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Q6R0H1

- LHY_ARATH

UniProt

Q6R0H1 - LHY_ARATH

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Protein

Protein LHY

Gene

LHY

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.4 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi46 – 6924H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. chromatin binding Source: InterPro
  2. sequence-specific DNA binding transcription factor activity Source: UniProtKB
  3. transcription regulatory region DNA binding Source: UniProtKB

GO - Biological processi

  1. circadian rhythm Source: TAIR
  2. long-day photoperiodism, flowering Source: TAIR
  3. negative regulation of circadian rhythm Source: TAIR
  4. negative regulation of sequence-specific DNA binding transcription factor activity Source: UniProtKB
  5. regulation of circadian rhythm Source: UniProtKB
  6. regulation of transcription, DNA-templated Source: TAIR
  7. response to abscisic acid Source: TAIR
  8. response to auxin Source: TAIR
  9. response to cadmium ion Source: TAIR
  10. response to cold Source: TAIR
  11. response to ethylene Source: TAIR
  12. response to gibberellin Source: TAIR
  13. response to jasmonic acid Source: TAIR
  14. response to salicylic acid Source: TAIR
  15. response to salt stress Source: TAIR
  16. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Protein LHY
Alternative name(s):
MYB-related transcription factor LHY
Protein LATE ELONGATED HYPOCOTYL
Gene namesi
Name:LHY
Ordered Locus Names:At1g01060
ORF Names:T25K16.6
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548: Chromosome 1

Organism-specific databases

TAIRiAT1G01060.

Subcellular locationi

Nucleus 1 PublicationPROSITE-ProRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Shorter circadian oscillations.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 645645Protein LHYPRO_0000388998Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61PhosphoserineBy similarity

Post-translational modificationi

Phosphorylated by CK2.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ6R0H1.
PRIDEiQ6R0H1.

Expressioni

Tissue specificityi

Expressed in leaves, roots, stems, flowers and siliques.2 Publications

Inductioni

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 APRR9.6 Publications

Gene expression databases

ExpressionAtlasiQ6R0H1. baseline and differential.

Interactioni

Subunit structurei

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 CKB3.3 Publications

Protein-protein interaction databases

BioGridi24576. 13 interactions.
IntActiQ6R0H1. 2 interactions.
STRINGi3702.AT1G01060.3-P.

Structurei

3D structure databases

ProteinModelPortaliQ6R0H1.
SMRiQ6R0H1. Positions 22-75.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini19 – 7355HTH myb-typePROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi310 – 36051Ala-richAdd
BLAST

Sequence similaritiesi

Contains 1 HTH myb-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG269073.
HOGENOMiHOG000084594.
InParanoidiQ6R0H1.
KOiK12133.
OMAiMDEPRAS.
PhylomeDBiQ6R0H1.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
InterProiIPR009057. Homeodomain-like.
IPR017930. Myb_dom.
IPR006447. Myb_dom_plants.
IPR001005. SANT/Myb.
[Graphical view]
PfamiPF00249. Myb_DNA-binding. 1 hit.
[Graphical view]
SMARTiSM00717. SANT. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
TIGRFAMsiTIGR01557. myb_SHAQKYF. 1 hit.
PROSITEiPS51294. HTH_MYB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

This entry describes 1 isoform i produced by alternative splicing. Align

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q6R0H1-1) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MDTNTSGEEL LAKARKPYTI TKQRERWTED EHERFLEALR LYGRAWQRIE
60 70 80 90 100
EHIGTKTAVQ IRSHAQKFFT KLEKEAEVKG IPVCQALDIE IPPPRPKRKP
110 120 130 140 150
NTPYPRKPGN NGTSSSQVSS AKDAKLVSSA SSSQLNQAFL DLEKMPFSEK
160 170 180 190 200
TSTGKENQDE NCSGVSTVNK YPLPTKQVSG DIETSKTSTV DNAVQDVPKK
210 220 230 240 250
NKDKDGNDGT TVHSMQNYPW HFHADIVNGN IAKCPQNHPS GMVSQDFMFH
260 270 280 290 300
PMREETHGHA NLQATTASAT TTASHQAFPA CHSQDDYRSF LQISSTFSNL
310 320 330 340 350
IMSTLLQNPA AHAAATFAAS VWPYASVGNS GDSSTPMSSS PPSITAIAAA
360 370 380 390 400
TVAAATAWWA SHGLLPVCAP APITCVPFST VAVPTPAMTE MDTVENTQPF
410 420 430 440 450
EKQNTALQDQ NLASKSPASS SDDSDETGVT KLNADSKTND DKIEEVVVTA
460 470 480 490 500
AVHDSNTAQK KNLVDRSSCG SNTPSGSDAE TDALDKMEKD KEDVKETDEN
510 520 530 540 550
QPDVIELNNR KIKMRDNNSN NNATTDSWKE VSEEGRIAFQ ALFARERLPQ
560 570 580 590 600
SFSPPQVAEN VNRKQSDTSM PLAPNFKSQD SCAADQEGVV MIGVGTCKSL
610 620 630 640
KTRQTGFKPY KRCSMEVKES QVGNINNQSD EKVCKRLRLE GEAST
Length:645
Mass (Da):70,438
Last modified:November 24, 2009 - v2
Checksum:iDC327F40AB75AAF5
GO

