIR

response to salicylic acid

Inferred from expression pattern Ref.2. Source: TAIR

response to salt stress

Inferred from expression pattern Ref.2. Source: TAIR

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionchromatin binding

Inferred from electronic annotation. Source: InterPro

sequence-specific DNA binding transcription factor activity

Inferred from direct assay Ref.12. Source: UniProtKB

transcription regulatory region DNA binding

Inferred from direct assay Ref.12. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.
Isoform 1 (identifier: Q6R0H1-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 645645Protein LHY
PRO_0000388998

Regions

Domain19 – 7355HTH myb-type
DNA binding46 – 6924H-T-H motif By similarity
Compositional bias310 – 36051Ala-rich

Amino acid modifications

Modified residue61Phosphoserine By similarity

Experimental info

Sequence conflict981R → Q in BAH19541. Ref.5
Sequence conflict4081Q → R in AAS09977. Ref.2
Sequence conflict4111N → T in CAA07004. Ref.1
Sequence conflict5371I → V in BAH19541. Ref.5

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 24, 2009. Version 2.
Checksum: DC327F40AB75AAF5

FASTA64570,438
        10         20         30         40         50         60 
MDTNTSGEEL LAKARKPYTI TKQRERWTED EHERFLEALR LYGRAWQRIE EHIGTKTAVQ 

        70         80         90        100        110        120 
IRSHAQKFFT KLEKEAEVKG IPVCQALDIE IPPPRPKRKP NTPYPRKPGN NGTSSSQVSS 

       130        140        150        160        170        180 
AKDAKLVSSA SSSQLNQAFL DLEKMPFSEK TSTGKENQDE NCSGVSTVNK YPLPTKQVSG 

       190        200        210        220        230        240 
DIETSKTSTV DNAVQDVPKK NKDKDGNDGT TVHSMQNYPW HFHADIVNGN IAKCPQNHPS 

       250        260        270        280        290        300 
GMVSQDFMFH PMREETHGHA NLQATTASAT TTASHQAFPA CHSQDDYRSF LQISSTFSNL 

       310        320        330        340        350        360 
IMSTLLQNPA AHAAATFAAS VWPYASVGNS GDSSTPMSSS PPSITAIAAA TVAAATAWWA 

       370        380        390        400        410        420 
SHGLLPVCAP APITCVPFST VAVPTPAMTE MDTVENTQPF EKQNTALQDQ NLASKSPASS 

       430        440        450        460        470        480 
SDDSDETGVT KLNADSKTND DKIEEVVVTA AVHDSNTAQK KNLVDRSSCG SNTPSGSDAE 

       490        500        510        520        530        540 
TDALDKMEKD KEDVKETDEN QPDVIELNNR KIKMRDNNSN NNATTDSWKE VSEEGRIAFQ 

       550        560        570        580        590        600 
ALFARERLPQ SFSPPQVAEN VNRKQSDTSM PLAPNFKSQD SCAADQEGVV MIGVGTCKSL 

