LXL04_011821 | RubberDandelionOmics

Gene overview

LXL04_011821

Reference: OH-1004 Chr: Chr03 Coordinates: 874823-876398 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1194 bp · LXL04_011821|LXL04_011821|OH1004|cDNA

ATGGCAGTACATGGGAAGCTGTTAAATGTACAAGTTCCTTCACCAACCAACTATGGTGGTCAGAATGGGTCAGCATCACCTAATGTTGGTAAGGCCATGGATGCATTCTCTCAGGCAGAATCACTTGTCTCTTCTTCAAAGAAACTTGAGAATGAAGTGGTATTGCTAGGACAGAATATAAAAGATCATGAAGAAAACATTGAATATCTAAAGACTCGTATAAGCAGCTTGGATGACCAGATTACAGATATTCAAGTAAC...

CDS

Download CDS FASTA

1194 bp · LXL04_011821|LXL04_011821|OH1004|CDS

ATGGCAGTACATGGGAAGCTGTTAAATGTACAAGTTCCTTCACCAACCAACTATGGTGGTCAGAATGGGTCAGCATCACCTAATGTTGGTAAGGCCATGGATGCATTCTCTCAGGCAGAATCACTTGTCTCTTCTTCAAAGAAACTTGAGAATGAAGTGGTATTGCTAGGACAGAATATAAAAGATCATGAAGAAAACATTGAATATCTAAAGACTCGTATAAGCAGCTTGGATGACCAGATTACAGATATTCAAGTAAC...

Protein

Download Protein FASTA

397 aa · LXL04_011821|LXL04_011821|OH1004|PROTEIN

MAVHGKLLNVQVPSPTNYGGQNGSASPNVGKAMDAFSQAESLVSSSKKLENEVVLLGQNIKDHEENIEYLKTRISSLDDQITDIQVTLGKSQSSNSSTHTTLTEDKDLSQHIIQQHQKSAGAIVSKLKSHEDPTCIKDVLGVVATLGKLYDDNLSRIVSEYLGLDTMLALVCMTYDGVKALETYFGLYGIERRLEVICLENMRPYVGEVMGDDPQRRLALVKPKLPNGKSPLGFLGFAVNMIHIDIPHLLPSTSNGYGLR...

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_011821`
TK1151 ID	TkA02G610360
OH-1004 ID	LXL04_011821
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 98.267 / 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_011821

Location Chr03:874823-876398 (+)

Description Similar to DMS3: Protein DEFECTIVE IN MERISTEM SILENCING 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g49250`	Component of the RNA-directed DNA methylation (RdDM) machinery, probably by facilitating an RNAi-mediated epigenetic modification involving secondary siRNAs and spreading of DNA methylation, thus leading to gene silencing.	A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.2008 · DOI: 10.1038/ng.119 RNA polymerase V transcription guides ARGONAUTE4 to chromatin.2009 · DOI: 10.1038/ng.365 IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.2009 · DOI: 10.1038/nsmb.1690 RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.2012 · DOI: 10.4161/epi.20290
`At5g24280`	Contributes to DNA double-strand break (DSB) repair via somatic homologous recombination.	GMI1, a structural-maintenance-of-chromosomes-hinge domain-containing protein, is involved in somatic homologous recombination in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2011.04604.x

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_011821 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

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

GO:0000419 RNA polymerase V complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0042803 protein homodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT3G49250

ath:AT5G24280

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.

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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.

Nucleus0.743

Rank 1 · LXL04_011821 · OH-1004

Cytoplasm0.324

Rank 2 · LXL04_011821 · OH-1004

Mitochondrion0.031

Rank 3 · LXL04_011821 · OH-1004

Cell membrane0.029

Rank 4 · LXL04_011821 · OH-1004

Endoplasmic reticulum0.020

Rank 5 · LXL04_011821 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

No result was found for this query.

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
`Q94A79`	Arabidopsis thaliana	Protein DEFECTIVE IN MERISTEM SILENCING 3	45.844%	Swiss-Prot	moderate database homology
`F4KFS5`	Arabidopsis thaliana	Structural maintenance of chromosomes flexible hinge domain-containing protein GMI1	36.782%	Swiss-Prot	moderate database homology

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