LXL04_015823 | RubberDandelionOmics

Gene overview

LXL04_015823

Reference: OH-1004 Chr: Chr03 Coordinates: 87485806-87493569 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2400 bp · LXL04_015823|LXL04_015823|OH1004|cDNA

ATGGAGACCAAACGGACAAACAAACGCAAAGAACCGTCAGGCCAACGAGACGCTGCCATTGCTCCGATGATCGTTCTTCCTTGGCCAAATAAAACATCCGGTGGAAACCATAAGACGAGAGCCAAGAGATGTGGTAAAGACGTAACGTGTTCAGCAACAAGTAGGGCGAGCAAGGATCATGAAACTGACGTAAACCGTGAGACGCCGTCGACCAAATTGAAAGCCAAATTTAGGCCCAAAGTGATGGCGGTTTCCCCAAT...

CDS

Download CDS FASTA

2400 bp · LXL04_015823|LXL04_015823|OH1004|CDS

ATGGAGACCAAACGGACAAACAAACGCAAAGAACCGTCAGGCCAACGAGACGCTGCCATTGCTCCGATGATCGTTCTTCCTTGGCCAAATAAAACATCCGGTGGAAACCATAAGACGAGAGCCAAGAGATGTGGTAAAGACGTAACGTGTTCAGCAACAAGTAGGGCGAGCAAGGATCATGAAACTGACGTAAACCGTGAGACGCCGTCGACCAAATTGAAAGCCAAATTTAGGCCCAAAGTGATGGCGGTTTCCCCAAT...

Protein

Download Protein FASTA

799 aa · LXL04_015823|LXL04_015823|OH1004|PROTEIN

METKRTNKRKEPSGQRDAAIAPMIVLPWPNKTSGGNHKTRAKRCGKDVTCSATSRASKDHETDVNRETPSTKLKAKFRPKVMAVSPITKPTTPEPLSSRGRRRGHSSMKTSRSRRRLEFDSPYIQTKTMQIFTKGGSCFTRKVKNYIAHDQHKSLECNEKEEDEWCKKEQELFRERALSFINSMRLVQGNRGFMGWKGSVVDSVVGVFLTQNTADSYSSCAFMSLAAKYPNQDGTEGVDWNAVRCAKPHVISHAIQERGM...

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_015823`
TK1151 ID	TkA02G210460
OH-1004 ID	LXL04_015823
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	74.000
Protein coverage (%)	TK1151 100.000 / OH-1004 77.096 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_015823

Location Chr03:87485806-87493569 (+)

Description Similar to DME: Transcriptional activator DEMETER

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q8LK56`	Transcriptional activator involved in gene imprinting.	No verified direct reference in this release
`At2g36490`	Bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity.	ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.2002 · DOI: 10.1016/s0092-8674(02)01133-9 DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases.2006 · DOI: 10.1073/pnas.0601109103 ROS1 5-methylcytosine DNA glycosylase is a slow-turnover catalyst that initiates DNA demethylation in a distributive fashion.2009 · DOI: 10.1093/nar/gkp390 Methylation-independent DNA binding modulates specificity of Repressor of Silencing 1 (ROS1) and facilitates demethylation in long substrates.2010 · DOI: 10.1074/jbc.m110.124578 DDM1 and ROS1 have a role in UV-B induced- and oxidative DNA damage in A. thaliana.2013 · DOI: 10.3389/fpls.2013.00420 AP endonucleases process 5-methylcytosine excision intermediates during active DNA demethylation in Arabidopsis.2014 · DOI: 10.1093/nar/gku834 The carboxy-terminal domain of ROS1 is essential for 5-methylcytosine DNA glycosylase activity.2014 · DOI: 10.1016/j.jmb.2014.09.010
`At3g10010`	Potential transcriptional activator that may act by nicking the target promoter.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0445900`	Bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity.	A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice.2011 · DOI: 10.1073/pnas.1112704108
`Os01g0218032`	Bifunctional DNA glycosylase/lyase, which excises 5-methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an apyrimidinic (AP) site that is subsequently incised by the lyase activity (Probable).	A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny.2012 · DOI: 10.1111/j.1365-313x.2012.05009.x Mutations in the DNA demethylase OsROS1 result in a thickened aleurone and improved nutritional value in rice grains.2018 · DOI: 10.1073/pnas.1806304115

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015823 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006284 base-excision repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0141044 epigenetic programming in the endosperm Biological Process

GO:0141166 chromosomal 5-methylcytosine DNA demethylation pathway Biological Process

GO:0141169 chromosomal 5-methylcytosine DNA demethylation, direct 5-methylcytosine excision pathway Biological Process

GO:0005634 nucleus Cellular Component

GO:0043078 polar nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity Molecular Function

GO:0016829 lyase activity Molecular Function

KEGG gene cross-reference

ath:AT5G04560

dosa:Os05g0445900

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.

Nucleus0.861

Rank 1 · LXL04_015823 · OH-1004

Cytoplasm0.149

Rank 2 · LXL04_015823 · OH-1004

Mitochondrion0.060

Rank 3 · LXL04_015823 · OH-1004

Cell membrane0.025

Rank 4 · LXL04_015823 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_015823 · 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.

PF15628.12RRM_DME646-711 aa

PF15628.12RRM_DME734-770 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015823	`PF15628.12`	RRM_DME	646	711	1.1e-36	125.8
LXL04_015823	`PF15628.12`	RRM_DME	734	770	1.1e-36	125.8

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
`Q8LK56`	Arabidopsis thaliana	Transcriptional activator DEMETER	52.778%	Swiss-Prot	weak database homology
`Q9SJQ6`	Arabidopsis thaliana	DNA glycosylase/AP lyase ROS1	55.233%	Swiss-Prot	weak database homology
`Q9SR66`	Arabidopsis thaliana	DEMETER-like protein 2	52.874%	Swiss-Prot	weak database homology
`B8YIE8`	Oryza sativa subsp. japonica	Protein ROS1C	56.098%	Swiss-Prot	weak database homology
`C7IW64`	Oryza sativa subsp. japonica	Protein ROS1A	52.542%	Swiss-Prot	weak database homology

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