LXL04_003348 | RubberDandelionOmics

Gene overview

LXL04_003348

Reference: OH-1004 Chr: Chr01 Coordinates: 75702078-75709917 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3660 bp · LXL04_003348|LXL04_003348|OH1004|cDNA

ATGTCCAGACTTTGTGAAACCGGCGATGTCGAAGTTGAACAGGCGGGAATACCTCTTTTGAGCAATCCCCCACAAATTTCAAAAACCCTAATTACACCCATActcttttcttttcttcggGATACATTCCATTTTTTTTCTCGATTATCAAGAATTAGCGTATTGATCATGTCGACAACGACCAAGAAGAACGGGAATCCAGTGGAGGCCaaagatgatggtgatggaGGCGAAGAACAAAATGGGCGTTCTGATTCTGA...

CDS

Download CDS FASTA

3660 bp · LXL04_003348|LXL04_003348|OH1004|CDS

ATGTCCAGACTTTGTGAAACCGGCGATGTCGAAGTTGAACAGGCGGGAATACCTCTTTTGAGCAATCCCCCACAAATTTCAAAAACCCTAATTACACCCATACTCTTTTCTTTTCTTCGGGATACATTCCATTTTTTTTCTCGATTATCAAGAATTAGCGTATTGATCATGTCGACAACGACCAAGAAGAACGGGAATCCAGTGGAGGCCAAAGATGATGGTGATGGAGGCGAAGAACAAAATGGGCGTTCTGATTCTGA...

Protein

Download Protein FASTA

1219 aa · LXL04_003348|LXL04_003348|OH1004|PROTEIN

MSRLCETGDVEVEQAGIPLLSNPPQISKTLITPILFSFLRDTFHFFSRLSRISVLIMSTTTKKNGNPVEAKDDGDGGEEQNGRSDSEIDAKEDVQKRRCMKRGREDNNGNTSTGTKYREKKHKPLEHQKQAVSVKVEKEMPMVVLLSSDDEDTFPEETEEGMIDAETDLATSDREGNVTNEEINSKEDKTESERHKRSTRNEGINYAIFNDDDDDVEEDVGKKTQQRSTSKKERMGEKRNHTPSNLNRKDGSKPKYYAKK...

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_003348`
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_003348

Location Chr01:75702078-75709917 (-)

Description Similar to JMJ25: Lysine-specific demethylase JMJ25

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g07610`	Histone demethylase that demethylates 'Lys-9' (H3K9me) of histone H3 with a specific activity for H3K9me2 and H3K9me1.	Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana.2008 · DOI: 10.1126/science.1150987 An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites.2009 · DOI: 10.1038/emboj.2009.59 Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.2010 · DOI: 10.1038/emboj.2010.227 DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns.2012 · DOI: 10.1038/emboj.2012.141 IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis.2012 · DOI: 10.1093/nar/gks647 SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1.2014 · DOI: 10.1371/journal.pone.0084687 Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development.2016 · DOI: 10.1242/dev.129932 Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis.2021 · DOI: 10.1038/s41467-021-22995-3 The arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation.2025 · DOI: 10.1093/nar/gkaf985
`At1g11950`	May function as histone H3 lysine demethylase and be involved in regulation of gene expression.	No verified direct reference in this release
`At1g62310`	May function as histone H3 lysine demethylase and be involved in regulation of gene expression.	No verified direct reference in this release
`At4g00990`	Histone demethylase that demethylates 'Lys-9' (H3K9me) of histone H3 with a specific activity for H3K9me1 and H3K9me2.	JMJ27, an Arabidopsis H3K9 histone demethylase, modulates defense against Pseudomonas syringae and flowering time.2017 · DOI: 10.1111/tpj.13623 JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis.2021 · DOI: 10.1111/nph.17593
`At1g09060`	May bind histone H3 but appears to lack demethylase activity because it cannot bind Fe²⁺.	JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis.2015 · DOI: 10.1111/tpj.12924 JMJ24 targets CHROMOMETHYLASE3 for proteasomal degradation in Arabidopsis.2016 · DOI: 10.1101/gad.274647.115 A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis.2016 · DOI: 10.1104/pp.15.01688

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003348 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009555 pollen development Biological Process

GO:0009617 response to bacterium Biological Process

GO:0009908 flower development Biological Process

GO:0010440 stomatal lineage progression Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0042742 defense response to bacterium Biological Process

KEGG gene cross-reference

ath:AT1G09060

ath:AT1G11950

ath:AT1G62310

ath:AT3G07610

ath:AT4G00990

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.

Nucleus0.914

Rank 1 · LXL04_003348 · OH-1004

Cytoplasm0.104

Rank 2 · LXL04_003348 · OH-1004

Cell membrane0.051

Rank 3 · LXL04_003348 · OH-1004

Endoplasmic reticulum0.026

Rank 4 · LXL04_003348 · OH-1004

Plastid0.015

Rank 5 · LXL04_003348 · 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.

PF10497.15zf-4CXXC_R1273-335 aa

PF02373.29JmjC831-927 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003348	`PF10497.15`	zf-4CXXC_R1	273	335	3.5e-06	27.8
LXL04_003348	`PF02373.29`	JmjC	831	927	2.7e-15	57.5

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
`Q9SSE9`	Arabidopsis thaliana	Lysine-specific demethylase JMJ25	47.553%	Swiss-Prot	moderate database homology
`C0SUU8`	Arabidopsis thaliana	Lysine-specific demethylase JMJ26	48.515%	Swiss-Prot	moderate database homology
`C0SV12`	Arabidopsis thaliana	Lysine-specific demethylase JMJ29	47.908%	Swiss-Prot	moderate database homology
`Q8VYB9`	Arabidopsis thaliana	Lysine-specific demethylase JMJ27	43.257%	Swiss-Prot	moderate database homology
`F4HZD1`	Arabidopsis thaliana	E3 ubiquitin-protein ligase JMJ24	34.417%	Swiss-Prot	moderate database homology

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