LXL04_026202 | RubberDandelionOmics

Gene overview

LXL04_026202

Reference: OH-1004 Chr: Chr05 Coordinates: 122691961-122695987 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3786 bp · LXL04_026202|LXL04_026202|OH1004|cDNA

ATGTTCTCCGACGTCGGCGTAAGTTTTCATGTGGGCAATGCAGTTTTAATCGATTTGTATTTTGGTATAATGCATGATTTAGTGTCACTTCCTCGTACTGTGTTCAATCTGACGGGTGTGTCTGGTATTTTACTATATGTGATTGAAGGGGATAGAGTTGATACGGTGATGGATTTCTCGAGAACTAAGATAAGTCAGCGGACGCGTTCTTGCTATGACAAGCTTTACTTAGAGTTCAATGAGAAAAAAAATAACGGAAG...

CDS

Download CDS FASTA

3786 bp · LXL04_026202|LXL04_026202|OH1004|CDS

ATGTTCTCCGACGTCGGCGTAAGTTTTCATGTGGGCAATGCAGTTTTAATCGATTTGTATTTTGGTATAATGCATGATTTAGTGTCACTTCCTCGTACTGTGTTCAATCTGACGGGTGTGTCTGGTATTTTACTATATGTGATTGAAGGGGATAGAGTTGATACGGTGATGGATTTCTCGAGAACTAAGATAAGTCAGCGGACGCGTTCTTGCTATGACAAGCTTTACTTAGAGTTCAATGAGAAAAAAAATAACGGAAG...

Protein

Download Protein FASTA

1261 aa · LXL04_026202|LXL04_026202|OH1004|PROTEIN

MFSDVGVSFHVGNAVLIDLYFGIMHDLVSLPRTVFNLTGVSGILLYVIEGDRVDTVMDFSRTKISQRTRSCYDKLYLEFNEKKNNGRPRNPRRGSGGGGEDRIDSVGESSAKSSDGLKGSGGKRDGIKVRSCKINKGRKGKEELGKASKKGNNETPICVIEDSEDDDDDDDRVGLNESSPGTEETSGRGKVKSSERGKKVSRKSLIDEVEDDCGHDDKCGQTNDSHHNKNNDDDDDDDVVSLLGDNPMSSKSPERNDSYG...

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	`LXL04_026202`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_026202

Location Chr05:122691961-122695987 (+)

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.

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.

Nucleus0.955

Rank 1 · LXL04_026202 · OH-1004

Cytoplasm0.091

Rank 2 · LXL04_026202 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_026202 · OH-1004

Mitochondrion0.015

Rank 4 · LXL04_026202 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_026202 · OH-1004

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.

PF04851.22ResIII713-908 aa

PF00176.30SNF2-rel_dom721-1012 aa

PF00271.38Helicase_C1060-1178 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026202	`PF04851.22`	ResIII	713	908	5.7e-07	30.3
LXL04_026202	`PF00176.30`	SNF2-rel_dom	721	1012	1.5e-22	80.7
LXL04_026202	`PF00271.38`	Helicase_C	1060	1178	3.9e-18	66.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`F4I8S3`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 3	45.884%	Swiss-Prot	moderate database homology
`Q9LK10`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 4	42.490%	Swiss-Prot	moderate database homology
`F4K493`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 2	32.749%	Swiss-Prot	moderate database homology
`Q9M297`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 1	30.975%	Swiss-Prot	moderate database homology
`Q9SIW2`	Arabidopsis thaliana	Protein CHROMATIN REMODELING 35	30.560%	Swiss-Prot	weak database homology

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