TkA03G395290 | RubberDandelionOmics

Gene overview

TkA03G395290

Reference: TK1151 Chr: Chr03 Coordinates: 98198130-98199652 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

873 bp · TkA03G395290|TK1151|cDNA

ATGGCAATGTGCTCTTTAAACTTGGAGATGATGGCTATGTTCAGGCTGAAGAGGGCGAGGACAGCTACATACTTGGTGCCTTATTCAACCTACCAAAACTTTCCACGTGAAGTTGAAGGAGATGGGAATGAATCTGATTTCACTATATCATCTGAATTTGATGTTAATGCAACTGTTAATGAAGATTCCACAATTCAAAACAACAAAATATCAGAAATGAGAATGTTGGATCTTTATTCAGGATGTGGGGCCATGTCTAC...

CDS

Download CDS FASTA

873 bp · TkA03G395290|TK1151|CDS

ATGGCAATGTGCTCTTTAAACTTGGAGATGATGGCTATGTTCAGGCTGAAGAGGGCGAGGACAGCTACATACTTGGTGCCTTATTCAACCTACCAAAACTTTCCACGTGAAGTTGAAGGAGATGGGAATGAATCTGATTTCACTATATCATCTGAATTTGATGTTAATGCAACTGTTAATGAAGATTCCACAATTCAAAACAACAAAATATCAGAAATGAGAATGTTGGATCTTTATTCAGGATGTGGGGCCATGTCTAC...

Protein

Download Protein FASTA

290 aa · TkA03G395290|TK1151|PROTEIN

MAMCSLNLEMMAMFRLKRARTATYLVPYSTYQNFPREVEGDGNESDFTISSEFDVNATVNEDSTIQNNKISEMRMLDLYSGCGAMSTGLCLGANMANLNLVTVRNESAEDFLQLLKEWEKLCQSYSLIGGGDSQPKEPATIEEDEEVEEEDDNDVDNVEIFEVDQILSICYGDPKEIKKRDLYLKVRWKGYGPEEDTWEPLEGLNDCHDKIKEFVIRLCFAMTINKAQGQTIQNVGIYLPEPVFPHGQLYIALSRGISRG...

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	`TkA03G395290`
TK1151 ID	TkA03G395290
OH-1004 ID	LXL04_009054
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 95.172 / OH-1004 87.898 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 TkA03G395290

Location Chr03:98198130-98199652 (-)

Description Similar to CMT3: DNA (cytosine-5)-methyltransferase CMT3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g69770`	Involved in the CpXpG methylation (e.g. CHG cytosine) and in gene silencing.	Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.2001 · DOI: 10.1126/science.1059745 Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene.2001 · DOI: 10.1101/gad.905701 Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.2002 · DOI: 10.1016/s0960-9822(01)00622-4 JMJ24 targets CHROMOMETHYLASE3 for proteasomal degradation in Arabidopsis.2016 · DOI: 10.1101/gad.274647.115
`At1g80740`	May be involved in the CpXpG methylation and in gene silencing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0226800`	Involved in CpXpG DNA methylation (By similarity).	No verified direct reference in this release
`Os10g0104900`	Involved in CpXpG DNA methylation.	No verified direct reference in this release
`UniProt: Q5KQL9`	Involved in CpXpG DNA methylation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009054 · 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:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0010069 zygote asymmetric cytokinesis in embryo sac Biological Process

GO:0032259 methylation Biological Process

GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

GO:0141010 transposable element silencing by siRNA-mediated DNA methylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

GO:0003886 DNA (cytosine-5-)-methyltransferase activity Molecular Function

GO:0031625 ubiquitin protein ligase binding Molecular Function

KEGG gene cross-reference

ath:AT1G69770

dosa:Os03g0226800

dosa:Os05g0224800

dosa:Os05g0224900

dosa:Os10g0104900

osa:4338140

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.

Nucleus0.525

Rank 1 · TkA03G395290 · TK1151

Cytoplasm0.377

Rank 2 · TkA03G395290 · TK1151

Mitochondrion0.074

Rank 3 · TkA03G395290 · TK1151

Extracellular0.067

Rank 4 · TkA03G395290 · TK1151

Endoplasmic reticulum0.054

Rank 5 · TkA03G395290 · 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.

PF22589SPMIP1138-195 aa

PF00385Chromo161-215 aa

PF02689Herpes_Helicase218-283 aa

PF13538UvrD_C_2219-255 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G395290	`PF22589`	SPMIP1	138	195	0.27	12.1
TkA03G395290	`PF00385`	Chromo	161	215	3.7e-12	46.7
TkA03G395290	`PF02689`	Herpes_Helicase	218	283	0.0024	16.7
TkA03G395290	`PF13538`	UvrD_C_2	219	255	0.032	14.8

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
`Q94F88`	Arabidopsis thaliana	sp\|Q94F88\|CMT3_ARATH DNA (cytosine-5)-methyltransferase CMT3	42.000%	Swiss-Prot	Medium
`O49139`	Arabidopsis thaliana	sp\|O49139\|CMT1_ARATH Putative DNA (cytosine-5)-methyltransferase CMT1	37.200%	Swiss-Prot	Medium
`A0A0P0VUY4`	Oryza sativa subsp. japonica	sp\|A0A0P0VUY4\|CMT1_ORYSJ DNA (cytosine-5)-methyltransferase CMT1	38.600%	Swiss-Prot	Medium
`C0SQ89`	Oryza sativa subsp. japonica	sp\|C0SQ89\|CMT3_ORYSJ DNA (cytosine-5)-methyltransferase CMT3	39.500%	Swiss-Prot	Medium
`Q5KQL9`	Oryza sativa subsp. japonica	sp\|Q5KQL9\|CMT2_ORYSJ DNA (cytosine-5)-methyltransferase CMT2	43.800%	Swiss-Prot	Medium

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