LHY Homeodomain-like superfamily protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: LHY
Official Full Name: Homeodomain-like superfamily protein
Primary source: TAIR:AT1G01060
Locus tag: AT1G01060
See related: Araport:AT1G01060
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: LATE ELONGATED HYPOCOTYL; LATE ELONGATED HYPOCOTYL 1; LHY1; T25K16.6; T25K16_6
Summary: LHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1
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Genomic context

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See LHY in Genome Data Viewer

Location:: chromosome: 1

Exon count:: 11

Sequence:: Chromosome: 1; NC_003070.9 (33365..37871, complement)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Twilight length alters growth and flowering time in Arabidopsis via LHY/CCA1.
Title: Twilight length alters growth and flowering time in Arabidopsis via LHY/CCA1.
XAP5 CIRCADIAN TIMEKEEPER specifically modulates 3' splice site recognition and is important for circadian clock regulation partly by alternative splicing of LHY and TIC.
Title: XAP5 CIRCADIAN TIMEKEEPER specifically modulates 3' splice site recognition and is important for circadian clock regulation partly by alternative splicing of LHY and TIC.
LHY positively regulates post-penetration resistance in Arabidopsis thaliana.
Title: CCA1 and LHY contribute to nonhost resistance to Pyricularia oryzae (syn. Magnaporthe oryzae) in Arabidopsis thaliana.
we also found that CCA1 is required for both a short- and long-term response of the circadian oscillator to sucrose, while LHY acts to attenuate the effects of sucrose on circadian period. Together, this work highlights new pathways for how sucrose could be signaling to the oscillator and reveals further functional separation of CCA1 and LHY.
Title: Physiological and Genetic Dissection of Sucrose Inputs to the Arabidopsis thaliana Circadian System.
LHY promoted expression of abscissic acid (ABA)-responsive genes responsible for increased tolerance to drought and osmotic stress but alleviated the inhibitory effect of ABA on seed germination and plant growth.
Title: Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets.
Transcriptional co-regulators PRR9, PRR7 and PRR5 inhibit morning loop LHY and CCA1 expression by binding to their promoters
Title: A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana.
Histone 3 activating marks associated with the translational start sites of CCA1/LHY and TOC1 are circadian regulated.
Title: Circadian clock regulates dynamic chromatin modifications associated with Arabidopsis CCA1/LHY and TOC1 transcriptional rhythms.
Rhythmic expression of LHY under light-dark cycling conditions correlates with histone modification.
Title: Rhythmic oscillation of histone acetylation and methylation at the Arabidopsis central clock loci.
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.
Title: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.
Functional interactions between the clock proteins LHY and CCA1 and the photoreceptor PhyB control organ elongation and flowering time.
Title: Suppression of late-flowering and semi-dwarf phenotypes in the Arabidopsis clock mutant lhy-12;cca1-101 by phyB under continuous light.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001035847.1

Supported by ESTs:

NM_001083968.1

Supported by ESTs:

NM_001197953.1

Supported by ESTs:

NM_001331247.1

Supported by ESTs:

NM_001331248.1

Supported by ESTs:

NM_099988.4

Supported by ESTs:

NM_179237.1

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within circadian rhythm	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within long-day photoperiodism, flowering	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to cold	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: Homeodomain-like superfamily protein

NP_001030924.1

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); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).

NP_001077437.1

LATE ELONGATED HYPOCOTYL (LHY); CONTAINS InterPro DOMAIN/s: SANT, DNA-binding (InterPro:IPR001005), Myb, DNA-binding (InterPro:IPR014778), Homeodomain-like (InterPro:IPR009057), Myb-like DNA-binding domain, SHAQKYF class (InterPro:IPR006447), HTH transcriptional regulator, Myb-type, DNA-binding (InterPro:IPR017930); BEST Arabidopsis thaliana protein match is: circadian clock associated 1 (TAIR:AT2G46830.1); Has 2567 Blast hits to 2041 proteins in 275 species: Archae - 2; Bacteria - 252; Metazoa - 294; Fungi - 166; Plants - 1044; Viruses - 30; Other Eukaryotes - 779 (source: NCBI BLink).

NP_001184882.1

LATE ELONGATED HYPOCOTYL (LHY); FUNCTIONS IN: DNA binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: in 11 processes; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; BEST Arabidopsis thaliana protein match is: circadian clock associated 1 (TAIR:AT2G46830.1).

NP_171614.1

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); Has 2469 Blast hits to 2022 proteins in 280 species: Archae - 2; Bacteria - 257; Metazoa - 292; Fungi - 162; Plants - 1048; Viruses - 29; Other Eukaryotes - 679 (source: NCBI BLink).

NP_849568.1

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); Has 2469 Blast hits to 2022 proteins in 280 species: Archae - 2; Bacteria - 257; Metazoa - 292; Fungi - 162; Plants - 1048; Viruses - 29; Other Eukaryotes - 679 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_003070.9 Reference assembly

Range

33365..37871 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001331246.1 → NP_001320628.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9S0S1, A0A654E6V0, F4HQH3
NM_001035847.1 → NP_001030924.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001030924.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DFD7, B9DFM4, O81713, Q6R0H1, Q9MAM8

UniProtKB/TrEMBL

A0A178W761, A0A5S9S0S1, A0A654E6V0

Conserved Domains (2) summary

TIGR01557
Location:22 → 72

myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

PTZ00121
Location:432 → 533

PTZ00121; MAEBL; Provisional
NM_001331247.1 → NP_001320627.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DFD7, B9DFM4, O81713, Q6R0H1, Q9MAM8

UniProtKB/TrEMBL

A0A178W761, A0A5S9S0S1, A0A654E6V0

Conserved Domains (2) summary

TIGR01557
Location:22 → 72

myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

PTZ00121
Location:432 → 533

PTZ00121; MAEBL; Provisional
NM_099988.4 → NP_171614.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_171614.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DFD7, B9DFM4, O81713, Q6R0H1, Q9MAM8

UniProtKB/TrEMBL

A0A178W761, A0A5S9S0S1, A0A654E6V0

Conserved Domains (2) summary

TIGR01557
Location:22 → 72

myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

PTZ00121
Location:432 → 533

PTZ00121; MAEBL; Provisional
NM_001083968.1 → NP_001077437.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001077437.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A178W696, A0A5S9S0S1, A0A654E6V0, F4HQG9

Conserved Domains (2) summary

TIGR01557
Location:22 → 72

myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

smart00717
Location:24 → 71

SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
NM_179237.1 → NP_849568.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_849568.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DFD7, B9DFM4, O81713, Q6R0H1, Q9MAM8

UniProtKB/TrEMBL

A0A178W761, A0A5S9S0S1, A0A654E6V0

Conserved Domains (2) summary

TIGR01557
Location:22 → 72

myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

PTZ00121
Location:432 → 533

PTZ00121; MAEBL; Provisional
NM_001197953.1 → NP_001184882.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001184882.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9S0S1, A0A654E6V0, F4HQH3

Conserved Domains (1) summary

PTZ00121
Location:430 → 531

PTZ00121; MAEBL; Provisional
NM_001331248.1 → NP_001320629.1 Homeodomain-like superfamily protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

B9DFD7, B9DFM4, O81713, Q6R0H1, Q9MAM8

UniProtKB/TrEMBL

A0A178W761, A0A5S9S0S1, A0A654E6V0

Conserved Domains (2) summary

TIGR01557
Location:22 → 72

myb_SHAQKYF; myb-like DNA-binding domain, SHAQKYF class

PTZ00121
Location:432 → 533

PTZ00121; MAEBL; Provisional