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Gene : LHY A. thaliana

Gene ID  ? AT1G01060
Brief Description  Homeodomain-like superfamily protein  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? LATE ELONGATED HYPOCOTYL (LHY); CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), Homeodomain-like (InterPro:IPR009057), Myb, DNA-binding (InterPro:IPR014778), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447); BEST Arabidopsis thaliana protein match is: circadian clock associated 1 (TAIR:AT2G46830.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? LHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1  Source: TAIR, Jun 30, 2015.
  • synonyms:
  • LHY1

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16 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
Accumulation of the LHY protein in the lhy-1 mutant was altered by the det1-1 mutation and through the proteasome pathway. 15988568
The function of ELF3 and ELF4 in their light-regulated expression associated with CCA1, LHY, and TOC1 as part of the central oscillator of the circadian clock in Arabidopsis is reported. 16212608
The linkages of TOC1, CCA1 and LHY genes and the canonical CO-FT flowering pathway were studied. 17540692
CCA1 and LHY delay flowering time under continuous light by reducing the accumulation of SVP. 19011118
CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis. 19218364
LHY/CCA1 regulates a pathway negatively controlling flowering locus T (FT), possibly via ELF3-SVP/FLC. 19383102
A conserved G-Box motif contributes to the rhythmic expression of LHY. 19789276
LHY ubiquitination by SINAT5 was inhibited by DET1. 20599732
Results reveal a role of PRR7 and PRR9 in regulating CCA1 and LHY activities in response to ambient temperature. 21098730
CCA1/LHY-mediated output from the circadian clock contributes to plant cold tolerance through regulation of the CBF cold-response pathway. 21471455
Functional interactions between the clock proteins LHY and CCA1 and the photoreceptor PhyB control organ elongation and flowering time. 21822060
Interaction of Arabidopsis DET1 with LHY in mediating transcriptional repression in the plant circadian clock 21884973
Our computational analysis suggests that TOC1 is a repressor of the morning genes Late Elongated Hypocotyl and Circadian Clock Associated1 rather than an activator as first conceived. 22395476
Rhythmic expression of LHY under light-dark cycling conditions correlates with histone modification. 22878891
Histone 3 activating marks associated with the translational start sites of CCA1/LHY and TOC1 are circadian regulated. 23128602
Transcriptional co-regulators PRR9, PRR7 and PRR5 inhibit morning loop LHY and CCA1 expression by binding to their promoters 24267177


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12 Flanking Regions

Flank size: from most upstream transcription start site, or most downstream transcription stop site

Region Name Flank Size Direction Length Gene Included? Chromosome Location
AT1G01060 0.5kb upstream 0.5kb upstream 5007   true Chr1: 33365-38371
AT1G01060 0.5kb upstream 0.5kb upstream 500   false Chr1: 37872-38371
AT1G01060 0.5kb downstream 0.5kb downstream 5007   true Chr1: 32865-37871
AT1G01060 0.5kb downstream 0.5kb downstream 500   false Chr1: 32865-33364
AT1G01060 1.0kb upstream 1.0kb upstream 5507   true Chr1: 33365-38871
AT1G01060 1.0kb upstream 1.0kb upstream 1000   false Chr1: 37872-38871
AT1G01060 1.0kb downstream 1.0kb downstream 5507   true Chr1: 32365-37871
AT1G01060 1.0kb downstream 1.0kb downstream 1000   false Chr1: 32365-33364
AT1G01060 3.0kb upstream 3.0kb upstream 7507   true Chr1: 33365-40871
AT1G01060 3.0kb upstream 3.0kb upstream 3000   false Chr1: 37872-40871
AT1G01060 3.0kb downstream 3.0kb downstream 7507   true Chr1: 30365-37871
AT1G01060 3.0kb downstream 3.0kb downstream 3000   false Chr1: 30365-33364


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1 Pathways

Data Source: KEGG

Identifier Name
04712 Circadian rhythm - plant

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12 Data Sets

Name Description Version
BAR Annotations Lookup Mapping(s) between AGI locus and Affy Probeset identifier 10/08/2013
Genome Annotation Araport11 protein-coding, non-coding and transposable element genes Araport11 (06/2016)
RNA-seq expression Measure of gene expression levels (Transcripts per Million, TPM) quantified by Salmon Araport11 (06/2016)
PubMed to gene mapping Curated associations between publications and NCBI Gene records 8/12/2016
GO Annotation from InterPro    
PO Annotation from TAIR Literature-based annotations of genes to Plant Ontology (PO) terms 06/30/2015
Swiss-Prot data set High-quality, manually annotated, non-redundant protein sequence database 2016_07
Panther data set PANTHER paralogs from Arabidopsis 11.0
KEGG pathways data set Wiring diagrams of molecular interactions, reactions, and relations 79.0
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
IntAct interactions data set Curated binary and complex protein-protein interactions for Arabidopsis thaliana 8/02/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139