LXL04_026108 | RubberDandelionOmics

Gene overview

LXL04_026108

Reference: OH-1004 Chr: Chr05 Coordinates: 121023339-121026178 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2131 bp · LXL04_026108|LXL04_026108|OH1004|cDNA

GGGGGAAGGAAGGGTTTGTTTCTCCAGAGAAGCTAAGCTTGAGTTTTTGAAGCACAAAAGGCTTCAACGAATGAAAACAGCCACAATGAATGACACTGCACATGTCACTAATCTGATGACAAGAAGCAGTGGAGATTCCTTAAGAGATCCCGCATCCTGTGGTCTGAGATCATTCAGAACTCCATATCCACATCCACAATCTGGCTATGGTCTGAATGAGTCAGACACAATATCAAAACAAAAGATTGACAAATTTGACA...

CDS

Download CDS FASTA

2085 bp · LXL04_026108|LXL04_026108|OH1004|CDS

TTGAAGCACAAAAGGCTTCAACGAATGAAAACAGCCACAATGAATGACACTGCACATGTCACTAATCTGATGACAAGAAGCAGTGGAGATTCCTTAAGAGATCCCGCATCCTGTGGTCTGAGATCATTCAGAACTCCATATCCACATCCACAATCTGGCTATGGTCTGAATGAGTCAGACACAATATCAAAACAAAAGATTGACAAATTTGACACAACTGATCTTGATTGGACAGATAACATGCCAGAATGTCCAGTATA...

Protein

Download Protein FASTA

694 aa · LXL04_026108|LXL04_026108|OH1004|PROTEIN

MKHKRLQRMKTATMNDTAHVTNLMTRSSGDSLRDPASCGLRSFRTPYPHPQSGYGLNESDTISKQKIDKFDTTDLDWTDNMPECPVYYPSKEEFEDPLAYLQKIAPEASKYGICKIVSPLNASVPAGIVLMKEKAGFRFTTRVQPLRLAEWNTEDKVTFFLSGRNYTFRDFEKMANKVFARRYYSAGCLPATYLEKEFWQEIASGKTESVEYACDVDGSAFSSAPSDQLGQSKWNLKKVARLSRSILRLLETTIPGVTEP...

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_026108`
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_026108

Location Chr05:121023339-121026178 (+)

Description Similar to JMJ706: Lysine-specific demethylase JMJ706

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os10g0577600`	Histone demethylase that demethylates 'Lys-9' (H3K9me) of histone H3 with a specific activity for H3K9me3 and H3K9me2.	Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development.2008 · DOI: 10.1073/pnas.0805901105
`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_026108 · 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:0009266 response to temperature stimulus 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

KEGG gene cross-reference

ath:AT3G48430

ath:AT5G46910

dosa:Os01g0907400

dosa:Os03g0151300

dosa:Os10g0577600

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.

Nucleus0.909

Rank 1 · LXL04_026108 · OH-1004

Cytoplasm0.106

Rank 2 · LXL04_026108 · OH-1004

Cell membrane0.039

Rank 3 · LXL04_026108 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_026108 · OH-1004

Plastid0.021

Rank 5 · LXL04_026108 · 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.

PF02375.24JmjN85-117 aa

PF02373.29JmjC261-384 aa

PF02928.22zf-C5HC2476-524 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026108	`PF02375.24`	JmjN	85	117	4.1e-17	62.4
LXL04_026108	`PF02373.29`	JmjC	261	384	1.6e-38	132.3
LXL04_026108	`PF02928.22`	zf-C5HC2	476	524	1.1e-07	32.8

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
`F4KIX0`	Arabidopsis thaliana	Lysine-specific demethylase JMJ13	61.264%	Swiss-Prot	strong database homology
`Q9STM3`	Arabidopsis thaliana	Lysine-specific demethylase REF6	33.779%	Swiss-Prot	moderate database homology
`Q336N8`	Oryza sativa subsp. japonica	Lysine-specific demethylase JMJ706	61.243%	Swiss-Prot	strong database homology
`Q10RP4`	Oryza sativa subsp. japonica	Probable lysine-specific demethylase SE14	37.879%	Swiss-Prot	weak database homology
`Q5N712`	Oryza sativa subsp. japonica	Lysine-specific demethylase JMJ705	39.744%	Swiss-Prot	moderate database homology

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