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Gene : REF6 A. thaliana

DB identifier  ? AT3G48430 Secondary Identifier  ? locus:504955644
Name  ? relative of early flowering 6 Brief Description  relative of early flowering 6
TAIR Computational Description  relative of early flowering 6;(source:Araport11)
TAIR 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. The mRNA is cell-to-cell mobile.
TAIR Short Description  relative of early flowering 6
TAIR Aliases  EIN6, JMJ12, REF6

12 Gene Rifs

1 Organism

31 Publications

0 Synonyms

Genomics

Genome feature

Region: gene ? Length: 5537  
Location: Chr3:17935256-17940792

Gene models - REF6 AT3G48430

? Gene models

Transcripts: 2  Exons: 13  Introns: 11 

Overlapping Features

? Genome features that overlap coordinates of this Gene

12 Child Features

1 Cross References

1 Downstream Intergenic Region

0 Located Features

1 Upstream Intergenic Region

Proteins

Curated comments from UniProt

Type Comment Proteins
REF6_ARATH developmental stage Accumulates during seed development, seed storage, and seed germination stages (PubMed:33037128). In roots, highly expressed in the stele, but barely detectable in the cortex and epidermis (PubMed:30267471). Not observed in lateral root primordia, but detected in both young and mature lateral roots (PubMed:30267471).
REF6_ARATH function Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3, thus acting as a positive regulator of gene expression (PubMed:33107825). Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035, PubMed:33107825). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTG(C/T)T(C/T)-3' (5'-CTCTGYTY-3'), with a preference for hypo-methylated status (e.g. cytosine methylation), to promote the demethylation of H3K27me3 and recruit the chromatin remodeler BRM in order to activate gene expression (PubMed:27111034, PubMed:27111035, PubMed:31048693, PubMed:32257379). Participates in the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035, PubMed:31048693, PubMed:32257379). Bind mostly motifs located in active chromatin states which are depleted for heterochromatic modifications (PubMed:31048693). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760, PubMed:32392578, PubMed:33107825). Stimulates lateral roots formation (e.g. primordium initiation and emergence) via the epigenetic de-repression of PIN genes such as PIN1, PIN3 and PIN7 directly by modulating the methylation status of their loci (PubMed:30267471). Interacts with the NF-Y complex to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). Together with EEN, involved in the epigenetic chromatin-dependent regulatory mechanism that monitors the expression of the essential multifunctional plant stress regulator EIN2 via H3K27me3 repressive histone demethylation and histone variant H2A.Z eviction, thus modulating responses to ethylene (ET), especially during embryogenesis (PubMed:31418686). Eluviates seed dormancy by triggering abscisic acid (ABA) catabolism in seeds via the induction of CYP707A1 and CYP707A3 expression, genes involved in ABA degradation; binds directly to CYP707A1 and CYP707A3 loci to reduce their H3K27me3 levels in developing siliques (PubMed:33037128). Required for systemic acquired resistance (SAR) toward pathogenic bacteria (e.g. Pseudomonas syringae pv tomato DC3000 (avrPto)) (PubMed:32392578). Together with FLD and MSI4/FVE, contributes to dehydroabietinal-dependent (DA, a diterpenoid tricyclic diterpene) activation of flowering ans SAR (PubMed:32392578). Binds to the HSFA2 chromatin region to alleviate H3K27me3 repressive marks and trigger its expression in resp...
REF6_ARATH function Involved in the maintenance of H3K27me1 histone marks on euchromatin in a PRC2-dependent manner, to maintain low-level basal expression of corresponding genes (PubMed:33107825). Together with ELF6, required for H3K27me3 resetting (especially in constitutive heterochromatin within the pericentromeric regions) and transgenerational inheritance of histone marks, thus acting in safeguarding genome and epigenome integrity during sexual reproduction (PubMed:33107825).
REF6_ARATH similarity Belongs to the JHDM3 histone demethylase family.
REF6_ARATH tissue specificity Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues (PubMed:30267471). Detected in inflorescences, stems and siliques. Present in seeds (PubMed:33037128).

2 Proteins

Function

Interactions

Interaction Network

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Expression

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Co-expression

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Data Source: ATTED-II
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LS: LS is a monotonic transformation (negative logit) of MR index. Larger LS indicates stronger co-expression.

 

Homology

Phytozome Homologs

Data Source: Phytozome


0 Homologues

 

Other

9 Data Sets