LXL04_014603 | RubberDandelionOmics

Gene overview

LXL04_014603

Reference: OH-1004 Chr: Chr03 Coordinates: 53600881-53603428 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2049 bp · LXL04_014603|LXL04_014603|OH1004|cDNA

ATGAGCGTACCACATCAAAAGTTGTTGCGTTTCATTTCTAGTAATTGTTTCTCTCCTGTTGCCGGCGGAATCGCCGTTTCAGCACCGTCAAGGGACAGAGCTGATGTCGCCGGTGGTAACATCCAGCAAGCCACCCCTTTCTTAACCCTAAATATCCCTAAACTCGAACCTAAAGACGAACCTTTCGACGACCCACCCCATCCCCACCATTCTCATACCAATTATGCAAACCCTAACCTTAATTTCACTCTCAACACACA...

CDS

Download CDS FASTA

2049 bp · LXL04_014603|LXL04_014603|OH1004|CDS

ATGAGCGTACCACATCAAAAGTTGTTGCGTTTCATTTCTAGTAATTGTTTCTCTCCTGTTGCCGGCGGAATCGCCGTTTCAGCACCGTCAAGGGACAGAGCTGATGTCGCCGGTGGTAACATCCAGCAAGCCACCCCTTTCTTAACCCTAAATATCCCTAAACTCGAACCTAAAGACGAACCTTTCGACGACCCACCCCATCCCCACCATTCTCATACCAATTATGCAAACCCTAACCTTAATTTCACTCTCAACACACA...

Protein

Download Protein FASTA

682 aa · LXL04_014603|LXL04_014603|OH1004|PROTEIN

MSVPHQKLLRFISSNCFSPVAGGIAVSAPSRDRADVAGGNIQQATPFLTLNIPKLEPKDEPFDDPPHPHHSHTNYANPNLNFTLNTQPDTSQPVAQPAVGENDVYSEFSRIQEMFRTAFSNNTDKYDAPGFIDPDAQAIVPVPEENHLSAVADSSRRKYQQRSGELVRVTNLGVEDERYFRDVVRKTRMMYDSLRVFVTMEDEKRRNNVFGRIPRARGDLKASSVMKDRGLWLNRDKRIVGAIPGVYVGDIFFFRMEICV...

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_014603`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_014603

Location Chr03:53600881-53603428 (+)

Description Similar to SUVH9: Histone-lysine N-methyltransferase family member SUVH9

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g13460`	Histone methyltransferase family member that plays a role in gene silencing.	SRA-domain proteins required for DRM2-mediated de novo DNA methylation.2008 · DOI: 10.1371/journal.pgen.1000280 SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.2014 · DOI: 10.1038/nature12931 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
`At2g33290`	Histone methyltransferase family member that plays a central role in gene silencing.	Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis.2005 · DOI: 10.1038/sj.emboj.7600604 SRA-domain proteins required for DRM2-mediated de novo DNA methylation.2008 · DOI: 10.1371/journal.pgen.1000280 SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.2014 · DOI: 10.1038/nature12931 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
`At5g04940`	Histone methyltransferase.	Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis.2005 · DOI: 10.1038/sj.emboj.7600604
`At1g73100`	Histone methyltransferase.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014603 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009294 DNA-mediated transformation Biological Process

GO:0032259 methylation Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

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

GO:0000775 chromosome, centromeric region Cellular Component

GO:0000792 heterochromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005694 chromosome Cellular Component

GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific Molecular Function

GO:0003690 double-stranded DNA binding Molecular Function

GO:0008168 methyltransferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G73100

ath:AT2G33290

ath:AT4G13460

ath:AT5G04940

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.

Nucleus0.918

Rank 1 · LXL04_014603 · OH-1004

Cytoplasm0.105

Rank 2 · LXL04_014603 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_014603 · OH-1004

Plastid0.026

Rank 4 · LXL04_014603 · OH-1004

Endoplasmic reticulum0.019

Rank 5 · LXL04_014603 · 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.

PF02182.24SAD_SRA240-392 aa

PF05033.23Pre-SET423-518 aa

PF00856.34SET537-668 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014603	`PF02182.24`	SAD_SRA	240	392	1.5e-51	174.7
LXL04_014603	`PF05033.23`	Pre-SET	423	518	1.7e-22	80.6
LXL04_014603	`PF00856.34`	SET	537	668	9.9e-13	49.2

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
`Q9T0G7`	Arabidopsis thaliana	Histone-lysine N-methyltransferase family member SUVH9	57.680%	Swiss-Prot	strong database homology
`O22781`	Arabidopsis thaliana	Histone-lysine N-methyltransferase family member SUVH2	52.895%	Swiss-Prot	strong database homology
`Q9FF80`	Arabidopsis thaliana	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH1	41.468%	Swiss-Prot	moderate database homology
`Q9C5P4`	Arabidopsis thaliana	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH3	39.278%	Swiss-Prot	moderate database homology

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