LXL04_021814 | RubberDandelionOmics

Gene overview

LXL04_021814

Reference: OH-1004 Chr: Chr04 Coordinates: 137516826-137520965 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3822 bp · LXL04_021814|LXL04_021814|OH1004|cDNA

ATGAAGAGGAAGCTCATAAATTTACACCAAAACACACACCAATTTGATGCACATCCTTTTGAAGCATACTGGTGTGGTTCATGGTTGCCTGTAGAATGCTTACGAATCAGAAATGGAGTTGTTAGCATGTTAATCATAAACGAAGAAAAGTCAACCGAAGAAACCCTTCCCATGTCTGACCTTCGAATAAAGTCAAGAAAAGCAAATTTAGCTGACTGTACATGCTTTTTAAGACCTGGAACAGATGTCTGTGTGCTTTC...

CDS

Download CDS FASTA

3822 bp · LXL04_021814|LXL04_021814|OH1004|CDS

ATGAAGAGGAAGCTCATAAATTTACACCAAAACACACACCAATTTGATGCACATCCTTTTGAAGCATACTGGTGTGGTTCATGGTTGCCTGTAGAATGCTTACGAATCAGAAATGGAGTTGTTAGCATGTTAATCATAAACGAAGAAAAGTCAACCGAAGAAACCCTTCCCATGTCTGACCTTCGAATAAAGTCAAGAAAAGCAAATTTAGCTGACTGTACATGCTTTTTAAGACCTGGAACAGATGTCTGTGTGCTTTC...

Protein

Download Protein FASTA

1273 aa · LXL04_021814|LXL04_021814|OH1004|PROTEIN

MKRKLINLHQNTHQFDAHPFEAYWCGSWLPVECLRIRNGVVSMLIINEEKSTEETLPMSDLRIKSRKANLADCTCFLRPGTDVCVLSTIPLTEEDSTNNNPKPIWIDARINSIERKPHENDKCVCEFHVSIYQKQGPVGMIKKAVHKDTKLVHIDQITILQKLEGKPCEINQYRWHLSEDCNSRRIFKLFTGKFSADISWLIVASVFKQLVFDVKSVDNQIVYQILNDDNDNSNSSQTAVNFKLQIDTSTPFIIPFTKSE...

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_021814`
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_021814

Location Chr04:137516826-137520965 (+)

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

Arabidopsis / Rice Reference Genes and Papers

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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.

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.

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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.

Nucleus0.916

Rank 1 · LXL04_021814 · OH-1004

Cytoplasm0.129

Rank 2 · LXL04_021814 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_021814 · OH-1004

Mitochondrion0.023

Rank 4 · LXL04_021814 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_021814 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF16719.12SAWADEE47-132 aa

PF04851.22ResIII686-894 aa

PF00176.30SNF2-rel_dom690-1007 aa

PF00271.38Helicase_C1071-1187 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021814	`PF16719.12`	SAWADEE	47	132	4.4e-06	27.5
LXL04_021814	`PF04851.22`	ResIII	686	894	1.1e-07	32.6
LXL04_021814	`PF00176.30`	SNF2-rel_dom	690	1007	2e-20	73.8
LXL04_021814	`PF00271.38`	Helicase_C	1071	1187	6.3e-17	62.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9M297`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 1	58.232%	Swiss-Prot	moderate database homology
`F4K493`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 2	55.402%	Swiss-Prot	moderate database homology
`Q9LK10`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 4	32.517%	Swiss-Prot	moderate database homology
`F4I8S3`	Arabidopsis thaliana	SNF2 domain-containing protein CLASSY 3	30.254%	Swiss-Prot	moderate database homology
`Q9SIW2`	Arabidopsis thaliana	Protein CHROMATIN REMODELING 35	31.161%	Swiss-Prot	moderate database homology

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