LXL04_032023 | RubberDandelionOmics

Gene overview

LXL04_032023

Reference: OH-1004 Chr: Chr07 Coordinates: 15109657-15111999 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1902 bp · LXL04_032023|LXL04_032023|OH1004|cDNA

ATGGATCCCAGCTCCGGTGAAGAGTCTGAGTTCAGTGATTCCGAGTATGCTGATTACAAAGACAAACCACTAGAACAACTGAGAAACGGAACCTTAAAGGTCAAATTCCCCAACGGCATACTTAGGTGTCCATTCTGTGCTGGAAAGAAAAAACAGAACTTCAAATACAAAGATCTGTATCAGCATGCCTCGGGAGTAGGCAAGGGATCTTCAAACAGAAACGCCAAACAGAAAGCCAATCATCTCGCCCTAGCAATCTA...

CDS

Download CDS FASTA

1902 bp · LXL04_032023|LXL04_032023|OH1004|CDS

ATGGATCCCAGCTCCGGTGAAGAGTCTGAGTTCAGTGATTCCGAGTATGCTGATTACAAAGACAAACCACTAGAACAACTGAGAAACGGAACCTTAAAGGTCAAATTCCCCAACGGCATACTTAGGTGTCCATTCTGTGCTGGAAAGAAAAAACAGAACTTCAAATACAAAGATCTGTATCAGCATGCCTCGGGAGTAGGCAAGGGATCTTCAAACAGAAACGCCAAACAGAAAGCCAATCATCTCGCCCTAGCAATCTA...

Protein

Download Protein FASTA

633 aa · LXL04_032023|LXL04_032023|OH1004|PROTEIN

MDPSSGEESEFSDSEYADYKDKPLEQLRNGTLKVKFPNGILRCPFCAGKKKQNFKYKDLYQHASGVGKGSSNRNAKQKANHLALAIYLENDLAHESEQPLKVAAPTPVAPVSEKTELYCWPWTGIVVNIVKDPDNEQDVENTEYWMKRFSKYKPEQVEISWDNQTKVAQALVRFNNDWTGFKNAMEFEKAFEVSHHSKREWFASEKSSGSSIYAWLARSNDFESQGAIGDFLRKNRELKTISDLVQEAVQTRNKPVVELA...

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_032023`
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_032023

Location Chr07:15109657-15111999 (-)

Description Similar to FDM1: Factor of DNA methylation 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g15910`	Forms a complex with IDN2 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway.	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034 IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.2012 · DOI: 10.1371/journal.pgen.1002693 INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.2012 · DOI: 10.1073/pnas.1206638109
`At4g00380`	Forms a complex with IDN2 and FDM1/IDNL1 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway.	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034 IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.2012 · DOI: 10.1371/journal.pgen.1002693 INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.2012 · DOI: 10.1073/pnas.1206638109
`At1g80790`	Acts in association with FDM3 and FDM4 for RNA-directed DNA methylation (RdDM).	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034
`At3g48670`	Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway and downstream of small interfering RNA (siRNA) formation.	IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.2009 · DOI: 10.1038/nsmb.1690 An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis.2010 · DOI: 10.1111/j.1365-313x.2010.04130.x IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.2012 · DOI: 10.1371/journal.pgen.1002693 INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.2012 · DOI: 10.1073/pnas.1206638109 IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation.2012 · DOI: 10.4161/epi.21237 A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing.2013 · DOI: 10.1016/j.molcel.2012.11.011 RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA.2014 · DOI: 10.1111/tpj.12563 Two Components of the RNA-Directed DNA Methylation Pathway Associate with MORC6 and Silence Loci Targeted by MORC6 in Arabidopsis.2016 · DOI: 10.1371/journal.pgen.1006026
`At3g12550`	Acts in association with FDM4 and FDM5 for RNA-directed DNA methylation (RdDM).	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_032023 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010569 regulation of double-strand break repair via homologous recombination Biological Process

GO:0046686 response to cadmium ion Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0003725 double-stranded RNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G15910

ath:AT1G80790

ath:AT3G12550

ath:AT3G48670

ath:AT4G00380

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.

Cytoplasm0.552

Rank 1 · LXL04_032023 · OH-1004

Nucleus0.458

Rank 2 · LXL04_032023 · OH-1004

Cell membrane0.081

Rank 3 · LXL04_032023 · OH-1004

Endoplasmic reticulum0.039

Rank 4 · LXL04_032023 · OH-1004

Lysosome / Vacuole0.022

Rank 5 · LXL04_032023 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF03470.20zf-XS43-85 aa

PF03468.21XS116-223 aa

PF03469.20XH502-632 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032023	`PF03470.20`	zf-XS	43	85	1.2e-20	74.1
LXL04_032023	`PF03468.21`	XS	116	223	1.1e-30	107.0
LXL04_032023	`PF03469.20`	XH	502	632	1.3e-55	187.6

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
`Q9S9P3`	Arabidopsis thaliana	Factor of DNA methylation 1	53.440%	Swiss-Prot	strong database homology
`F4JH53`	Arabidopsis thaliana	Factor of DNA methylation 2	51.942%	Swiss-Prot	strong database homology
`Q9SAI1`	Arabidopsis thaliana	Factor of DNA methylation 5	49.029%	Swiss-Prot	moderate database homology
`Q8VZ79`	Arabidopsis thaliana	Protein INVOLVED IN DE NOVO 2	38.644%	Swiss-Prot	moderate database homology
`Q9LHB1`	Arabidopsis thaliana	Factor of DNA methylation 3	36.562%	Swiss-Prot	moderate database homology

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