LXL04_018805 | RubberDandelionOmics

Gene overview

LXL04_018805

Reference: OH-1004 Chr: Chr04 Coordinates: 18474421-18482790 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4002 bp · LXL04_018805|LXL04_018805|OH1004|cDNA

TTGGTCGTTAGGGTTTGTAACCTCTCTATCTCGACTACTCAGCGGAACAAAGAGCAAACGCCGCCGTTCGTCGGAGTAGCTGATCCGAGTGAAAAAATGGCGGACACCAAAGCAGTCACAATTCGAACAAGGAAGTTCATGACAAACAGGCTTCTATCCAGGAAACAATTCGTCATTGATGTGCTCCATCCAGGAAGGCCCAATGTCTCCAAGGCTGAACTCAAGGAGAAGTTGGCTAGGATGTATGAGGTGAAAGATCC...

CDS

Download CDS FASTA

4002 bp · LXL04_018805|LXL04_018805|OH1004|CDS

TTGGTCGTTAGGGTTTGTAACCTCTCTATCTCGACTACTCAGCGGAACAAAGAGCAAACGCCGCCGTTCGTCGGAGTAGCTGATCCGAGTGAAAAAATGGCGGACACCAAAGCAGTCACAATTCGAACAAGGAAGTTCATGACAAACAGGCTTCTATCCAGGAAACAATTCGTCATTGATGTGCTCCATCCAGGAAGGCCCAATGTCTCCAAGGCTGAACTCAAGGAGAAGTTGGCTAGGATGTATGAGGTGAAAGATCC...

Protein

Download Protein FASTA

1333 aa · LXL04_018805|LXL04_018805|OH1004|PROTEIN

MVVRVCNLSISTTQRNKEQTPPFVGVADPSEKMADTKAVTIRTRKFMTNRLLSRKQFVIDVLHPGRPNVSKAELKEKLARMYEVKDPNGIFVFKFRTHFGGGKSTGFGLIYDSVENAKKYEPKYRLVRNGLDTKVEKSRKQLKERKNRAKKIRDQGWRCCQEEEMSFKTLLVLLNPENIRINTKQKPKKLLILSPPSLQSPIHIPSALFQHIDGLKSSSISTINRSFFTSLPVMLLSSTELSNSEKAVSDITLENCDAVD...

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_018805`
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_018805

Location Chr04:18474421-18482790 (-)

Description Similar to IDM1: Increased DNA methylation 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g14980`	Histone H3 acetyltransferase that binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and catalyzes H3K18 and H3K23 acetylation.	A histone acetyltransferase regulates active DNA demethylation in Arabidopsis.2012 · DOI: 10.1126/science.1219416 Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis.2012 · DOI: 10.1073/pnas.1208557109 Regulation of active DNA demethylation by an α-crystallin domain protein in Arabidopsis.2014 · DOI: 10.1016/j.molcel.2014.06.008
`At5g28060`	Small ribosomal subunit protein eS24y.	No verified direct reference in this release
`At3g04920`	Small ribosomal subunit protein eS24z.	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_018805 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002181 cytoplasmic translation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006412 translation Biological Process

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

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009505 plant-type cell wall Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT3G04920

ath:AT3G14980

ath:AT5G28060

ddi:DDB_G0275473

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.

Nucleus0.958

Rank 1 · LXL04_018805 · OH-1004

Cytoplasm0.082

Rank 2 · LXL04_018805 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_018805 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_018805 · OH-1004

Plastid0.013

Rank 5 · LXL04_018805 · 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.

PF01282.26Ribosomal_S24e39-130 aa

PF22970.3DUF7028641-699 aa

PF16135.11TDBD850-906 aa

PF23209.2IDM1_C1082-1221 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018805	`PF01282.26`	Ribosomal_S24e	39	130	7.7e-38	129.2
LXL04_018805	`PF22970.3`	DUF7028	641	699	4.8e-06	27.1
LXL04_018805	`PF16135.11`	TDBD	850	906	3.5e-10	40.4
LXL04_018805	`PF23209.2`	IDM1_C	1082	1221	3.1e-59	199.8

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
`F4IXE7`	Arabidopsis thaliana	Increased DNA methylation 1	37.236%	Swiss-Prot	weak database homology
`Q8LC83`	Arabidopsis thaliana	Small ribosomal subunit protein eS24y	88.430%	Swiss-Prot	weak database homology
`Q9SS17`	Arabidopsis thaliana	Small ribosomal subunit protein eS24z	90.909%	Swiss-Prot	weak database homology

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