LXL04_009054 | RubberDandelionOmics

Gene overview

LXL04_009054

Reference: OH-1004 Chr: Chr02 Coordinates: 117007573-117009132 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

945 bp · LXL04_009054|LXL04_009054|OH1004|cDNA

ATGCAGGCTAAAAGACACTTTACAGAAGCTCTTGTTGATGGCAATGTGCTCTTTAAACTTGGAGATGATGGCTATGTTCAGCTTTTCAAGTATACTTATTTGGTTTCTAAATGTAGGCTGAAGAGGGCGAGGACAGCTACATACTTGGTGCCTTATTCAACCTACCAAAACTTTCCACGTGAAGTTGAAGGAGATGGGAATGAATCTGATTTCACTATATCATCTGAATTTGATGTTAATGCAACTGTTAATGAAGATTC...

CDS

Download CDS FASTA

945 bp · LXL04_009054|LXL04_009054|OH1004|CDS

ATGCAGGCTAAAAGACACTTTACAGAAGCTCTTGTTGATGGCAATGTGCTCTTTAAACTTGGAGATGATGGCTATGTTCAGCTTTTCAAGTATACTTATTTGGTTTCTAAATGTAGGCTGAAGAGGGCGAGGACAGCTACATACTTGGTGCCTTATTCAACCTACCAAAACTTTCCACGTGAAGTTGAAGGAGATGGGAATGAATCTGATTTCACTATATCATCTGAATTTGATGTTAATGCAACTGTTAATGAAGATTC...

Protein

Download Protein FASTA

314 aa · LXL04_009054|LXL04_009054|OH1004|PROTEIN

MQAKRHFTEALVDGNVLFKLGDDGYVQLFKYTYLVSKCRLKRARTATYLVPYSTYQNFPREVEGDGNESDFTISSEFDVNATVNEDSTIQNNKISEMRMLDLYSGCGAMSTGLCLGANMANLNLVTVRNESAEDFLQLLKEWEKLCQSYSLIGGGDSQPKEPATIEEDEEVEEEDDNDVDNVEIFEVDQILSICYGDPKEIKKRDLYLKVRWKGYGPEEDTWEPLEGLNDCHDKIKEFVIRLCFAMTINKAQGQTIQNVG...

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_009054`
TK1151 ID	TkA03G395290
OH-1004 ID	LXL04_009054
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 95.172 / OH-1004 87.898 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_009054

Location Chr02:117007573-117009132 (-)

Description Similar to CMT3: DNA (cytosine-5)-methyltransferase CMT3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g69770`	Involved in the CpXpG methylation (e.g. CHG cytosine) and in gene silencing.	Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.2001 · DOI: 10.1126/science.1059745 Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.2001 · DOI: 10.1101/gad.905701 Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.2002 · DOI: 10.1016/s0960-9822(01)00622-4 JMJ24 targets CHROMOMETHYLASE3 for proteasomal degradation in Arabidopsis.2016 · DOI: 10.1101/gad.274647.115

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0226800`	Involved in CpXpG DNA methylation (By similarity).	No verified direct reference in this release
`UniProt: Q5KQL9`	Involved in CpXpG DNA methylation.	No verified direct reference in this release
`Os10g0104900`	Involved in CpXpG DNA methylation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009054 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0010069 zygote asymmetric cytokinesis in embryo sac Biological Process

GO:0032259 methylation Biological Process

GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation Biological Process

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

GO:0141010 transposable element silencing by siRNA-mediated DNA methylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

GO:0003886 DNA (cytosine-5-)-methyltransferase activity Molecular Function

GO:0031625 ubiquitin protein ligase binding Molecular Function

KEGG gene cross-reference

ath:AT1G69770

dosa:Os03g0226800

dosa:Os05g0224800

dosa:Os05g0224900

dosa:Os10g0104900

osa:4338140

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.

Nucleus0.578

Rank 1 · LXL04_009054 · OH-1004

Cytoplasm0.350

Rank 2 · LXL04_009054 · OH-1004

Mitochondrion0.062

Rank 3 · LXL04_009054 · OH-1004

Extracellular0.061

Rank 4 · LXL04_009054 · OH-1004

Cell membrane0.048

Rank 5 · LXL04_009054 · 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.

PF00385.31Chromo185-239 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009054	`PF00385.31`	Chromo	185	239	3.9e-12	46.6

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
`Q94F88`	Arabidopsis thaliana	DNA (cytosine-5)-methyltransferase CMT3	43.556%	Swiss-Prot	moderate database homology
`A0A0P0VUY4`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT1	39.545%	Swiss-Prot	moderate database homology
`Q5KQL9`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT2	44.048%	Swiss-Prot	weak database homology
`C0SQ89`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT3	40.455%	Swiss-Prot	moderate database homology

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