LXL04_012742 | RubberDandelionOmics

Gene overview

LXL04_012742

Reference: OH-1004 Chr: Chr03 Coordinates: 18064907-18068909 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3195 bp · LXL04_012742|LXL04_012742|OH1004|cDNA

ATGATGGGGACAGAACTCATCAGACATCATGTGAAAGAAGAAACCATGGATATTCCATCAATTCCACCTGGATTTGAATCGATCACAGCTTTTTCTTTAAAAAGAGTTGAAGATACCAAAGTTTCTGTCCCTGTGACTTCTGAACAAAAACCACATCCAGTCAAAAACGAATCAGTGATTGAACAAAGTGATGATGAAAAGATTAAAAGGTCTGTTAGACCTAGACCTTGGATAAACTATGGCAAATTTGATAGCAATTC...

CDS

Download CDS FASTA

3195 bp · LXL04_012742|LXL04_012742|OH1004|CDS

ATGATGGGGACAGAACTCATCAGACATCATGTGAAAGAAGAAACCATGGATATTCCATCAATTCCACCTGGATTTGAATCGATCACAGCTTTTTCTTTAAAAAGAGTTGAAGATACCAAAGTTTCTGTCCCTGTGACTTCTGAACAAAAACCACATCCAGTCAAAAACGAATCAGTGATTGAACAAAGTGATGATGAAAAGATTAAAAGGTCTGTTAGACCTAGACCTTGGATAAACTATGGCAAATTTGATAGCAATTC...

Protein

Download Protein FASTA

1064 aa · LXL04_012742|LXL04_012742|OH1004|PROTEIN

MMGTELIRHHVKEETMDIPSIPPGFESITAFSLKRVEDTKVSVPVTSEQKPHPVKNESVIEQSDDEKIKRSVRPRPWINYGKFDSNSGDESESVQNQTSSNQITKGVIRGCEECSNCQKVIAKWRPEEARIPDLVEAPVFYPTEEEFEDTLKYISSIREKAESYGICRIVPPSSWKPPCPLKEKTVWENSTFATRIQRVDKLQNRDSLSKMLLAPVYHKKAKKRRCVKTEFDQKTSHGSDPVDPMVPAPGFGFEPGPLFT...

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_012742`
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_012742

Location Chr03:18064907-18068909 (+)

Description Similar to JMJ16: Putative lysine-specific demethylase JMJ16

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08620`	Functions as a histone H3 'Lys-4' (H3K4me) demethylase involved in the negative regulation of gene expression.	The Histone H3K4 Demethylase JMJ16 Represses Leaf Senescence in Arabidopsis.2019 · DOI: 10.1105/tpc.18.00693 Cell-type-dependent histone demethylase specificity promotes meiotic chromosome condensation in Arabidopsis.2020 · DOI: 10.1038/s41477-020-0697-0
`At4g20400`	Transcriptional repressor.	Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis.2009 · DOI: 10.1371/journal.pone.0008033 A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis.2010 · DOI: 10.1111/j.1365-313x.2010.04182.x JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis.2010 · DOI: 10.1101/gad.579910 Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation.2010 · DOI: 10.1038/embor.2010.158 Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14.2015 · DOI: 10.1093/nar/gku1382 C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association.2015 · DOI: 10.1038/celldisc.2015.3 Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases.2018 · DOI: 10.1105/tpc.17.00666 Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis.2019 · DOI: 10.1186/s13059-019-1777-1 JMJ14 encoded H3K4 demethylase modulates immune responses by regulating defence gene expression and pipecolic acid levels.2020 · DOI: 10.1111/nph.16270 Conditional effects of the epigenetic regulator JUMONJI 14 in Arabidopsis root growth.2019 · DOI: 10.1242/dev.183905 Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis.2021 · DOI: 10.1038/s41467-021-22995-3
`At1g30810`	Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a specific activity for H3K4me3 and H3K4me2.	A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression.2012 · DOI: 10.1371/journal.pgen.1002664
`At2g34880`	Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a specific activity for H3K4me3.	Overexpression of a histone H3K4 demethylase, JMJ15, accelerates flowering time in Arabidopsis.2012 · DOI: 10.1007/s00299-012-1249-5 Over-expression of histone H3K4 demethylase gene JMJ15 enhances salt tolerance in Arabidopsis.2014 · DOI: 10.3389/fpls.2014.00290

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0196500`	Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a specific activity for H3K4me3, H3K4me2 and H3K4me1.	Control of transposon activity by a histone H3K4 demethylase in rice.2013 · DOI: 10.1073/pnas.1217020110 Structural basis of a histone H3 lysine 4 demethylase required for stem elongation in rice.2013 · DOI: 10.1371/journal.pgen.1003239

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012742 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009626 plant-type hypersensitive response Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0009908 flower development Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010032 meiotic chromosome condensation Biological Process

GO:0010082 regulation of root meristem growth Biological Process

GO:0010468 regulation of gene expression Biological Process

KEGG gene cross-reference

ath:AT1G08620

ath:AT4G20400

dosa:Os05g0196500

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.

Nucleus0.932

Rank 1 · LXL04_012742 · OH-1004

Cytoplasm0.136

Rank 2 · LXL04_012742 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_012742 · OH-1004

Mitochondrion0.025

Rank 4 · LXL04_012742 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_012742 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF02375.24JmjN138-171 aa

PF02373.29JmjC373-489 aa

PF02928.22zf-C5HC2596-647 aa

PF05964.20FYRN853-893 aa

PF05965.20FYRC898-982 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012742	`PF02375.24`	JmjN	138	171	1.6e-17	63.7
LXL04_012742	`PF02373.29`	JmjC	373	489	1.5e-45	155.1
LXL04_012742	`PF02928.22`	zf-C5HC2	596	647	1.7e-14	54.5
LXL04_012742	`PF05964.20`	FYRN	853	893	5.8e-10	39.3
LXL04_012742	`PF05965.20`	FYRC	898	982	4.6e-19	69.1

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
`C0SUT9`	Arabidopsis thaliana	Putative lysine-specific demethylase JMJ16	65.014%	Swiss-Prot	moderate database homology
`Q8GUI6`	Arabidopsis thaliana	Lysine-specific demethylase JMJ14	45.000%	Swiss-Prot	moderate database homology
`F4I6G4`	Arabidopsis thaliana	Lysine-specific demethylase JMJ18	56.649%	Swiss-Prot	moderate database homology
`O64752`	Arabidopsis thaliana	Lysine-specific demethylase JMJ15	54.966%	Swiss-Prot	moderate database homology
`Q53WJ1`	Oryza sativa subsp. japonica	Lysine-specific demethylase JMJ703	59.854%	Swiss-Prot	moderate database homology

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