LXL04_033209 | RubberDandelionOmics

Gene overview

LXL04_033209

Reference: OH-1004 Chr: Chr07 Coordinates: 38328629-38329659 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

485 bp · LXL04_033209|LXL04_033209|OH1004|cDNA

atgaaTGAGTGTTGCAACGCCAGATTAGTCGAACTCGTCAAGCTCTTATACAACAGTTGGATCGTAACAGTGGCGGGTTCATCTCAGCGATTATTCAGGATGATTGATGGATTGAATTTCAAGgagtttgttttatttttatctgCATTTAGTTCCCGTGCCACCTTACAACATAAAGTGGAATGGAGCTTCTTCTTGACTTTTATACAAATTCTGCTAAGCGAAAGCCAGATCAGATTATCATCTTCAGAAGTGAGTGA...

CDS

Download CDS FASTA

387 bp · LXL04_033209|LXL04_033209|OH1004|CDS

ATGAATGAGTGTTGCAACGCCAGATTAGTCGAACTCGTCAAGCTCTTATACAACAGTTGGATCGTAACAGTGGCGGGTTCATCTCAGCGATTATTCAGGATGATTGATGGATTGAATTTCAAGGAGTTTGTTTTATTTTTATCTGCATTTAGTTCCCGTGCCACCTTACAACATAAAGTGGAATGGAGCTTCTTCTTGACTTTTATACAAATTCTGCTAAGCGAAAGCCAGATCAGATTATCATCTTCAGAAGTGAGTGA...

Protein

Download Protein FASTA

128 aa · LXL04_033209|LXL04_033209|OH1004|PROTEIN

MNECCNARLVELVKLLYNSWIVTVAGSSQRLFRMIDGLNFKEFVLFLSAFSSRATLQHKVEWSFFLTFIQILLSESQIRLSSSEVSESQFSQVLNIELDQIIEACKMLRRITIPSFPSPEVTTMCNLV

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_033209`
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_033209

Location Chr07:38328629-38329659 (-)

Description Protein of unknown function

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g27040`	Together with RDM3, required for transcriptional gene silencing (TGS) by DNA methylation and repressive histone modifications (H3K9me2) of several chromatin loci.	ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation.2003 · DOI: 10.1126/science.1079695 Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.2004 · DOI: 10.1016/j.cub.2004.06.055 The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.2006 · DOI: 10.1016/j.cell.2006.05.031 An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.2006 · DOI: 10.1016/j.cell.2006.05.032 Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.2006 · DOI: 10.1038/nature05198 Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components.2007 · DOI: 10.1101/gad.451207 ARGONAUTE4 is required for resistance to Pseudomonas syringae in Arabidopsis.2007 · DOI: 10.1105/tpc.107.054494 Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide.2008 · DOI: 10.1016/j.cell.2008.02.034 Viral genome methylation as an epigenetic defense against geminiviruses.2008 · DOI: 10.1128/jvi.00719-08 RNA polymerase V transcription guides ARGONAUTE4 to chromatin.2009 · DOI: 10.1038/ng.365 The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci.2010 · DOI: 10.1105/tpc.109.072199 Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing.2011 · DOI: 10.1371/journal.pgen.1002120

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0275600`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release
`Os04g0151800`	Probably involved in the RNA silencing pathway.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_033209 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006417 regulation of translation Biological Process

GO:0030422 siRNA processing Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0031048 regulatory ncRNA-mediated heterochromatin formation Biological Process

GO:0031507 heterochromatin formation Biological Process

GO:0042742 defense response to bacterium Biological Process

GO:0051607 defense response to virus Biological Process

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

GO:0000791 euchromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

KEGG gene cross-reference

ath:AT2G27040

dosa:Os01g0275600

dosa:Os04g0151800

osa:4324438

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.

Cytoplasm0.475

Rank 1 · LXL04_033209 · OH-1004

Nucleus0.376

Rank 2 · LXL04_033209 · OH-1004

Mitochondrion0.139

Rank 3 · LXL04_033209 · OH-1004

Endoplasmic reticulum0.082

Rank 4 · LXL04_033209 · OH-1004

Cell membrane0.067

Rank 5 · LXL04_033209 · 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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9ZVD5`	Arabidopsis thaliana	Protein argonaute 4	75.000%	Swiss-Prot	weak database homology
`Q9SDG8`	Oryza sativa subsp. japonica	Protein argonaute 4A	62.500%	Swiss-Prot	weak database homology
`Q0JF58`	Oryza sativa subsp. japonica	Protein argonaute 4B	71.875%	Swiss-Prot	weak database homology

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