TkA03G472030 | RubberDandelionOmics

Gene overview

TkA03G472030

Reference: TK1151 Chr: Chr03 Coordinates: 117988640-117993594 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2982 bp · TkA03G472030|TK1151|cDNA

CAATTCAAATCTAAACTAAAACCCTTTTTGATTCCCGCTCAAAACGTCCCGCTTATAAAACCCTCGCGACCATTCTCTCTCTACACGCTCTCTTTCGACAGTCTCTTCGCCGCACTCTTCCGTCGTTTTCTCTCTCATCGCCGCCAGAAAATGACGAGGGCAAAGAGAAGGTCTTCATCTGCCTCCAAGGATGATACATTGGTTTCTTCGGAGAAACGCCCAAAAATAGAAGAAGAAAAGAAGGAAGAGGGAGAAGAAGC...

CDS

Download CDS FASTA

2754 bp · TkA03G472030|TK1151|CDS

CAATTCAAATCTAAACTAAAACCCTTTTTGATTCCCGCTCAAAACGTCCCGCTTATAAAACCCTCGCGACCATTCTCTCTCTACACGCTCTCTTTCGACAGTCTCTTCGCCGCACTCTTCCGTCGTTTTCTCTCTCATCGCCGCCAGAAAATGACGAGGGCAAAGAGAAGGTCTTCATCTGCCTCCAAGGATGATACATTGGTTTCTTCGGAGAAACGCCCAAAAATAGAAGAAGAAAAGAAGGAAGAGGGAGAAGAAGC...

Protein

Download Protein FASTA

917 aa · TkA03G472030|TK1151|PROTEIN

QFKSKLKPFLIPAQNVPLIKPSRPFSLYTLSFDSLFAALFRRFLSHRRQKMTRAKRRSSSASKDDTLVSSEKRPKIEEEKKEEGEEASAVPDPVSLVKSSGEKSEKPKAKAKANVKNEEDDAEESRFVGDPVPADEARQRWPLRYLPKNKAGKTQSLETTYGVQPPKDLMQAKRHFTEALVDGNVLFKLGDDGYVQAEEGEDSYICKVVEMFEGVDGTSYFSAQWFYRAKDTIIQACSNLVDDKRIFLSEIKDDNPLDCL...

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	`TkA03G472030`
TK1151 ID	TkA03G472030
OH-1004 ID	LXL04_009794
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 90.840 / OH-1004 96.078 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G472030

Location Chr03:117988640-117993594 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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

Rice

Reference gene ID	Possible function	Papers / DOI
`Os10g0104900`	Involved in CpXpG DNA methylation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009794 · 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:Os10g0104900

zma:542060

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.912

Rank 1 · TkA03G472030 · TK1151

Cytoplasm0.120

Rank 2 · TkA03G472030 · TK1151

Cell membrane0.035

Rank 3 · TkA03G472030 · TK1151

Endoplasmic reticulum0.024

Rank 4 · TkA03G472030 · TK1151

Mitochondrion0.023

Rank 5 · TkA03G472030 · 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.

PF09747CCD97-like_C35-124 aa

PF00145DNA_methylase63-111 aa

PF01426BAH187-293 aa

PF00145DNA_methylase342-395 aa

PF09747CCD97-like_C429-446 aa

PF00385Chromo454-507 aa

PF00145DNA_methylase518-879 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G472030	`PF09747`	CCD97-like_C	35	124	0.13	13.1
TkA03G472030	`PF00145`	DNA_methylase	63	111	6.6e-39	134.9
TkA03G472030	`PF01426`	BAH	187	293	3.6e-10	40.5
TkA03G472030	`PF00145`	DNA_methylase	342	395	6.6e-39	134.9
TkA03G472030	`PF09747`	CCD97-like_C	429	446	0.13	13.1
TkA03G472030	`PF00385`	Chromo	454	507	1.8e-11	44.5
TkA03G472030	`PF00145`	DNA_methylase	518	879	6.6e-39	134.9

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
`Q94F88`	Arabidopsis thaliana	sp\|Q94F88\|CMT3_ARATH DNA (cytosine-5)-methyltransferase CMT3	53.400%	Swiss-Prot	High
`C0SQ89`	Oryza sativa subsp. japonica	sp\|C0SQ89\|CMT3_ORYSJ DNA (cytosine-5)-methyltransferase CMT3	55.800%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card