LXL04_004774 | RubberDandelionOmics

Gene overview

LXL04_004774

Reference: OH-1004 Chr: Chr01 Coordinates: 145801244-145805887 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2484 bp · LXL04_004774|LXL04_004774|OH1004|cDNA

ATGGCGAAAGGAGTTAAGAGAGATATGAAGCAGTCAGAGGAAGCCATTGATTCGTCGGTACCTACTTCCGATTCCAAACAATCACCTCCGTCAAAGAAATCCAAAGTCTCTTCAGCCACCGCCGCAGCCGAAGACGACACCCGTTTCACCGGAAAACCAGTTCCGGCTGACCAAGCCAGAGAAAAATGGCCTCATCGCTACCAATCCAAGAGCAGAGTCGTTATAGCTTCTTCAAACGGTGAACTGAATGGAAAGGAGAT...

CDS

Download CDS FASTA

2484 bp · LXL04_004774|LXL04_004774|OH1004|CDS

ATGGCGAAAGGAGTTAAGAGAGATATGAAGCAGTCAGAGGAAGCCATTGATTCGTCGGTACCTACTTCCGATTCCAAACAATCACCTCCGTCAAAGAAATCCAAAGTCTCTTCAGCCACCGCCGCAGCCGAAGACGACACCCGTTTCACCGGAAAACCAGTTCCGGCTGACCAAGCCAGAGAAAAATGGCCTCATCGCTACCAATCCAAGAGCAGAGTCGTTATAGCTTCTTCAAACGGTGAACTGAATGGAAAGGAGAT...

Protein

Download Protein FASTA

827 aa · LXL04_004774|LXL04_004774|OH1004|PROTEIN

MAKGVKRDMKQSEEAIDSSVPTSDSKQSPPSKKSKVSSATAAAEDDTRFTGKPVPADQAREKWPHRYQSKSRVVIASSNGELNGKEIIQAKCHYTKAVVDGVAFDLYDDAFVKAEEGHPDFIARIVEMFETVDKELYCSAQWFFRAEDTVIKSQAHLIDKRRVFYSEMKDDNPLDSILSKVKIVQLPPNVDLAEKEKALSSYDLYYDMQYSMPVTFTTLHKESLITESDESSVISDDDCLNVVVEKTNKKYANKTKINKS...

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_004774`
TK1151 ID	TkA01G113090
OH-1004 ID	LXL04_004774
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_004774

Location Chr01:145801244-145805887 (+)

Description Similar to MET2A: DNA (cytosine-5)-methyltransferase 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

No hit for this species in the current source table.

Rice

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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004774 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0032259 methylation Biological Process

GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation 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:0051720 DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates Molecular Function

KEGG gene cross-reference

dosa:Os03g0226800

dosa:Os10g0104900

zma:542060

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.

Nucleus0.908

Rank 1 · LXL04_004774 · OH-1004

Cytoplasm0.138

Rank 2 · LXL04_004774 · OH-1004

Mitochondrion0.031

Rank 3 · LXL04_004774 · OH-1004

Cell membrane0.029

Rank 4 · LXL04_004774 · OH-1004

Endoplasmic reticulum0.017

Rank 5 · LXL04_004774 · 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.

PF01426.25BAH112-211 aa

PF00385.31Chromo374-428 aa

PF00145.24DNA_methylase437-791 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004774	`PF01426.25`	BAH	112	211	1.2e-12	48.5
LXL04_004774	`PF00385.31`	Chromo	374	428	3.3e-10	40.4
LXL04_004774	`PF00145.24`	DNA_methylase	437	791	3.5e-39	135.9

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
`C0SQ89`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT3	52.086%	Swiss-Prot	strong database homology
`A0A0P0VUY4`	Oryza sativa subsp. japonica	DNA (cytosine-5)-methyltransferase CMT1	51.075%	Swiss-Prot	strong database homology

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