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Gene : REF6 A. thaliana

Gene ID  ? AT3G48430
Brief Description  relative of early flowering 6  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? relative of early flowering 6 (REF6); FUNCTIONS IN: sequence-specific DNA binding transcription factor activity, zinc ion binding, nucleic acid binding; INVOLVED IN: in 6 processes; LOCATED IN: nucleus; EXPRESSED IN: 8 plant structures; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347), Zinc finger, C2H2-like (InterPro:IPR015880), Transcription factor jumonji (InterPro:IPR013129), Zinc finger, C2H2-type (InterPro:IPR007087), Transcription factor jumonji, JmjN (InterPro:IPR003349), Zinc finger, C2H2-type/integrase, DNA-binding (InterPro:IPR013087); BEST Arabidopsis thaliana protein match is: Zinc finger (C2H2 type) family protein / transcription factor jumonji (jmj) family protein (TAIR:AT5G04240.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? Relative of Early Flowering 6 (REF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a positive regulator of flowering in an FLC-dependent pathway. REF6 mutants have hyperacetylation of histone H4 at the FLC locus. REF6 interacts with BES1 in a Y2H assay and in vitro. REF6 may play a role in brassinoteroid signaling by affecting histone methylation in the promoters of BR-responsive genes. It is most closely related to the JHDM3 subfamily of JmjN/C proteins.  Source: TAIR, Jun 30, 2015.
Name  ? relative of early flowering 6
  • synonyms:
  • JMJ12,
  • Jumonji domain-containing protein 12

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1 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
BES1 recruits transcriptional regulators ELF6 and REF6 to regulate target gene expression and coordinate brassinosteroids responses with other developmental processes such as control of flowering time. 18467490

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
AT3G48430 0.5kb upstream 0.5kb upstream 6037   true Chr3: 17934756-17940792
AT3G48430 0.5kb upstream 0.5kb upstream 500   false Chr3: 17934756-17935255
AT3G48430 0.5kb downstream 0.5kb downstream 6037   true Chr3: 17935256-17941292
AT3G48430 0.5kb downstream 0.5kb downstream 500   false Chr3: 17940793-17941292
AT3G48430 1.0kb upstream 1.0kb upstream 6537   true Chr3: 17934256-17940792
AT3G48430 1.0kb upstream 1.0kb upstream 1000   false Chr3: 17934256-17935255
AT3G48430 1.0kb downstream 1.0kb downstream 6537   true Chr3: 17935256-17941792
AT3G48430 1.0kb downstream 1.0kb downstream 1000   false Chr3: 17940793-17941792
AT3G48430 3.0kb upstream 3.0kb upstream 8537   true Chr3: 17932256-17940792
AT3G48430 3.0kb upstream 3.0kb upstream 3000   false Chr3: 17932256-17935255
AT3G48430 3.0kb downstream 3.0kb downstream 8537   true Chr3: 17935256-17943792
AT3G48430 3.0kb downstream 3.0kb downstream 3000   false Chr3: 17940793-17943792

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0 Pathways

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 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
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