LXL04_032350 | RubberDandelionOmics

Gene overview

LXL04_032350

Reference: OH-1004 Chr: Chr07 Coordinates: 21111454-21118985 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4636 bp · LXL04_032350|LXL04_032350|OH1004|cDNA

ATGGCCAGCAAAGATGCTACTCCATCCACCAATGAACCTTCAAAATCCGCTTTGCAAGTGCAACCAAAGTCGGCACCTTCCGAAACAGAGTAACCAGAACTTGATCCCATCAAGTATTCAAGGAAAAGGCAAAAGACTGAGAAATCAGCTTCACCGAAGGTTGGAAATGGGGTTAACCAACAGCAGAAATGGTGCCATCAATGCCGGACCAAAAGAGATCGCGTGGTACCCAAATATATCCGAAGAGGAGTTTACCAAGG...

CDS

Download CDS FASTA

4623 bp · LXL04_032350|LXL04_032350|OH1004|CDS

ATGCTACTCCATCCACCAATGAACCTTCAAAATCCGCTTTGCAAGTGCAACCAAAGTCGGCACCTTCCGAAACAGAGTAACCAGAACTTGATCCCATCAAGTATTCAAGGAAAAGGCAAAAGACTGAGAAATCAGCTTCACCGAAGGTTGGAAATGGGGTTAACCAACAGCAGAAATGGTGCCATCAATGCCGGACCAAAAGAGATCGCGTGGTACCCAAATATATCCGAAGAGGAGTTTACCAAGGCTTGCCCTTTTTG...

Protein

Download Protein FASTA

1540 aa · LXL04_032350|LXL04_032350|OH1004|PROTEIN

MLLHPPMNLQNPLCKCNQSRHLPKQSNQNLIPSSIQGKGKRLRNQLHRRLEMGLTNSRNGAINAGPKEIAWYPNISEEEFTKACPFCLNKCNCKACLRAFSPKFIQGYSCSKSDKIRYSKLIIQKVLPFVRRLHEDQLMEKLIEASVKGLPRSELQLQDAECEVDDNIFCDKCGAYVYDFYRSCACGYDVCLVCTQDLHKGKKLCTNGGIHCPPIEIGGCNEGVLELKHIMPVDWVENMLEKAQRIYKINTRDDNDNDNN...

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_032350`
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_032350

Location Chr07:21111454-21118985 (+)

Description Similar to CCR4-6: Carbon catabolite repressor protein 4 homolog 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At5g11350`	Acts as a catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover.	No verified direct reference in this release
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032350 · 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:0009555 pollen development Biological Process

GO:0009908 flower development Biological Process

GO:0010440 stomatal lineage progression Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0048366 leaf development Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

GO:2000039 regulation of trichome morphogenesis Biological Process

GO:0000118 histone deacetylase complex Cellular Component

GO:0000785 chromatin Cellular Component

KEGG gene cross-reference

ath:AT1G11950

ath:AT1G62310

ath:AT3G07610

ath:AT5G11350

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.

Nucleus0.527

Rank 1 · LXL04_032350 · OH-1004

Cytoplasm0.333

Rank 2 · LXL04_032350 · OH-1004

Cell membrane0.115

Rank 3 · LXL04_032350 · OH-1004

Endoplasmic reticulum0.070

Rank 4 · LXL04_032350 · OH-1004

Plastid0.069

Rank 5 · LXL04_032350 · 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.

PF02373.29JmjC493-561 aa

PF03372.30Exo_endo_phos1070-1292 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032350	`PF02373.29`	JmjC	493	561	1.4e-10	42.4
LXL04_032350	`PF03372.30`	Exo_endo_phos	1070	1292	3.3e-16	60.4

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
`C0SUU8`	Arabidopsis thaliana	Lysine-specific demethylase JMJ26	37.558%	Swiss-Prot	weak database homology
`C0SV12`	Arabidopsis thaliana	Lysine-specific demethylase JMJ29	37.774%	Swiss-Prot	weak database homology
`Q8VYU4`	Arabidopsis thaliana	Carbon catabolite repressor protein 4 homolog 6	48.509%	Swiss-Prot	weak database homology
`Q9SSE9`	Arabidopsis thaliana	Lysine-specific demethylase JMJ25	40.257%	Swiss-Prot	weak database homology
`Q8VYB9`	Arabidopsis thaliana	Lysine-specific demethylase JMJ27	35.622%	Swiss-Prot	weak database homology

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