LXL04_005054 | RubberDandelionOmics

Gene overview

LXL04_005054

Reference: OH-1004 Chr: Chr01 Coordinates: 153890884-153896764 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4083 bp · LXL04_005054|LXL04_005054|OH1004|cDNA

ATGGATAATAAGGGGGAAAGTTCGTCCTCTCACCAAGTTGACCCAGCTGACGGCGTTTATGCTCCGGTGACACCAGCAAAACCAGCCGGATCGGAAACAACGATCATGAAAGATTGGCTAAGAACCCCGTTTGATGAAGCGTTATTTGAAGATACACCTGCGAACAACAATTTCAGCTGCTGGGAGCGTAATTTGGGGCCAACAATGTACAATCCTAGGGTTTCCATGGACGATTTAGGAATTTGGAATATTCCGTGTCG...

CDS

Download CDS FASTA

4083 bp · LXL04_005054|LXL04_005054|OH1004|CDS

ATGGATAATAAGGGGGAAAGTTCGTCCTCTCACCAAGTTGACCCAGCTGACGGCGTTTATGCTCCGGTGACACCAGCAAAACCAGCCGGATCGGAAACAACGATCATGAAAGATTGGCTAAGAACCCCGTTTGATGAAGCGTTATTTGAAGATACACCTGCGAACAACAATTTCAGCTGCTGGGAGCGTAATTTGGGGCCAACAATGTACAATCCTAGGGTTTCCATGGACGATTTAGGAATTTGGAATATTCCGTGTCG...

Protein

Download Protein FASTA

1360 aa · LXL04_005054|LXL04_005054|OH1004|PROTEIN

MDNKGESSSSHQVDPADGVYAPVTPAKPAGSETTIMKDWLRTPFDEALFEDTPANNNFSCWERNLGPTMYNPRVSMDDLGIWNIPCRDLLALADANGSLKLHNFISDLNAPPPPEPDVITQFTPVTPDQSKKANVHQQSHLIIEQSQEADSSTVVQSNQDTEKGLSDQINLNETPQQTKQRRRKHRPKVIKERKPRTAKKPATPNPDGSSTGKRKYVRKKPVEKSPIAEGEIIDLTTDEQQSEKSCKRKINFDEVEAIQV...

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_005054`
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_005054

Location Chr01:153890884-153896764 (-)

Description Similar to ROS1: DNA glycosylase/AP lyase ROS1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`UniProt: Q8LK56`	Transcriptional activator involved in gene imprinting.	No verified direct reference in this release
`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
`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_005054 · 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: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:0050832 defense response to fungus Biological Process

GO:0141044 epigenetic programming in the endosperm Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0043078 polar nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G36490

ath:AT5G04560

dosa:Os01g0217900

osa:9271145

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.

Nucleus0.902

Rank 1 · LXL04_005054 · OH-1004

Cytoplasm0.193

Rank 2 · LXL04_005054 · OH-1004

Mitochondrion0.031

Rank 3 · LXL04_005054 · OH-1004

Cell membrane0.024

Rank 4 · LXL04_005054 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_005054 · 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-GPD829-951 aa

PF15629.12Perm-CXXC1213-1244 aa

PF15628.12RRM_DME1247-1347 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005054	`PF00730.32`	HhH-GPD	829	951	2.7e-06	28.4
LXL04_005054	`PF15629.12`	Perm-CXXC	1213	1244	3.2e-14	53.6
LXL04_005054	`PF15628.12`	RRM_DME	1247	1347	1.2e-53	180.2

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
`Q9SJQ6`	Arabidopsis thaliana	DNA glycosylase/AP lyase ROS1	54.088%	Swiss-Prot	moderate database homology
`Q8LK56`	Arabidopsis thaliana	Transcriptional activator DEMETER	66.549%	Swiss-Prot	weak database homology
`Q9SR66`	Arabidopsis thaliana	DEMETER-like protein 2	57.018%	Swiss-Prot	weak database homology
`C7IW64`	Oryza sativa subsp. japonica	Protein ROS1A	65.913%	Swiss-Prot	weak database homology
`B8YIE8`	Oryza sativa subsp. japonica	Protein ROS1C	61.160%	Swiss-Prot	weak database homology

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