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Gene : LEC1 A. thaliana

Gene ID  ? AT1G21970
Brief Description  Histone superfamily protein  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? LEAFY COTYLEDON 1 (LEC1); FUNCTIONS IN: transcription activator activity, sequence-specific DNA binding transcription factor activity; INVOLVED IN: in 6 processes; LOCATED IN: nucleus, intracellular; EXPRESSED IN: seed, endosperm, cultured somatic embryo; EXPRESSED DURING: C globular stage, B proembryo stage, D bilateral stage, E expanded cotyledon stage; CONTAINS InterPro DOMAIN/s: Transcription factor, CBFA/NFYB, DNA topoisomerase (InterPro:IPR003957), Histone-fold (InterPro:IPR009072), Transcription factor CBF/NF-Y/archaeal histone (InterPro:IPR003958), Transcription factor, NFYB/HAP3, conserved site (InterPro:IPR003956); BEST Arabidopsis thaliana protein match is: nuclear factor Y, subunit B6 (TAIR:AT5G47670.2).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Transcriptional activator of genes required for both embryo maturation and cellular differentiation. Sequence is similar to HAP3 subunit of the CCAAT-box binding factor. HAP3 subunit is divided into three domains: an amino-terminal A domain, a central B domain, and a carboxyl-terminal C domain. LEC1 shared high similarity with other HAP3 homologs only in central, B domain. LEC1 is required for the specification of cotyledon identity and the completion of embryo maturation. It was sufficient to induce embryogenic programs in vegetative cells, suggesting that LEC1 is a major embryonic regulator that mediates the switch between embryo and vegetative development. Mutants are desiccation intolerant, have trichomes on cotyledons and exhibit precocious meristem activation. Levels of the ABI3 and FUS3 transcripts were significantly reduced in developing siliques of the lec1-1 mutants, indicating that LEC1 down-regulates FUS3 and ABI3.When LEC1 is overexpressed from an inducible promoter, the expression of numerous genes involved in fatty acid biosynthesis is increased suggesting a role in positive regulation of FA biosynthesis.  Source: TAIR, Jun 30, 2015.
Name  ? LEAFY COTYLEDON 1
  • synonyms:
  • EMBRYO DEFECTIVE 212,
  • EMBRYO DEFECTIVE 212,
  • EMB212,
  • AtLEC1,
  • NF-YB9,
  • NUCLEAR FACTOR Y%2C SUBUNIT B9,
  • EMB 212

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10 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
We suggest that LEC1 controls the expression of the SSP genes in a hierarchical manner, which involves ABI3 and FUS3. 15695450
Cultures of the lec mutants formed somatic embryos at a low frequency. Moreover, somatic embryos were formed from callus tissue through an indirect route. 16034595
A study of the network of transcription factors that regulates gene expression in A. thaliana is described and discussed. 17158584
LEC1 positively regulates fatty acid biosynthesis genes. Genes involved in glycolysis and lipid accumulation are also up-regulated. 18689444
LEC1 and LEC1-LIKE activate the CRC and SUCROSE SYNTHASE 2 (SUS2) promoters in combination with an NF-YC subunit through the interaction with a seed-specific ABA-response element (ABRE) binding bZIP factor, bZIP67. 19207209
LEC1 appears to be an integrator of various regulatory events, involving the transcription factor itself as well as light and hormone signalling, especially during somatic and early zygotic embryogenesis. 22429691
Data confirms LEC1's known participation in the regulation of somatic embryogenesis, but also indicates additional roles in embryonic and extra-embryonic cell elongation 23073004
NUCLEAR FACTOR Y transcription factors have both opposing and additive roles in abscisic acid-mediated seed germination. 23527203
NUCLEAR FACTOR Y (NF-Y) binds a CCAAT box in the distal enhancer element and that CCAAT disruption dramatically reduces FT promoter activity 24610724
In addition to VAL B3 factors, epigenetic mechanisms are implicated in maintaining repression of LEC1/AFL (LAFL)network during vegetative development 24902838

Genomics

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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
AT1G21970 0.5kb upstream 0.5kb upstream 2573   true Chr1: 7727577-7730149
AT1G21970 0.5kb upstream 0.5kb upstream 500   false Chr1: 7729650-7730149
AT1G21970 0.5kb downstream 0.5kb downstream 2573   true Chr1: 7727077-7729649
AT1G21970 0.5kb downstream 0.5kb downstream 500   false Chr1: 7727077-7727576
AT1G21970 1.0kb upstream 1.0kb upstream 3073   true Chr1: 7727577-7730649
AT1G21970 1.0kb upstream 1.0kb upstream 1000   false Chr1: 7729650-7730649
AT1G21970 1.0kb downstream 1.0kb downstream 3073   true Chr1: 7726577-7729649
AT1G21970 1.0kb downstream 1.0kb downstream 1000   false Chr1: 7726577-7727576
AT1G21970 3.0kb upstream 3.0kb upstream 5073   true Chr1: 7727577-7732649
AT1G21970 3.0kb upstream 3.0kb upstream 3000   false Chr1: 7729650-7732649
AT1G21970 3.0kb downstream 3.0kb downstream 5073   true Chr1: 7724577-7729649
AT1G21970 3.0kb downstream 3.0kb downstream 3000   false Chr1: 7724577-7727576

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Data Source: KEGG

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11 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 UniProt GO annotations assigned by UniProt 8/01/2016
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
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