LXL04_006456 | RubberDandelionOmics

Gene overview

LXL04_006456

Reference: OH-1004 Chr: Chr02 Coordinates: 11164123-11179329 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6084 bp · LXL04_006456|LXL04_006456|OH1004|cDNA

ATGGCGGCTATTGAGGAATGCCAAAAGGAATTATCGGAAGCAAGAGCGCTGGTTGAAGAAGCTGAACGCTCTCTCGTCGGAGATACAGATACGATGATGACAGAGACAGAAAGAGAAGCGATGTTAAAAAACAAAGAGAGATTTGAATCGGTAAAAGCTCCGTCTATCTACGCCATAGTCGGCACAATCGCGAGCTTGCAGATTTCCATAGCTCAGGCATCCGGCACATCACAGTTAATCCTTCCGTCAGCTATCACTTT...

CDS

Download CDS FASTA

6084 bp · LXL04_006456|LXL04_006456|OH1004|CDS

ATGGCGGCTATTGAGGAATGCCAAAAGGAATTATCGGAAGCAAGAGCGCTGGTTGAAGAAGCTGAACGCTCTCTCGTCGGAGATACAGATACGATGATGACAGAGACAGAAAGAGAAGCGATGTTAAAAAACAAAGAGAGATTTGAATCGGTAAAAGCTCCGTCTATCTACGCCATAGTCGGCACAATCGCGAGCTTGCAGATTTCCATAGCTCAGGCATCCGGCACATCACAGTTAATCCTTCCGTCAGCTATCACTTT...

Protein

Download Protein FASTA

2027 aa · LXL04_006456|LXL04_006456|OH1004|PROTEIN

MAAIEECQKELSEARALVEEAERSLVGDTDTMMTETEREAMLKNKERFESVKAPSIYAIVGTIASLQISIAQASGTSQLILPSAITLISCALFGVTFRYAVRRDLDNFQLKTGTSAAFGFVKGLATRAGGPPMELEINSNVAYVGMYGMNPSSVCNHRRKLQNSTDCPCLDVGKPKRPVYIPLELCDLISLQRYTKSLSNLQRASLVEKSMRALTGTTASAGIRRYSTPLLPSAVRNQAPPHISNAYISVWMLLNSFGLL...

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_006456`
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_006456

Location Chr02:11164123-11179329 (+)

Description Similar to AGO4A: Protein argonaute 4A

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
`At5g21150`	Involved in RNA-mediated post-transcriptional gene silencing (PTGS).	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 Control of female gamete formation by a small RNA pathway in Arabidopsis.2010 · DOI: 10.1038/nature08828 ARGONAUTE9-dependent silencing of transposable elements in pericentromeric regions of Arabidopsis.2010 · DOI: 10.1038/nature08828

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
`UniProt: Q5NBN9`	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_006456 · 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:0009554 megasporogenesis Biological Process

GO:0010526 transposable element silencing 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:0048481 plant ovule development Biological Process

GO:0051607 defense response to virus Biological Process

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

KEGG gene cross-reference

ath:AT2G27040

ath:AT5G21150

dosa:Os01g0275200

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.

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.

Nucleus0.936

Rank 1 · LXL04_006456 · OH-1004

Cytoplasm0.145

Rank 2 · LXL04_006456 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_006456 · OH-1004

Mitochondrion0.018

Rank 4 · LXL04_006456 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_006456 · 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.

PF02170.29PAZ158-206 aa

PF13963.12Transpos_assoc278-366 aa

PF02992.21Transposase_21582-793 aa

PF13960.12DUF4218980-1093 aa

PF13952.12DUF42161257-1331 aa

PF03004.20Transposase_241780-1925 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006456	`PF02170.29`	PAZ	158	206	1e-07	32.7
LXL04_006456	`PF13963.12`	Transpos_assoc	278	366	1.5e-15	57.8
LXL04_006456	`PF02992.21`	Transposase_21	582	793	2e-77	259.9
LXL04_006456	`PF13960.12`	DUF4218	980	1093	1.3e-42	144.9
LXL04_006456	`PF13952.12`	DUF4216	1257	1331	5e-17	62.9
LXL04_006456	`PF03004.20`	Transposase_24	1780	1925	3.6e-15	57.0

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
`Q9ZVD5`	Arabidopsis thaliana	Protein argonaute 4	70.000%	Swiss-Prot	weak database homology
`Q84VQ0`	Arabidopsis thaliana	Protein argonaute 9	72.340%	Swiss-Prot	weak database homology
`Q9SDG8`	Oryza sativa subsp. japonica	Protein argonaute 4A	39.344%	Swiss-Prot	weak database homology
`Q0JF58`	Oryza sativa subsp. japonica	Protein argonaute 4B	64.912%	Swiss-Prot	weak database homology
`Q5NBN9`	Oryza sativa subsp. japonica	Protein argonaute 15	63.636%	Swiss-Prot	weak database homology

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