TkA02G360120 | RubberDandelionOmics

Gene overview

TkA02G360120

Reference: TK1151 Chr: Chr02 Coordinates: 91533229-91541661 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

6726 bp · TkA02G360120|TK1151|cDNA

CTGGTGCCCAAGACTGAGCGGTGGTCCTAGCGAAGCCATATTATGAGAAACAAACAAAACCTTCTTCCCCTAAACCTTCTTCTCCTAAGCATCATCGAAACCCTAAATTGCTTCAAAAAGTCTTGAATTCGTCTTCAAACCGCCGGCGCCCTGGCGATCCGATTCCCCTACGCCAGCGCAACTTTGGTTGCATAAGATTTGCCATATTTGTTCAAATTCAACACTCTATTTTTTTCTTCAATTCTTCCGGCCAATTCCAA...

CDS

Download CDS FASTA

4707 bp · TkA02G360120|TK1151|CDS

ATGAACTATGGGAGGGGTTTTCCACTCCCTCATTACAGAAATGATGATTCATGGAATCAGGCAAGAGGGATTCCGCCAGGGAGAGGAATTGGACCAATTAGGGGCTCTTGGACTGCTGCCATGCTTGGAGGACCAATCCCAGAGAGTGGCGGCTTAAGTGAGACTCCAAGAAGGGTGATTCCCATAGATGACGAGGTTATTTGTGGTACGGAATCATGGATTCCAATTCCAAAGGGAAATGGGATTGGGATTATGGGTCA...

Protein

Download Protein FASTA

1568 aa · TkA02G360120|TK1151|PROTEIN

MNYGRGFPLPHYRNDDSWNQARGIPPGRGIGPIRGSWTAAMLGGPIPESGGLSETPRRVIPIDDEVICGTESWIPIPKGNGIGIMGHSDLLTTIHQENDIVQNGENWNPVILDGSSWTPVTPGKPISQRSNLISVNKPTNQVEQNENWKDLVGMYQDLLREEAINLNEVAQELHPSQNQNQNHVAKRNLNPIQSTQIQSNFVVRNQQSPTFTSDMINEYTSNQLPTNGFPVPYRPCYNLNSPPRSEPDAASSGITGHLPC...

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	`TkA02G360120`
TK1151 ID	TkA02G360120
OH-1004 ID	LXL04_015148
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	92.400
Protein coverage (%)	TK1151 100.000 / OH-1004 99.936 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA02G360120

Location Chr02:91533229-91541661 (-)

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
`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_015148 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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: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:0019104 DNA N-glycosylase activity Molecular Function

GO:0032183 SUMO binding Molecular Function

KEGG gene cross-reference

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.

Nucleus0.920

Rank 1 · TkA02G360120 · TK1151

Cytoplasm0.156

Rank 2 · TkA02G360120 · TK1151

Cell membrane0.023

Rank 3 · TkA02G360120 · TK1151

Mitochondrion0.020

Rank 4 · TkA02G360120 · TK1151

Endoplasmic reticulum0.011

Rank 5 · TkA02G360120 · TK1151

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.

PF00269SASP167-181 aa

PF00269SASP500-529 aa

PF00730HhH-GPD853-878 aa

PF00730HhH-GPD1061-1179 aa

PF27225AF_1859_N1212-1273 aa

PF10576EndIII_4Fe-2S1217-1233 aa

PF15629Perm-CXXC1420-1451 aa

PF15628RRM_DME1454-1554 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G360120	`PF00269`	SASP	167	181	0.27	12.0
TkA02G360120	`PF00269`	SASP	500	529	0.27	12.0
TkA02G360120	`PF00730`	HhH-GPD	853	878	0.001	20.1
TkA02G360120	`PF00730`	HhH-GPD	1061	1179	0.001	20.1
TkA02G360120	`PF27225`	AF_1859_N	1212	1273	0.078	13.5
TkA02G360120	`PF10576`	EndIII_4Fe-2S	1217	1233	5.0	8.3
TkA02G360120	`PF15629`	Perm-CXXC	1420	1451	3.2e-12	47.2
TkA02G360120	`PF15628`	RRM_DME	1454	1554	7.5e-53	177.7

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	sp\|Q8LK56\|DME_ARATH Transcriptional activator DEMETER	44.100%	Swiss-Prot	Medium
`Q9SJQ6`	Arabidopsis thaliana	sp\|Q9SJQ6\|ROS1_ARATH DNA glycosylase/AP lyase ROS1	52.400%	Swiss-Prot	Medium
`Q9SR66`	Arabidopsis thaliana	sp\|Q9SR66\|DML2_ARATH DEMETER-like protein 2	46.500%	Swiss-Prot	Medium
`C7IW64`	Oryza sativa subsp. japonica	sp\|C7IW64\|ROS1A_ORYSJ Protein ROS1A	46.300%	Swiss-Prot	Medium
`B8YIE8`	Oryza sativa subsp. japonica	sp\|B8YIE8\|ROS1C_ORYSJ Protein ROS1C	46.300%	Swiss-Prot	Medium

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