LXL04_022000 | RubberDandelionOmics

Gene overview

LXL04_022000

Reference: OH-1004 Chr: Chr04 Coordinates: 142257573-142258162 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

519 bp · LXL04_022000|LXL04_022000|OH1004|cDNA

ATGAAGAGAACATCACCAGTTCCTTTAGATATCTCATCCGATGAAGATGACAAACCTTCTCAATCCAACGGTATAAAAAACCTCTCTATTTCAAAACGCCCAAAACTCGAGCCCACATCCATCACCAACCCCGCCAAACAAGTAATCACCCAAGAACTGTTGACGAAAAGTGCGAAAATGTATCAAGAATACATGAAGGAGATGCCGATACCATCTCAACATATGTCGGTAATTCCGTTTAGTTCATGGACGGGATTGGC...

CDS

Download CDS FASTA

519 bp · LXL04_022000|LXL04_022000|OH1004|CDS

ATGAAGAGAACATCACCAGTTCCTTTAGATATCTCATCCGATGAAGATGACAAACCTTCTCAATCCAACGGTATAAAAAACCTCTCTATTTCAAAACGCCCAAAACTCGAGCCCACATCCATCACCAACCCCGCCAAACAAGTAATCACCCAAGAACTGTTGACGAAAAGTGCGAAAATGTATCAAGAATACATGAAGGAGATGCCGATACCATCTCAACATATGTCGGTAATTCCGTTTAGTTCATGGACGGGATTGGC...

Protein

Download Protein FASTA

172 aa · LXL04_022000|LXL04_022000|OH1004|PROTEIN

MKRTSPVPLDISSDEDDKPSQSNGIKNLSISKRPKLEPTSITNPAKQVITQELLTKSAKMYQEYMKEMPIPSQHMSVIPFSSWTGLAKSMKQMYKQPLHYLTNIRIKEWDQMREIVGNDVALDTVIHPCKAETNIWLMEEVHRLTSSYQYLAKLWIQDPMYYTFIDSDSPQL

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_022000`
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_022000

Location Chr04:142257573-142258162 (-)

Description Similar to RDM1: Protein RDM1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g22680`	Regulator of RNA-directed DNA methylation (RdDM).	A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis.2010 · DOI: 10.1016/j.cub.2010.03.062 An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation.2010 · DOI: 10.1038/nature09025

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022000 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0030422 siRNA processing 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:0005654 nucleoplasm Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT3G22680

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.

Nucleus0.842

Rank 1 · LXL04_022000 · OH-1004

Cytoplasm0.259

Rank 2 · LXL04_022000 · OH-1004

Mitochondrion0.043

Rank 3 · LXL04_022000 · OH-1004

Cell membrane0.018

Rank 4 · LXL04_022000 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_022000 · 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.

PF09187.16RdDM_RDM155-170 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022000	`PF09187.16`	RdDM_RDM1	55	170	1.6e-52	177.3

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
`Q9LUJ3`	Arabidopsis thaliana	Protein RDM1	45.860%	Swiss-Prot	moderate database homology

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