TkA05G426260 | RubberDandelionOmics

Gene overview

TkA05G426260

Reference: TK1151 Chr: Chr05 Coordinates: 106303060-106308846 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4383 bp · TkA05G426260|TK1151|cDNA

TTTACAGCACCCATTAGACTGGGCGGTGTGGAAGCCCCTTATGCATTGACTACACCACTCCACAGTCCACAACCACTGCAAAAACTTTACTCTCTCTAGTGTGTGTGTGTTCATGCAAACGAGAAAGAGTCGACAATGTACTCGAACATTGAGATTTACCGATAAAAGACCACAAAAATGTTGCATAAATTTCTCTGCAGTTTTGTCTTTCCTCTAACGCATTGATTCTCTGTTTAAGCATCGATTTCTGTGCTCCGTCG...

CDS

Download CDS FASTA

3816 bp · TkA05G426260|TK1151|CDS

ATGAAGAGGAGATATAATTATTTACACCAATACACACATCAGTTTGATCCACAGCCTTTTGAAGCATACTGGAGTGGTTCATGGGCACCTGTGGAGCGAATAAGAATCAGACATGGAGTTGTTAGCACATTTATTAGTAACGAAGGAGAGAAACTGGAAGAAAGCATTCCCATGTCAGATATTCGAATAAGATCCAGAAAAGCAACTTTGGCTGATTGCTTATGCTTTTTAAGACCTGGAACAGATGTCTGTGTGCATTC...

Protein

Download Protein FASTA

1271 aa · TkA05G426260|TK1151|PROTEIN

MKRRYNYLHQYTHQFDPQPFEAYWSGSWAPVERIRIRHGVVSTFISNEGEKLEESIPMSDIRIRSRKATLADCLCFLRPGTDVCVHSSIPLTEEESSNENPKPIWIDARISSVERKPHENDKCICEFHISIYMKQNPAGMIKKTVHKDTKIVHIDQISILQKLEIKPCDSNHYRWRFSEDCNSRLVYKLFTGKFSSDLSWLIVASVFKQLTFDVKSVDNQIVYQIFDDDSDNNSSQTAVNFKLQIDTSIPFVSSFTESQE...

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	`TkA05G426260`
TK1151 ID	TkA05G426260
OH-1004 ID	LXL04_021814
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	78.700
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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 TkA05G426260

Location Chr05:106303060-106308846 (+)

Description Similar to CLSY1: SNF2 domain-containing protein CLASSY 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g42670`	Probable chromatin remodeling factor.	Identification of genes required for de novo DNA methylation in Arabidopsis.2011 · DOI: 10.4161/epi.6.3.14242
`At5g20420`	Probable chromatin remodeling factor.	No verified direct reference in this release
`At3g24340`	Probable chromatin remodeling factor.	No verified direct reference in this release
`At1g05490`	Probable chromatin remodeling factor.	No verified direct reference in this release
`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_021814 · 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:0031047 regulatory ncRNA-mediated gene silencing Biological Process

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

GO:0140745 siRNA transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

GO:0004386 helicase activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0016787 hydrolase activity Molecular Function

KEGG gene cross-reference

ath:AT1G05490

ath:AT3G24340

ath:AT3G42670

ath:AT5G20420

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.

Nucleus0.914

Rank 1 · TkA05G426260 · TK1151

Cytoplasm0.141

Rank 2 · TkA05G426260 · TK1151

Cell membrane0.028

Rank 3 · TkA05G426260 · TK1151

Mitochondrion0.026

Rank 4 · TkA05G426260 · TK1151

Endoplasmic reticulum0.014

Rank 5 · TkA05G426260 · 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.

PF16719SAWADEE45-135 aa

PF16719SAWADEE194-233 aa

PF04081DNA_pol_delta_4373-425 aa

PF06420Mgm101p451-530 aa

PF04851ResIII500-531 aa

PF04081DNA_pol_delta_4508-590 aa

PF04851ResIII684-892 aa

PF00176SNF2-rel_dom688-1009 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G426260	`PF16719`	SAWADEE	45	135	6.3e-06	27.0
TkA05G426260	`PF16719`	SAWADEE	194	233	6.3e-06	27.0
TkA05G426260	`PF04081`	DNA_pol_delta_4	373	425	5.2	8.1
TkA05G426260	`PF06420`	Mgm101p	451	530	0.19	12.0
TkA05G426260	`PF04851`	ResIII	500	531	3.1e-07	31.2
TkA05G426260	`PF04081`	DNA_pol_delta_4	508	590	5.2	8.1
TkA05G426260	`PF04851`	ResIII	684	892	3.1e-07	31.2
TkA05G426260	`PF00176`	SNF2-rel_dom	688	1009	5e-20	72.5
TkA05G426260	`PF00271`	Helicase_C	745	787	1.7e-17	64.4
TkA05G426260	`PF00271`	Helicase_C	1068	1185	1.7e-17	64.4

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
`Q9M297`	Arabidopsis thaliana	sp\|Q9M297\|CLSY1_ARATH SNF2 domain-containing protein CLASSY 1	46.300%	Swiss-Prot	Medium
`F4K493`	Arabidopsis thaliana	sp\|F4K493\|CLSY2_ARATH SNF2 domain-containing protein CLASSY 2	46.100%	Swiss-Prot	Medium
`Q9LK10`	Arabidopsis thaliana	sp\|Q9LK10\|CLSY4_ARATH SNF2 domain-containing protein CLASSY 4	32.100%	Swiss-Prot	Medium
`F4I8S3`	Arabidopsis thaliana	sp\|F4I8S3\|CLSY3_ARATH SNF2 domain-containing protein CLASSY 3	32.100%	Swiss-Prot	Medium
`Q9SIW2`	Arabidopsis thaliana	sp\|Q9SIW2\|CHR35_ARATH Protein CHROMATIN REMODELING 35	29.700%	Swiss-Prot	Low

JBrowse

View in Genome Browser

Gene Card