LXL04_009589 | RubberDandelionOmics

Gene overview

LXL04_009589

Reference: OH-1004 Chr: Chr02 Coordinates: 129280301-129288553 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1920 bp · LXL04_009589|LXL04_009589|OH1004|cDNA

ATGTTGGTCACGGTTGGCACCTCTTTTCGGTCCAAGCCACCACTCCGAGACTTGTTGGTCACGGCTACGTTGGTCACGGTTGACACCCCTCTTTTCGGGTCCAAGCCACCACTCCAAGTGTTGGAACCTCGAAAGGTGGGGAttactctgataccaattgatacGAACTCATCCCATACTAGTGGTTCCGTCGGTCCTGGTGATCTCGTGACTTCGGATGGTGTGAACTTGCTGGCTAGCGGGTTGAGATGTCAGCCTGC...

CDS

Download CDS FASTA

1920 bp · LXL04_009589|LXL04_009589|OH1004|CDS

ATGTTGGTCACGGTTGGCACCTCTTTTCGGTCCAAGCCACCACTCCGAGACTTGTTGGTCACGGCTACGTTGGTCACGGTTGACACCCCTCTTTTCGGGTCCAAGCCACCACTCCAAGTGTTGGAACCTCGAAAGGTGGGGATTACTCTGATACCAATTGATACGAACTCATCCCATACTAGTGGTTCCGTCGGTCCTGGTGATCTCGTGACTTCGGATGGTGTGAACTTGCTGGCTAGCGGGTTGAGATGTCAGCCTGC...

Protein

Download Protein FASTA

639 aa · LXL04_009589|LXL04_009589|OH1004|PROTEIN

MLVTVGTSFRSKPPLRDLLVTATLVTVDTPLFGSKPPLQVLEPRKVGITLIPIDTNSSHTSGSVGPGDLVTSDGVNLLASGLRCQPAEPDEDGVIILANPPPAKPRFAISFLTFDLSRAHEPTPQIVFFFLRTRSGHLSWSAGHVLPPPILHFAMRSQPKMQKLEGRKRKPAELKCSPAKLLKNGTVTSLTVNDPYPNHPRPTSEECRAVRDDLLAFHGFPKQFLKYREQRLKLLPNADECGSTTSPQPEPAVSSKESVL...

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_009589`
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_009589

Location Chr02:129280301-129288553 (-)

Description Similar to At3g47830: Putative DNA glycosylase At3g47830

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g47830`	Putative DNA glycosylase At3g47830.	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

Rice

Reference gene ID	Possible function	Papers / DOI
`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
`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

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009589 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006284 base-excision repair Biological Process

GO:0006285 base-excision repair, AP site formation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0050832 defense response to fungus 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:0005730 nucleolus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G36490

ath:AT3G47830

dosa:Os01g0217900

dosa:Os05g0445900

osa:9271145

sai:Saci_1497

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.

Nucleus0.742

Rank 1 · LXL04_009589 · OH-1004

Cytoplasm0.214

Rank 2 · LXL04_009589 · OH-1004

Mitochondrion0.057

Rank 3 · LXL04_009589 · OH-1004

Plastid0.041

Rank 4 · LXL04_009589 · OH-1004

Cell membrane0.038

Rank 5 · LXL04_009589 · 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.

PF00730.32HhH-GPD264-407 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009589	`PF00730.32`	HhH-GPD	264	407	1.4e-11	45.4

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
`F4JCQ3`	Arabidopsis thaliana	Putative DNA glycosylase At3g47830	59.459%	Swiss-Prot	weak database homology
`Q9SJQ6`	Arabidopsis thaliana	DNA glycosylase/AP lyase ROS1	30.058%	Swiss-Prot	weak database homology
`C7IW64`	Oryza sativa subsp. japonica	Protein ROS1A	26.054%	Swiss-Prot	weak database homology
`B8YIE8`	Oryza sativa subsp. japonica	Protein ROS1C	30.636%	Swiss-Prot	weak database homology

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