TkA05G432040 | RubberDandelionOmics

Gene overview

TkA05G432040

Reference: TK1151 Chr: Chr05 Coordinates: 107737986-107740384 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1428 bp · TkA05G432040|TK1151|cDNA

AAGCCAAAAGACCCCTTCAGACTTCAGACATGACTCTCCTCTCTTGTTGACGACAGTCATCGGGAAAAATGGAGGACGGTAAAATGGTTTCCGAGCTTCGAAAGGCGCGTAGTTTGGTGGTAGGGCTGGCGAGAGAAGTCGACATGAAGAATCAAAGGCTGTGGGAAATGGAGCGCCATTCTGAAGAGATTTCTACACGCCTCCATTCCATGATTGCTGAGAAAGATCGGATGAACCATTCGTTTTCAGAAGAAATGAGA...

CDS

Download CDS FASTA

552 bp · TkA05G432040|TK1151|CDS

ATGGACAATTTAAACCAAACTCTTATACTTAGAGAACACATGAGTAACAATGAGCTACAAGCTGCTAGAAAGGAACTCATAAATGTTTTACCCCAAATTTTGGAGGGAAGCGCTATGATTGGACTGAAAAGAATGGGGGAGGTTGCTCAAAAACCTTTTCAAGATGTTTGCTTGCAGAGATTTTCTGCTCAAGATTGGGAATTGAGGTCAGTTGAGTTAAGTTCATTGTGGCAAGATAAGGTTAACAATCCAAATTGGCA...

Protein

Download Protein FASTA

183 aa · TkA05G432040|TK1151|PROTEIN

MDNLNQTLILREHMSNNELQAARKELINVLPQILEGSAMIGLKRMGEVAQKPFQDVCLQRFSAQDWELRSVELSSLWQDKVNNPNWHPFKHAVKDGKLQEIIDEDDTDLKELKSQWGEEPCKAVVNALLELNEYNSSGRYVVSELWNFKENKKATLKEVIDCLIQQLKTNKSLKRRRDTQRPN

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	`TkA05G432040`
TK1151 ID	TkA05G432040
OH-1004 ID	LXL04_021930
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.400
Protein coverage (%)	TK1151 96.175 / OH-1004 16.191 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA05G432040

Location Chr05:107737986-107740384 (-)

Description Similar to IDN2: Protein INVOLVED IN DE NOVO 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`At3g12550`	Acts in association with FDM4 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

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Functional annotation source: OH1004 · LXL04_021930 · 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:0010569 regulation of double-strand break repair via homologous recombination Biological Process

GO:0046686 response to cadmium ion Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003723 RNA binding Molecular Function

GO:0003725 double-stranded RNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G15910

ath:AT3G12550

ath:AT3G48670

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.

Nucleus0.618

Rank 1 · TkA05G432040 · TK1151

Cytoplasm0.505

Rank 2 · TkA05G432040 · TK1151

Cell membrane0.036

Rank 3 · TkA05G432040 · TK1151

Endoplasmic reticulum0.025

Rank 4 · TkA05G432040 · TK1151

Mitochondrion0.018

Rank 5 · TkA05G432040 · 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.

PF07133Merozoite_SPAM2-37 aa

PF18538DUF562436-94 aa

PF03469XH43-171 aa

PF18609SAM_Exu90-138 aa

PF07133Merozoite_SPAM90-150 aa

PF29031KH_KHD4141-170 aa

PF18538DUF5624142-174 aa

PF18609SAM_Exu148-171 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G432040	`PF07133`	Merozoite_SPAM	2	37	0.2	12.4
TkA05G432040	`PF18538`	DUF5624	36	94	0.21	12.4
TkA05G432040	`PF03469`	XH	43	171	7.2e-54	182.0
TkA05G432040	`PF18609`	SAM_Exu	90	138	0.008	17.1
TkA05G432040	`PF07133`	Merozoite_SPAM	90	150	0.2	12.4
TkA05G432040	`PF29031`	KH_KHD4	141	170	0.082	13.7
TkA05G432040	`PF18538`	DUF5624	142	174	0.21	12.4
TkA05G432040	`PF18609`	SAM_Exu	148	171	0.008	17.1
TkA05G432040	`PF07133`	Merozoite_SPAM	149	171	0.2	12.4

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
`Q9S9P3`	Arabidopsis thaliana	sp\|Q9S9P3\|FDM1_ARATH Factor of DNA methylation 1	49.200%	Swiss-Prot	Medium
`F4JH53`	Arabidopsis thaliana	sp\|F4JH53\|FDM2_ARATH Factor of DNA methylation 2	47.500%	Swiss-Prot	Medium
`Q8VZ79`	Arabidopsis thaliana	sp\|Q8VZ79\|IDN2_ARATH Protein INVOLVED IN DE NOVO 2	49.400%	Swiss-Prot	Medium
`Q9SAI1`	Arabidopsis thaliana	sp\|Q9SAI1\|FDM5_ARATH Factor of DNA methylation 5	46.100%	Swiss-Prot	Medium
`Q9LHB1`	Arabidopsis thaliana	sp\|Q9LHB1\|FDM3_ARATH Factor of DNA methylation 3	44.300%	Swiss-Prot	Medium

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