TkA06G021590 | RubberDandelionOmics

Gene overview

TkA06G021590

Reference: TK1151 Chr: Chr06 Coordinates: 5917464-5922132 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4294 bp · TkA06G021590|TK1151|cDNA

CTTGAATGCACAATATACATAACGTGAAGGCAAACGTAAGTAGGATTCTCAAGTCGCAGGCGCAGGTGGGGCCAACATAAGGTCTTTTTTCCAGATCTGAGTTACGCCGTCGAAATGTCGAATGCATTGCAATATAACTTTTGGCGCCCTTCGCGTTTCTTAGACGAGCGAACCCAAAAGATTCGACATTAATGCTGCTGTATCTCTCTAACTTTAGTTTCCTTCTCTTTCTAGAATACGAATTGACTTTTGACTACTCG...

CDS

Download CDS FASTA

3615 bp · TkA06G021590|TK1151|CDS

ATGGATTTCTCGAGAACTAAGATAAGTCAGCGGACGCGTTCTTGCTATGACAAGCTTTACTTAGAGTTCAATGAGAAAAAAAATAACGGAAGGCCTCGGAATCCTCGCCGCGGCAGCGGCGGTGGTGGTGAAGATCGAATCGATAGTGTTGGTGAGAGTTCTGCGAAATCAAGTGACGGCTTGAAGGGAAGCGGTGGAAAGAGAGATGGGATCAAAGTTAGGTCTTGTAAGATAAATAAAGGGCGTAAAGGGAAGGAGGA...

Protein

Download Protein FASTA

1204 aa · TkA06G021590|TK1151|PROTEIN

MDFSRTKISQRTRSCYDKLYLEFNEKKNNGRPRNPRRGSGGGGEDRIDSVGESSAKSSDGLKGSGGKRDGIKVRSCKINKGRKGKEELGKASKKGNNETPICVIEDSEDDDDDDRVGLNESSPGTEETSGRGKVKSSERGKKVSRKSLIDEVEDDCGHDDKCGQTNDSHHNKNNDDDDDDDVVSLLGDNPMSSKSPERNDSYGKTEKNSEKDFQCDITASNDDCLKEKNRITEDKSVTSNGCHPDESDDHEGITLGDDIT...

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	`TkA06G021590`
TK1151 ID	TkA06G021590
OH-1004 ID	LXL04_026202
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.100
Protein coverage (%)	TK1151 100.000 / OH-1004 95.559 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 TkA06G021590

Location Chr06:5917464-5922132 (-)

Description Similar to CLSY3: SNF2 domain-containing protein CLASSY 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g05490`	Probable chromatin remodeling factor.	No verified direct reference in this release
`At3g24340`	Probable chromatin remodeling factor.	No verified direct reference in this release
`At5g20420`	Probable chromatin remodeling factor.	No verified direct reference in this release
`At3g42670`	Probable chromatin remodeling factor.	Identification of genes required for de novo DNA methylation in Arabidopsis.2011 · DOI: 10.4161/epi.6.3.14242
`At2g16390`	Subunit of the chromatin-remodeling complex (DDR complex) that mediates RNA polymerases IV and V (Pol IV and Pol V) recruitment to chromatin.	Atypical RNA polymerase subunits required for RNA-directed DNA methylation.2005 · DOI: 10.1038/ng1580 A SNF2-like protein facilitates dynamic control of DNA methylation.2005 · DOI: 10.1038/sj.embor.7400446 Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis.2006 · DOI: 10.1038/sj.emboj.7601150 RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis.2006 · DOI: 10.1371/journal.pgen.0020083 A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.2008 · DOI: 10.1038/ng.119 Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes.2008 · DOI: 10.1016/j.cell.2008.09.035 NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation.2009 · DOI: 10.1101/gad.1765209 Defining the functional network of epigenetic regulators in Arabidopsis thaliana.2009 · DOI: 10.1093/mp/ssp017 RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway.2009 · DOI: 10.1093/mp/ssp006 The RNA silencing enzyme RNA polymerase v is required for plant immunity.2011 · DOI: 10.1371/journal.pgen.1002434 RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats.2012 · DOI: 10.4161/epi.20290 The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin.2013 · DOI: 10.1016/j.cell.2013.02.033

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026202 · 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:0001059 transcription by RNA polymerase IV Biological Process

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0035563 positive regulation of chromatin binding Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0070828 heterochromatin organization Biological Process

GO:0071360 cellular response to exogenous dsRNA Biological Process

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

GO:0140745 siRNA transcription Biological Process

GO:0000419 RNA polymerase V complex Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G05490

ath:AT2G16390

ath:AT3G24340

ath:AT3G42670

ath:AT5G20420

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.

Nucleus0.959

Rank 1 · TkA06G021590 · TK1151

Cytoplasm0.089

Rank 2 · TkA06G021590 · TK1151

Cell membrane0.023

Rank 3 · TkA06G021590 · TK1151

Mitochondrion0.014

Rank 4 · TkA06G021590 · TK1151

Endoplasmic reticulum0.012

Rank 5 · TkA06G021590 · 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.

PF04851ResIII656-851 aa

PF00176SNF2-rel_dom664-965 aa

PF13173AAA_14801-848 aa

PF13173AAA_14998-1081 aa

PF00271Helicase_C1003-1121 aa

PF13307Helicase_C_21011-1095 aa

PF13173AAA_141142-1192 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G021590	`PF04851`	ResIII	656	851	4.7e-07	30.6
TkA06G021590	`PF00176`	SNF2-rel_dom	664	965	7.7e-23	81.7
TkA06G021590	`PF13173`	AAA_14	801	848	0.095	13.4
TkA06G021590	`PF13173`	AAA_14	998	1081	0.095	13.4
TkA06G021590	`PF00271`	Helicase_C	1003	1121	3.7e-18	66.5
TkA06G021590	`PF13307`	Helicase_C_2	1011	1095	0.23	12.2
TkA06G021590	`PF13173`	AAA_14	1142	1192	0.095	13.4

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
`F4I8S3`	Arabidopsis thaliana	sp\|F4I8S3\|CLSY3_ARATH SNF2 domain-containing protein CLASSY 3	45.800%	Swiss-Prot	Medium
`Q9LK10`	Arabidopsis thaliana	sp\|Q9LK10\|CLSY4_ARATH SNF2 domain-containing protein CLASSY 4	42.800%	Swiss-Prot	Medium
`F4K493`	Arabidopsis thaliana	sp\|F4K493\|CLSY2_ARATH SNF2 domain-containing protein CLASSY 2	32.900%	Swiss-Prot	Medium
`Q9M297`	Arabidopsis thaliana	sp\|Q9M297\|CLSY1_ARATH SNF2 domain-containing protein CLASSY 1	31.200%	Swiss-Prot	Medium
`Q9SIW2`	Arabidopsis thaliana	sp\|Q9SIW2\|CHR35_ARATH Protein CHROMATIN REMODELING 35	29.400%	Swiss-Prot	Low

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