TkA03G286920 | RubberDandelionOmics

Gene overview

TkA03G286920

Reference: TK1151 Chr: Chr03 Coordinates: 70816377-70821590 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3906 bp · TkA03G286920|TK1151|cDNA

GCAGCAGCATTAAAATTTGATTTTTGGGTGTGGAAGCCATATGGGAGGGAAATGACAAAGAACAAATAAAACCCCCAAAATTTTGCAAAATCCCGCCTAATTTTTTACAGGTGTTGCTCAATCCAGAAAATATTCGTATCAACACGAAGCAAAAACCCAAAAAACTTCTCATTCTCTCTCCTCCATCACTTCAATCGCCGATTCATATTCCCTCTGCACTGTTTCAACATATCGATGGTCTGAAATCCAGCTCCATTTCA...

CDS

Download CDS FASTA

3303 bp · TkA03G286920|TK1151|CDS

ATGCTATTAAGTTCGACTGAGTTATCAAACTCGGAGAAAGCAGTATCTGATATTACTCTGGAGAATTGTGATGCCGTCGATGAAAAGATGGGTTTTTTGAACTGTGATTTCGAGCCTTTGCTGGATGGAATAGTTGAAAAGATGCCAAATGAGAAACCTTCAGATGATCTTGAAGTTGGCATGTGTAAGCTAGAAAAAAGTACAACCATCGAGGATAAAAAGGCTCTGGTTTCTACAGAAAATAGTATAGCTTCATGTGC...

Protein

Download Protein FASTA

1100 aa · TkA03G286920|TK1151|PROTEIN

MLLSSTELSNSEKAVSDITLENCDAVDEKMGFLNCDFEPLLDGIVEKMPNEKPSDDLEVGMCKLEKSTTIEDKKALVSTENSIASCAERETEKEMVECVTVNSNELDLCLKEEVKSSPMLLFPTSPHQEALEYKNWSANIEPKSIVDDDNDIKMVSEKEADNGCITINEVREDTVEVTRSKRGRKRKYLGSSECNGDARVKNEKVEKCGVEVSGRVLRSRPLTDSDSVKVDESVLNESLVGFKRKMEAECLNQTELKEVF...

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	`TkA03G286920`
TK1151 ID	TkA03G286920
OH-1004 ID	LXL04_018805
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.900
Protein coverage (%)	TK1151 100.000 / OH-1004 82.521 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 TkA03G286920

Location Chr03:70816377-70821590 (+)

Description Similar to IDM1: Increased DNA methylation 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14980`	Histone H3 acetyltransferase that binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and catalyzes H3K18 and H3K23 acetylation.	A histone acetyltransferase regulates active DNA demethylation in Arabidopsis.2012 · DOI: 10.1126/science.1219416 Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis.2012 · DOI: 10.1073/pnas.1208557109 Regulation of active DNA demethylation by an α-crystallin domain protein in Arabidopsis.2014 · DOI: 10.1016/j.molcel.2014.06.008

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018805 · 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:0002181 cytoplasmic translation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006412 translation Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT3G04920

ath:AT3G14980

ath:AT5G28060

ddi:DDB_G0275473

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.

Nucleus0.967

Rank 1 · TkA03G286920 · TK1151

Cytoplasm0.080

Rank 2 · TkA03G286920 · TK1151

Cell membrane0.026

Rank 3 · TkA03G286920 · TK1151

Endoplasmic reticulum0.013

Rank 4 · TkA03G286920 · TK1151

Plastid0.010

Rank 5 · TkA03G286920 · 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.

PF23004PHDvar_NSD84-100 aa

PF00628PHD86-100 aa

PF30811PHD_UBR7-like87-100 aa

PF22970DUF7028408-466 aa

PF22970DUF7028536-547 aa

PF16135TDBD617-673 aa

PF00628PHD623-633 aa

PF23011PHD-1st_NSD698-740 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G286920	`PF23004`	PHDvar_NSD	84	100	0.015	16.0
TkA03G286920	`PF00628`	PHD	86	100	3.9e-05	24.3
TkA03G286920	`PF30811`	PHD_UBR7-like	87	100	9.9	6.9
TkA03G286920	`PF22970`	DUF7028	408	466	3.8e-06	27.5
TkA03G286920	`PF22970`	DUF7028	536	547	3.8e-06	27.5
TkA03G286920	`PF16135`	TDBD	617	673	1e-10	42.1
TkA03G286920	`PF00628`	PHD	623	633	3.9e-05	24.3
TkA03G286920	`PF23011`	PHD-1st_NSD	698	740	0.0025	18.6
TkA03G286920	`PF23004`	PHDvar_NSD	700	725	0.015	16.0
TkA03G286920	`PF00628`	PHD	701	740	3.9e-05	24.3
TkA03G286920	`PF30811`	PHD_UBR7-like	710	745	9.9	6.9
TkA03G286920	`PF30811`	PHD_UBR7-like	736	801	9.9	6.9
TkA03G286920	`PF00628`	PHD	742	787	3.9e-05	24.3
TkA03G286920	`PF23004`	PHDvar_NSD	742	776	0.015	16.0
TkA03G286920	`PF23011`	PHD-1st_NSD	753	771	0.0025	18.6
TkA03G286920	`PF23209`	IDM1_C	849	988	2.4e-59	200.1

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
`F4IXE7`	Arabidopsis thaliana	sp\|F4IXE7\|IDM1_ARATH Increased DNA methylation 1	39.400%	Swiss-Prot	Low

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