LXL04_017609 | RubberDandelionOmics

Gene overview

LXL04_017609

Reference: OH-1004 Chr: Chr03 Coordinates: 155140510-155145283 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3087 bp · LXL04_017609|LXL04_017609|OH1004|cDNA

ATGGCATCTTCCGATGAAGAAGGCGAAATCGTGCCCGTTTGCGTCACAAACTACCACATTGTGAACGATCGTGATGTTCCGACTTCATTTTCGGAGTTACCGCTTCGTTGGAGCGATCAGGAGAACCGAATCGAAAGTAAAGAGCCATCGGTTATGTATCTGCGGGGAACTACGGACGGAGGTCTGCAAACAGTCCATAAGGAAGTGATCGCGTGGAAGTTGGACCTTTCGGATATAGTGCCTAAATTGTTCATGCTTTC...

CDS

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3087 bp · LXL04_017609|LXL04_017609|OH1004|CDS

ATGGCATCTTCCGATGAAGAAGGCGAAATCGTGCCCGTTTGCGTCACAAACTACCACATTGTGAACGATCGTGATGTTCCGACTTCATTTTCGGAGTTACCGCTTCGTTGGAGCGATCAGGAGAACCGAATCGAAAGTAAAGAGCCATCGGTTATGTATCTGCGGGGAACTACGGACGGAGGTCTGCAAACAGTCCATAAGGAAGTGATCGCGTGGAAGTTGGACCTTTCGGATATAGTGCCTAAATTGTTCATGCTTTC...

Protein

Download Protein FASTA

1028 aa · LXL04_017609|LXL04_017609|OH1004|PROTEIN

MASSDEEGEIVPVCVTNYHIVNDRDVPTSFSELPLRWSDQENRIESKEPSVMYLRGTTDGGLQTVHKEVIAWKLDLSDIVPKLFMLSKGKTWIKLQKPRKSYENVIKSVKIAVRCLHFVKRNADAGRDQISRHLVKTFSSYDEIGPVEEYLSAHLPLIRTAVARDKDLAKSKYFKTFLTEIENPRRRDYQLEQNHSKNKSKFIVSDDDEEHDEDFDDDNEDEDEEVLFYSVCAFCDNGGDVLPCEGNCMRSFHPTIDAGV...

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_017609`
TK1151 ID	TkA02G021500
OH-1004 ID	LXL04_017609
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.000
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_017609

Location Chr03:155140510-155145283 (-)

Description Similar to EDM2: Protein ENHANCED DOWNY MILDEW 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g55390`	Cellular antisilencing factor and regulator of genome DNA methylation patterns involved in the regulation of chromatin states.	EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels.2007 · DOI: 10.1111/j.1365-313x.2006.02999.x The Arabidopsis defense component EDM2 affects the floral transition in an FLC-dependent manner.2010 · DOI: 10.1111/j.1365-313x.2010.04169.x Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development.2010 · DOI: 10.1186/1471-2229-10-203 EMSY-like genes are required for full RPP7-mediated race-specific immunity and basal defense in Arabidopsis.2011 · DOI: 10.1094/mpmi-05-11-0123 Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity.2013 · DOI: 10.1038/srep01701 Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A.2013 · DOI: 10.1371/journal.pone.0067987 Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.2014 · DOI: 10.1073/pnas.1320106110 Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development.2016 · DOI: 10.1242/dev.129932 A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis .2017 · DOI: 10.1073/pnas.1710683114 The Arabidopsis RRM domain protein EDM3 mediates race-specific disease resistance by controlling H3K9me2-dependent alternative polyadenylation of RPP7 immune receptor transcripts.2019 · DOI: 10.1111/tpj.14148 The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression.2020 · DOI: 10.1371/journal.pgen.1008993 Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis.2021 · DOI: 10.1111/jipb.13068

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017609 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007165 signal transduction Biological Process

GO:0009911 positive regulation of flower development Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0010440 stomatal lineage progression Biological Process

GO:0031347 regulation of defense response Biological Process

GO:0031452 negative regulation of heterochromatin formation Biological Process

GO:0032259 methylation Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT5G55390

ddi:DDB_G0268158

hsa:54904

mmu:234135

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.

Nucleus0.950

Rank 1 · LXL04_017609 · OH-1004

Cytoplasm0.096

Rank 2 · LXL04_017609 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_017609 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_017609 · OH-1004

Plastid0.012

Rank 5 · LXL04_017609 · 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.

PF12047.14DNMT1-RFD15-124 aa

PF22908.3PHD_NSD289-357 aa

PF23004.3PHDvar_NSD369-395 aa

PF26055.1Mtase_EDM2675-846 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017609	`PF12047.14`	DNMT1-RFD	15	124	1.1e-07	32.7
LXL04_017609	`PF22908.3`	PHD_NSD	289	357	1.9e-19	70.4
LXL04_017609	`PF23004.3`	PHDvar_NSD	369	395	8.8e-06	26.3
LXL04_017609	`PF26055.1`	Mtase_EDM2	675	846	1.1e-85	286.1

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
`F4K3G5`	Arabidopsis thaliana	Protein ENHANCED DOWNY MILDEW 2	60.000%	Swiss-Prot	weak database homology

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