TkA08G049090 | RubberDandelionOmics

Gene overview

TkA08G049090

Reference: TK1151 Chr: Chr08 Coordinates: 12484125-12486685 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1639 bp · TkA08G049090|TK1151|cDNA

CTTATAGTTATCGGTTCCGATTTACAGCTTCTAGCTGCCTAGCTGGTTTTCAGTGTTTCAAACTCGCCCACGGTTGCAGAGAAAGTTAAATACTGATACTGTGGGTCCAAAATCCTACATACAAGCTTGATACGGGAATAGCCTACTGCAAGCAACATCAGGGAAGTGAAATCAGCGGGAAATGAACTCGACTCTAATAGCGAAACGCAATCGTCGCTGAAAATTCCATCACGTGTATGATGACTCAGCATATGGGACTT...

CDS

Download CDS FASTA

1110 bp · TkA08G049090|TK1151|CDS

ATGATGACTCAGCATATGGGACTTTTGGAGTTTTTAAGGTTGGAGGAAAAGAACAAAAGAAGGGAAGAACTTGAGAGTAAGATAAGGACGGCTGATTATCTAATGGCTTCTGTTATGAAACATAAAGAAATGATGGTTGAAAACTTCAATATAGAAGTTAAAATGAAGCAAGAAAAAGAGAATGAAGAGATTAAAGAGATTAGCATTGAGTATGAAGAGAGAAAATTGCAGCTTTATGACCATGAAAAGAAACTTAGAGC...

Protein

Download Protein FASTA

369 aa · TkA08G049090|TK1151|PROTEIN

MMTQHMGLLEFLRLEEKNKRREELESKIRTADYLMASVMKHKEMMVENFNIEVKMKQEKENEEIKEISIEYEERKLQLYDHEKKLRAREAINEHDNIIVDKEKKMIEMANLEKKKKANDRMLKLADDHKREKEKLYQKIIELQKKIDEKQRLELQINQMKGEIEVMKHMAEEDIEAKKKFDSIKEDLKEKEEELEDLEALNQALITKERQSNEELQDTRKELIAGMEHNPSRALIGVKRMGVLDKKPFIVAAKKRCLTQD...

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	`TkA08G049090`
TK1151 ID	TkA08G049090
OH-1004 ID	LXL04_017806
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	78.400
Protein coverage (%)	TK1151 98.916 / OH-1004 40.000 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 TkA08G049090

Location Chr08:12484125-12486685 (-)

Description Similar to FDM4: Factor of DNA methylation 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g48670`	Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway and downstream of small interfering RNA (siRNA) formation.	IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.2009 · DOI: 10.1038/nsmb.1690 An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis.2010 · DOI: 10.1111/j.1365-313x.2010.04130.x IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.2012 · DOI: 10.1371/journal.pgen.1002693 INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.2012 · DOI: 10.1073/pnas.1206638109 IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation.2012 · DOI: 10.4161/epi.21237 A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing.2013 · DOI: 10.1016/j.molcel.2012.11.011 RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA.2014 · DOI: 10.1111/tpj.12563 Two Components of the RNA-Directed DNA Methylation Pathway Associate with MORC6 and Silence Loci Targeted by MORC6 in Arabidopsis.2016 · DOI: 10.1371/journal.pgen.1006026
`At1g80790`	Acts in association with FDM3 and FDM4 for RNA-directed DNA methylation (RdDM).	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034
`At1g15910`	Forms a complex with IDN2 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway.	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034 IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.2012 · DOI: 10.1371/journal.pgen.1002693 INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.2012 · DOI: 10.1073/pnas.1206638109
`At4g00380`	Forms a complex with IDN2 and FDM1/IDNL1 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway.	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034 IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.2012 · DOI: 10.1371/journal.pgen.1002693 INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.2012 · DOI: 10.1073/pnas.1206638109
`At1g13790`	Acts in association with FDM3 and FDM5 for RNA-directed DNA methylation (RdDM).	A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation.2012 · DOI: 10.1093/nar/gks034

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017806 · 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:0032259 methylation Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0008168 methyltransferase activity Molecular Function

KEGG gene cross-reference

ath:AT1G13790

ath:AT3G12550

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.

Cytoplasm0.532

Rank 1 · TkA08G049090 · TK1151

Nucleus0.505

Rank 2 · TkA08G049090 · TK1151

Cell membrane0.041

Rank 3 · TkA08G049090 · TK1151

Endoplasmic reticulum0.033

Rank 4 · TkA08G049090 · TK1151

Mitochondrion0.019

Rank 5 · TkA08G049090 · 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.

PF23991DUF731013-29 aa

PF08681TacA132-47 aa

PF03469XH58-110 aa

PF08681TacA186-129 aa

PF23991DUF7310125-146 aa

PF08681TacA1145-160 aa

PF23991DUF7310170-204 aa

PF03469XH184-190 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G049090	`PF23991`	DUF7310	13	29	6.1	8.1
TkA08G049090	`PF08681`	TacA1	32	47	0.7	10.6
TkA08G049090	`PF03469`	XH	58	110	6.3e-47	159.5
TkA08G049090	`PF08681`	TacA1	86	129	0.7	10.6
TkA08G049090	`PF23991`	DUF7310	125	146	6.1	8.1
TkA08G049090	`PF08681`	TacA1	145	160	0.7	10.6
TkA08G049090	`PF23991`	DUF7310	170	204	6.1	8.1
TkA08G049090	`PF03469`	XH	184	190	6.3e-47	159.5
TkA08G049090	`PF03469`	XH	238	366	6.3e-47	159.5

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
`Q8VZ79`	Arabidopsis thaliana	sp\|Q8VZ79\|IDN2_ARATH Protein INVOLVED IN DE NOVO 2	46.700%	Swiss-Prot	Medium
`Q9SAI1`	Arabidopsis thaliana	sp\|Q9SAI1\|FDM5_ARATH Factor of DNA methylation 5	46.300%	Swiss-Prot	Medium
`Q9S9P3`	Arabidopsis thaliana	sp\|Q9S9P3\|FDM1_ARATH Factor of DNA methylation 1	45.500%	Swiss-Prot	Medium
`F4JH53`	Arabidopsis thaliana	sp\|F4JH53\|FDM2_ARATH Factor of DNA methylation 2	44.700%	Swiss-Prot	Medium
`Q9LMH6`	Arabidopsis thaliana	sp\|Q9LMH6\|FDM4_ARATH Factor of DNA methylation 4	48.000%	Swiss-Prot	Medium

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