LXL04_014337 | RubberDandelionOmics

Gene overview

LXL04_014337

Reference: OH-1004 Chr: Chr03 Coordinates: 46550694-46552396 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

948 bp · LXL04_014337|LXL04_014337|OH1004|cDNA

ATGGTGTTTTTTTGGAGCGTTCTTGTTTGCAGCGACGTCGGGAGTTCATCCGAGAGCTTCGCTTCTTCTTTCTATCATCGAGAGTTCATCGAGGGGGGAAAAGCTCGTAGGAAGTCGGAGGTTGCTGGTCAGAACTGTGTGTATGCTCGACCGAGAAAGAAAGGGCTCCGGCGGATAGCACTCGGCGATTTCAGCGAGCTTCCGGCGACTGTAGAAGGGAACCGTGGGTTTAGTTATACTTTCCGGGCAGAACTCATCAG...

CDS

Download CDS FASTA

948 bp · LXL04_014337|LXL04_014337|OH1004|CDS

ATGGTGTTTTTTTGGAGCGTTCTTGTTTGCAGCGACGTCGGGAGTTCATCCGAGAGCTTCGCTTCTTCTTTCTATCATCGAGAGTTCATCGAGGGGGGAAAAGCTCGTAGGAAGTCGGAGGTTGCTGGTCAGAACTGTGTGTATGCTCGACCGAGAAAGAAAGGGCTCCGGCGGATAGCACTCGGCGATTTCAGCGAGCTTCCGGCGACTGTAGAAGGGAACCGTGGGTTTAGTTATACTTTCCGGGCAGAACTCATCAG...

Protein

Download Protein FASTA

315 aa · LXL04_014337|LXL04_014337|OH1004|PROTEIN

MVFFWSVLVCSDVGSSSESFASSFYHREFIEGGKARRKSEVAGQNCVYARPRKKGLRRIALGDFSELPATVEGNRGFSYTFRAELIRHHVKEETMDNPSIPPGFESITAFSLKRVEDTKVSVPVTSEQKPHPVKNESVIEQSDDEKIKRSVRPRPWINYGKFDSNSGDESESVQNQTSSNQITKGVIRGCEECSNCQKVIAKWRPEEARIPDLVDAPVFYPTEEEFEDTLKYISSISGVLVPWLYIGMCFSSFCWMLLRS...

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_014337`
TK1151 ID	TkA08G026890
OH-1004 ID	LXL04_014337
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	98.200
Protein coverage (%)	TK1151 93.355 / OH-1004 89.206 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_014337

Location Chr03:46550694-46552396 (-)

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
`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
`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

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_014337 · 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:0009555 pollen development Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010032 meiotic chromosome condensation Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0040010 positive regulation of growth rate Biological Process

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

GO:0045892 negative regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT1G08620

ath:AT1G30810

ath:AT2G34880

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.

Nucleus0.663

Rank 1 · LXL04_014337 · OH-1004

Cytoplasm0.298

Rank 2 · LXL04_014337 · OH-1004

Cell membrane0.067

Rank 3 · LXL04_014337 · OH-1004

Mitochondrion0.051

Rank 4 · LXL04_014337 · OH-1004

Endoplasmic reticulum0.051

Rank 5 · LXL04_014337 · 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.

PF02375.24JmjN217-237 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014337	`PF02375.24`	JmjN	217	237	5.3e-09	36.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`C0SUT9`	Arabidopsis thaliana	Putative lysine-specific demethylase JMJ16	49.708%	Swiss-Prot	weak database homology
`O64752`	Arabidopsis thaliana	Lysine-specific demethylase JMJ15	58.974%	Swiss-Prot	weak database homology
`F4I6G4`	Arabidopsis thaliana	Lysine-specific demethylase JMJ18	37.037%	Swiss-Prot	weak database homology
`Q53WJ1`	Oryza sativa subsp. japonica	Lysine-specific demethylase JMJ703	43.103%	Swiss-Prot	weak database homology

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