LXL04_031920 | RubberDandelionOmics

Gene overview

LXL04_031920

Reference: OH-1004 Chr: Chr07 Coordinates: 13288163-13292989 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3318 bp · LXL04_031920|LXL04_031920|OH1004|cDNA

ATGGGTGAAGAGGTGTTTCCATGGTTGAAATCTCTGCCATTAGCACCAGAGTACCACCCAACCCTAGCCGAGTTTCAGGATCCTATTTCGTATATTTTCAAAATCGAAAAAGATGCTTCCAATTATGGAATCTGTAAAATCATCCCACCTGTCTCCACTTCTCCCAAAAAAACCATAACTGCGAACCTAAACCAGTCTCTGTCATCCCAAAGCCCTGATTCATCACCTACATTCACCACCAGGCAGCAGCAGATCGGTTT...

CDS

Download CDS FASTA

3318 bp · LXL04_031920|LXL04_031920|OH1004|CDS

ATGGGTGAAGAGGTGTTTCCATGGTTGAAATCTCTGCCATTAGCACCAGAGTACCACCCAACCCTAGCCGAGTTTCAGGATCCTATTTCGTATATTTTCAAAATCGAAAAAGATGCTTCCAATTATGGAATCTGTAAAATCATCCCACCTGTCTCCACTTCTCCCAAAAAAACCATAACTGCGAACCTAAACCAGTCTCTGTCATCCCAAAGCCCTGATTCATCACCTACATTCACCACCAGGCAGCAGCAGATCGGTTT...

Protein

Download Protein FASTA

1105 aa · LXL04_031920|LXL04_031920|OH1004|PROTEIN

MGEEVFPWLKSLPLAPEYHPTLAEFQDPISYIFKIEKDASNYGICKIIPPVSTSPKKTITANLNQSLSSQSPDSSPTFTTRQQQIGFCPRNHERPVQKSVWESGEYYTLPQFESKAKTFEKSYKKKRSNPTTALTALEVETLYWKAQMGKPFSIEYANDMPGTAFDQTVGENGGGKQGTKEINDVMTVEGSQWNMNVASRAKGSLLTFMKDELPGVNSPMVYISMLFSWFAWHVEDHDFHSLNYMHMGASKTWYGVPKDA...

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_031920`
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_031920

Location Chr07:13288163-13292989 (+)

Description Similar to REF6: Lysine-specific demethylase REF6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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
`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
`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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031920 · 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:0006952 defense response Biological Process

GO:0009408 response to heat Biological Process

GO:0009612 response to mechanical stimulus Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009741 response to brassinosteroid Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

KEGG gene cross-reference

ath:AT3G48430

dosa:Os01g0907400

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.

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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.

Nucleus0.906

Rank 1 · LXL04_031920 · OH-1004

Cytoplasm0.130

Rank 2 · LXL04_031920 · OH-1004

Cell membrane0.036

Rank 3 · LXL04_031920 · OH-1004

Endoplasmic reticulum0.021

Rank 4 · LXL04_031920 · OH-1004

Mitochondrion0.021

Rank 5 · LXL04_031920 · 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.

PF02375.24JmjN16-49 aa

PF02373.29JmjC221-338 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031920	`PF02375.24`	JmjN	16	49	1.6e-13	50.9
LXL04_031920	`PF02373.29`	JmjC	221	338	1.6e-38	132.4

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
`Q9STM3`	Arabidopsis thaliana	Lysine-specific demethylase REF6	46.968%	Swiss-Prot	moderate database homology
`Q6BDA0`	Arabidopsis thaliana	Lysine-specific demethylase ELF6	35.766%	Swiss-Prot	moderate database homology
`F4KIX0`	Arabidopsis thaliana	Lysine-specific demethylase JMJ13	40.945%	Swiss-Prot	weak database homology
`Q5N712`	Oryza sativa subsp. japonica	Lysine-specific demethylase JMJ705	48.298%	Swiss-Prot	moderate database homology
`Q10RP4`	Oryza sativa subsp. japonica	Probable lysine-specific demethylase SE14	37.681%	Swiss-Prot	moderate database homology

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