Sequence cautioni

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti98 – 981R → Q in BAH19541. (PubMed:19423640)Curated
Sequence conflicti408 – 4081Q → R in AAS09977. (PubMed:16463103)Curated
Sequence conflicti411 – 4111N → T in CAA07004. (PubMed:9657154)Curated
Sequence conflicti537 – 5371I → V in BAH19541. (PubMed:19423640)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
RefSeqiNP_001030924.1. NM_001035847.1. [Q6R0H1-1]
NP_171614.1. NM_099988.3. [Q6R0H1-1]
NP_849568.1. NM_179237.1. [Q6R0H1-1]
UniGeneiAt.25466.

Genome annotation databases

EnsemblPlantsiAT1G01060.1; AT1G01060.1; AT1G01060. [Q6R0H1-1]
AT1G01060.2; AT1G01060.2; AT1G01060. [Q6R0H1-1]
AT1G01060.3; AT1G01060.3; AT1G01060. [Q6R0H1-1]
GeneIDi839341.
KEGGiath:AT1G01060.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
RefSeqi NP_001030924.1. NM_001035847.1. [Q6R0H1-1 ]
NP_171614.1. NM_099988.3. [Q6R0H1-1 ]
NP_849568.1. NM_179237.1. [Q6R0H1-1 ]
UniGenei At.25466.

3D structure databases

ProteinModelPortali Q6R0H1.
SMRi Q6R0H1. Positions 22-75.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 24576. 13 interactions.
IntActi Q6R0H1. 2 interactions.
STRINGi 3702.AT1G01060.3-P.

Proteomic databases

PaxDbi Q6R0H1.
PRIDEi Q6R0H1.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblPlantsi AT1G01060.1 ; AT1G01060.1 ; AT1G01060 . [Q6R0H1-1 ]
AT1G01060.2 ; AT1G01060.2 ; AT1G01060 . [Q6R0H1-1 ]
AT1G01060.3 ; AT1G01060.3 ; AT1G01060 . [Q6R0H1-1 ]
GeneIDi 839341.
KEGGi ath:AT1G01060.

Organism-specific databases

GeneFarmi 1653. 100.
TAIRi AT1G01060.

Phylogenomic databases

eggNOGi NOG269073.
HOGENOMi HOG000084594.
InParanoidi Q6R0H1.
KOi K12133.
OMAi MDEPRAS.
PhylomeDBi Q6R0H1.

Gene expression databases

ExpressionAtlasi Q6R0H1. baseline and differential.

Family and domain databases

Gene3Di 1.10.10.60. 1 hit.
InterProi IPR009057. Homeodomain-like.
IPR017930. Myb_dom.
IPR006447. Myb_dom_plants.
IPR001005. SANT/Myb.
[Graphical view ]
Pfami PF00249. Myb_DNA-binding. 1 hit.
[Graphical view ]
SMARTi SM00717. SANT. 1 hit.
[Graphical view ]
SUPFAMi SSF46689. SSF46689. 1 hit.
TIGRFAMsi TIGR01557. myb_SHAQKYF. 1 hit.
PROSITEi PS51294. HTH_MYB. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiLHY_ARATH
AccessioniPrimary (citable) accession number: Q6R0H1
Secondary accession number(s): B9DFD7
, B9DFM4, O81713, Q9MAM8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 24, 2009
Last sequence update: November 24, 2009
Last modified: October 29, 2014
This is version 89 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3