LXL04_014712 | RubberDandelionOmics

Gene overview

LXL04_014712

Reference: OH-1004 Chr: Chr03 Coordinates: 55311806-55316246 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2736 bp · LXL04_014712|LXL04_014712|OH1004|cDNA

ATGGATTCACAAGAAACCGACGGCAATGGAACAACGGAGGCTCTGCCACCTCCTCCACCTGTACCGGAAGACGTGGTCCCCGAACAAGCTCTTCAACCTGTTAAGAAAAAGGTCATGCGAGTGCCAATGGCTCGACGTGGGTTAGCCACCAAGGGCCAAAAGGTCCAGCTCTTGACCAACCACTTCAAAGTCAGCGTCTCCAATGTTGACGGACACTTCTTTCACTACAGCGTTGCGCTTTTTTACGAAGATGGCCGTCC...

CDS

Download CDS FASTA

2736 bp · LXL04_014712|LXL04_014712|OH1004|CDS

ATGGATTCACAAGAAACCGACGGCAATGGAACAACGGAGGCTCTGCCACCTCCTCCACCTGTACCGGAAGACGTGGTCCCCGAACAAGCTCTTCAACCTGTTAAGAAAAAGGTCATGCGAGTGCCAATGGCTCGACGTGGGTTAGCCACCAAGGGCCAAAAGGTCCAGCTCTTGACCAACCACTTCAAAGTCAGCGTCTCCAATGTTGACGGACACTTCTTTCACTACAGCGTTGCGCTTTTTTACGAAGATGGCCGTCC...

Protein

Download Protein FASTA

911 aa · LXL04_014712|LXL04_014712|OH1004|PROTEIN

MDSQETDGNGTTEALPPPPPVPEDVVPEQALQPVKKKVMRVPMARRGLATKGQKVQLLTNHFKVSVSNVDGHFFHYSVALFYEDGRPVDGKGVGRKVLDRVHETYDSELAGKEFAYDGEKSLFTIGALPRNKLEFTVVLEDVTSNRNNGNASPDHGSPNDKDKKRIRRQYQSKTFKVELSFAAKIPMQAIAQALRGQESENSQEALRVLDIILRQHAARQGCLLVRQSFFHNDVKNFADVGGGVLGCRGFHSSFRTSQGG...

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_014712`
TK1151 ID	TkA02G403020
OH-1004 ID	LXL04_014712
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.900
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_014712

Location Chr03:55311806-55316246 (-)

Description Similar to AGO4: Protein argonaute 4

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
`Os07g0265600`	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_014712 · 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:Os01g0275600

dosa:Os04g0151800

dosa:Os07g0265600

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.

Cytoplasm0.657

Rank 1 · LXL04_014712 · OH-1004

Nucleus0.370

Rank 2 · LXL04_014712 · OH-1004

Mitochondrion0.081

Rank 3 · LXL04_014712 · OH-1004

Cell membrane0.073

Rank 4 · LXL04_014712 · OH-1004

Endoplasmic reticulum0.053

Rank 5 · LXL04_014712 · 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.

PF16486.12ArgoN53-213 aa

PF08699.16ArgoL1225-274 aa

PF02170.29PAZ279-409 aa

PF16488.11ArgoL2419-464 aa

PF16487.11ArgoMid473-525 aa

PF02171.24Piwi562-870 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014712	`PF16486.12`	ArgoN	53	213	6.7e-32	111.6
LXL04_014712	`PF08699.16`	ArgoL1	225	274	4.4e-18	65.4
LXL04_014712	`PF02170.29`	PAZ	279	409	6.9e-29	101.0
LXL04_014712	`PF16488.11`	ArgoL2	419	464	4.8e-14	53.0
LXL04_014712	`PF16487.11`	ArgoMid	473	525	7.8e-08	33.2
LXL04_014712	`PF02171.24`	Piwi	562	870	2.2e-105	352.9

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9ZVD5`	Arabidopsis thaliana	Protein argonaute 4	75.768%	Swiss-Prot	strong database homology
`Q84VQ0`	Arabidopsis thaliana	Protein argonaute 9	67.834%	Swiss-Prot	strong database homology
`Q9SDG8`	Oryza sativa subsp. japonica	Protein argonaute 4A	74.772%	Swiss-Prot	strong database homology
`Q0JF58`	Oryza sativa subsp. japonica	Protein argonaute 4B	73.483%	Swiss-Prot	strong database homology
`Q6YSJ5`	Oryza sativa subsp. japonica	Protein argonaute 16	63.771%	Swiss-Prot	strong database homology

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