LXL04_012568 | RubberDandelionOmics

Gene overview

LXL04_012568

Reference: OH-1004 Chr: Chr03 Coordinates: 14766711-14770482 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3366 bp · LXL04_012568|LXL04_012568|OH1004|cDNA

ATGAGGGACGTAGAAATCCCCAATTGGCTCGATAAATTGCCATTGGCACCGGTATTTTACCCAACCGAGACAGAATTTGCAGACCCAATTGCATACATCTCCAAGATTGAGAAAGAAGCCGGTGCATTTGGTATATGTAAAGTAATCCCACCCTTGCCAAAACCTTCCAAAAAGTACGTAGTAGGTAACCTAAATAAGTCCCTCCTGAAGTCTCCAGAATTGGGGAACGATGTAAAATTGAATAACATAGAAACAGTCAA...

CDS

Download CDS FASTA

3366 bp · LXL04_012568|LXL04_012568|OH1004|CDS

ATGAGGGACGTAGAAATCCCCAATTGGCTCGATAAATTGCCATTGGCACCGGTATTTTACCCAACCGAGACAGAATTTGCAGACCCAATTGCATACATCTCCAAGATTGAGAAAGAAGCCGGTGCATTTGGTATATGTAAAGTAATCCCACCCTTGCCAAAACCTTCCAAAAAGTACGTAGTAGGTAACCTAAATAAGTCCCTCCTGAAGTCTCCAGAATTGGGGAACGATGTAAAATTGAATAACATAGAAACAGTCAA...

Protein

Download Protein FASTA

1121 aa · LXL04_012568|LXL04_012568|OH1004|PROTEIN

MRDVEIPNWLDKLPLAPVFYPTETEFADPIAYISKIEKEAGAFGICKVIPPLPKPSKKYVVGNLNKSLLKSPELGNDVKLNNIETVNDGEIRAVFTTRHQELGQSSGKRTKEVGIGTSHPIPLNRQVWQSGEIYTLEQFESKSKNFARSQLSSIKEVSSLAIESLFWKAACEKPIYIEYANDVPGSGFGEPVGPSRLVHRHTRRRRTFDRNNKEDKSNDNENQKGESIRCSGSPSSSSSSSKVDMLKKDTNSNTNSSSML...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_012568`
TK1151 ID	TkA02G552670
OH-1004 ID	LXL04_012568
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_012568

Location Chr03:14766711-14770482 (+)

Description Similar to ELF6: Probable lysine-specific demethylase ELF6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g04240`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3, thus acting as a positive regulator of gene expression.	Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time.2004 · DOI: 10.1105/tpc.104.025353 Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis.2008 · DOI: 10.1073/pnas.0802254105 Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis.2009 · DOI: 10.1371/journal.pone.0008033 Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.2014 · DOI: 10.1038/nature13722 A new role for histone demethylases in the maintenance of plant genome integrity.2020 · DOI: 10.7554/elife.58533
`At3g48430`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3, thus acting as a positive regulator of gene expression.	Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time.2004 · DOI: 10.1105/tpc.104.025353 Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis.2008 · DOI: 10.1073/pnas.0802254105 Arabidopsis REF6 is a histone H3 lysine 27 demethylase.2011 · DOI: 10.1038/ng.854 Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis.2014 · DOI: 10.1038/ncomms5601 Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.2016 · DOI: 10.1038/ng.3555 REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.2016 · DOI: 10.1038/ng.3556 An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis.2019 · DOI: 10.1038/s41422-019-0145-8 DNA methylation repels targeting of Arabidopsis REF6.2019 · DOI: 10.1038/s41467-019-10026-1 Epigenetic silencing of a multifunctional plant stress regulator.2019 · DOI: 10.7554/elife.47835 Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.2020 · DOI: 10.1038/s41421-020-0150-6 Dehydroabietinal promotes flowering time and plant defense in Arabidopsis via the autonomous pathway genes FLOWERING LOCUS D, FVE, and RELATIVE OF EARLY FLOWERING 6.2020 · DOI: 10.1093/jxb/eraa232 The H3K27me3 Demethylase RELATIVE OF EARLY FLOWERING6 Suppresses Seed Dormancy by Inducing Abscisic Acid Catabolism.2020 · DOI: 10.1104/pp.20.01255 A new role for histone demethylases in the maintenance of plant genome integrity.2020 · DOI: 10.7554/elife.58533
`At5g46910`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and involved in the regulation of gene expression.	The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.2019 · DOI: 10.1038/s41467-019-09310-x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0151300`	Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3.	Se14, encoding a JmjC domain-containing protein, plays key roles in long-day suppression of rice flowering through the demethylation of H3K4me3 of RFT1.2014 · DOI: 10.1371/journal.pone.0096064
`Os01g0907400`	Histone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and H3K27me2.	Jumonji C domain protein JMJ705-mediated removal of histone H3 lysine 27 trimethylation is involved in defense-related gene activation in rice.2013 · DOI: 10.1105/tpc.113.118802

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012568 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009908 flower development Biological Process

GO:0010219 regulation of vernalization response Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

GO:0048577 negative regulation of short-day photoperiodism, flowering Biological Process

KEGG gene cross-reference

ath:AT5G04240

dosa:Os03g0151300

osa:9268736

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.948

Rank 1 · LXL04_012568 · OH-1004

Cytoplasm0.106

Rank 2 · LXL04_012568 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_012568 · OH-1004

Mitochondrion0.015

Rank 4 · LXL04_012568 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_012568 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF02375.24JmjN17-50 aa

PF02373.29JmjC310-428 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012568	`PF02375.24`	JmjN	17	50	2.8e-16	59.8
LXL04_012568	`PF02373.29`	JmjC	310	428	1.3e-35	123.0

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

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Protein	Organism	Description	Identity	Database	Confidence
`Q6BDA0`	Arabidopsis thaliana	Lysine-specific demethylase ELF6	55.882%	Swiss-Prot	strong database homology
`Q9STM3`	Arabidopsis thaliana	Lysine-specific demethylase REF6	45.055%	Swiss-Prot	weak database homology
`F4KIX0`	Arabidopsis thaliana	Lysine-specific demethylase JMJ13	47.264%	Swiss-Prot	weak database homology
`Q10RP4`	Oryza sativa subsp. japonica	Probable lysine-specific demethylase SE14	50.310%	Swiss-Prot	moderate database homology
`Q5N712`	Oryza sativa subsp. japonica	Lysine-specific demethylase JMJ705	47.851%	Swiss-Prot	weak database homology

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