       610        620        630        640 
KTRQTGFKPY KRCSMEVKES QVGNINNQSD EKVCKRLRLE GEAST 

« Hide

References

« Hide 'large scale' references
[1]"The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering."
Schaffer R., Ramsay N., Samach A., Corden S., Putterill J., Carre I.A., Coupland G.
Cell 93:1219-1229(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INDUCTION.
[2]"The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family."
Chen Y., Yang X., He K., Liu M., Li J., Gao Z., Lin Z., Zhang Y., Wang X., Qiu X., Shen Y., Zhang L., Deng X., Luo J., Deng X.-W., Chen Z., Gu H., Qu L.-J.
Plant Mol. Biol. 60:107-124(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY.
[3]"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. expand/collapse author list , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[4]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[5]"Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Strain: cv. Columbia.
[6]"The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis."
Sugano S., Andronis C., Ong M.S., Green R.M., Tobin E.M.
Proc. Natl. Acad. Sci. U.S.A. 96:12362-12366(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION, INTERACTION WITH CKB1 AND CKB3.
[7]"LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis."
Mizoguchi T., Wheatley K., Hanzawa Y., Wright L., Mizoguchi M., Song H.-R., Carre I.A., Coupland G.
Dev. Cell 2:629-641(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[8]"Light-regulated translation mediates gated induction of the Arabidopsis clock protein LHY."
Kim J.Y., Song H.R., Taylor B.L., Carre I.A.
EMBO J. 22:935-944(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION BY LIGHT.
[9]"The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots."
James A.B., Monreal J.A., Nimmo G.A., Kelly C.L., Herzyk P., Jenkins G.I., Nimmo H.G.
Science 322:1832-1835(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY, INDUCTION.
[10]"CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL function synergistically in the circadian clock of Arabidopsis."
Lu S.X., Knowles S.M., Andronis C., Ong M.S., Tobin E.M.
Plant Physiol. 150:834-843(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INDUCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, SUBUNIT, INTERACTION WITH CCA1, DNA-BINDING, DISRUPTION PHENOTYPE.
[11]"Posttranslational regulation of CIRCADIAN CLOCK ASSOCIATED1 in the circadian oscillator of Arabidopsis."
Yakir E., Hilman D., Kron I., Hassidim M., Melamed-Book N., Green R.M.
Plant Physiol. 150:844-857(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CCA1.
[12]"A functional genomics approach reveals CHE as a component of the Arabidopsis circadian clock."
Pruneda-Paz J.L., Breton G., Para A., Kay S.A.
Science 323:1481-1485(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
[13]"PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock."
Nakamichi N., Kiba T., Henriques R., Mizuno T., Chua N.H., Sakakibara H.
Plant Cell 22:594-605(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AJ006404 mRNA. Translation: CAA07004.1.
AY519507 mRNA. Translation: AAS09977.1.
AC007323 Genomic DNA. Translation: AAF26474.1. Sequence problems.
CP002684 Genomic DNA. Translation: AEE27223.1.
CP002684 Genomic DNA. Translation: AEE27224.1.
CP002684 Genomic DNA. Translation: AEE27225.1.
AK316728 mRNA. Translation: BAH19454.1.
AK316829 mRNA. Translation: BAH19541.1.
RefSeqNP_001030924.1. NM_001035847.1. [Q6R0H1-1]
NP_171614.1. NM_099988.3. [Q6R0H1-1]
NP_849568.1. NM_179237.1. [Q6R0H1-1]
UniGeneAt.25466.

3D structure databases

ProteinModelPortalQ6R0H1.
SMRQ6R0H1. Positions 22-75.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid24576. 13 interactions.
IntActQ6R0H1. 2 interactions.
STRING3702.AT1G01060.3-P.

Proteomic databases

PaxDbQ6R0H1.
PRIDEQ6R0H1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G01060.1; AT1G01060.1; AT1G01060. [Q6R0H1-1]
AT1G01060.2; AT1G01060.2; AT1G01060. [Q6R0H1-1]
AT1G01060.3; AT1G01060.3; AT1G01060. [Q6R0H1-1]
GeneID839341.
KEGGath:AT1G01060.

Organism-specific databases

GeneFarm1653. 100.
TAIRAT1G01060.

Phylogenomic databases

eggNOGNOG269073.
HOGENOMHOG000084594.
InParanoidQ6R0H1.
KOK12133.
OMAMDEPRAS.
PhylomeDBQ6R0H1.

Gene expression databases

ArrayExpressQ6R0H1.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
InterProIPR009057. Homeodomain-like.
IPR017930. Myb_dom.
IPR006447. Myb_dom_plants.
IPR001005. SANT/Myb.
[Graphical view]
PfamPF00249. Myb_DNA-binding. 1 hit.
[Graphical view]
SMARTSM00717. SANT. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
TIGRFAMsTIGR01557. myb_SHAQKYF. 1 hit.
PROSITEPS51294. HTH_MYB. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameLHY_ARATH
AccessionPrimary (citable) accession number: Q6R0H1
Secondary accession number(s): B9DFD7 expand/collapse secondary AC list , B9DFM4, O81713, Q9MAM8
Entry history
Integrated into UniProtKB/Swiss-Prot: November 24, 2009
Last sequence update: November 24, 2009
Last modified: May 14, 2014
This is version 87 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names