LXL04_029823 | RubberDandelionOmics

Gene overview

LXL04_029823

Reference: OH-1004 Chr: Chr06 Coordinates: 101203736-101206721 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1474 bp · LXL04_029823|LXL04_029823|OH1004|cDNA

ATGAGGACTTTGAAGCCTATGAACCGAAATCATAGCAACAAAGAGGATTTGCAAAGAGGATCACTGAATATAAAACAAAGACCTGATGGTTCTTCAAAATCACAAAGAATCGGTACTCGTAAAACAAAAAGGCTAGAGATTAACAACCCAAGAGAAACACAAAAAAGCGCGACAATTCTATCATGGCTAGTCGATTCCAAAGTAGTCCCAGAAAACGCAACTATCTATTATACAGGCGCAACTAGTCAAGATGGTTTCAA...

CDS

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1467 bp · LXL04_029823|LXL04_029823|OH1004|CDS

ATGAGGACTTTGAAGCCTATGAACCGAAATCATAGCAACAAAGAGGATTTGCAAAGAGGATCACTGAATATAAAACAAAGACCTGATGGTTCTTCAAAATCACAAAGAATCGGTACTCGTAAAACAAAAAGGCTAGAGATTAACAACCCAAGAGAAACACAAAAAAGCGCGACAATTCTATCATGGCTAGTCGATTCCAAAGTAGTCCCAGAAAACGCAACTATCTATTATACAGGCGCAACTAGTCAAGATGGTTTCAA...

Protein

Download Protein FASTA

488 aa · LXL04_029823|LXL04_029823|OH1004|PROTEIN

MRTLKPMNRNHSNKEDLQRGSLNIKQRPDGSSKSQRIGTRKTKRLEINNPRETQKSATILSWLVDSKVVPENATIYYTGATSQDGFKKGTIEHNGILCTCCRSFFTIRGFQLHTGGRVCDNPYDATGVDGIQGDGSITPLSQCMKLALQKRDGPEHHGIKYVTTKGSEDGDVYDDACILCADGGNLICCEQCNSTFHVKCLGMQVVPDEPYYCSYCVCKLCGKPITKKDYSCLTCSLCEKQYHVRCSNESLKIDINCFPR...

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_029823`
TK1151 ID	TkA07G350620
OH-1004 ID	LXL04_029823
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	97.700
Protein coverage (%)	TK1151 98.721 / OH-1004 79.098 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	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_029823

Location Chr06:101203736-101206721 (+)

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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029823 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0004402 histone acetyltransferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0010385 double-stranded methylated DNA binding Molecular Function

GO:0042393 histone binding Molecular Function

GO:0043993 histone H3K18 acetyltransferase activity Molecular Function

KEGG gene cross-reference

ath:AT3G14980

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.

Nucleus0.789

Rank 1 · LXL04_029823 · OH-1004

Cytoplasm0.265

Rank 2 · LXL04_029823 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_029823 · OH-1004

Endoplasmic reticulum0.023

Rank 4 · LXL04_029823 · OH-1004

Mitochondrion0.017

Rank 5 · LXL04_029823 · 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.

PF16135.11TDBD89-128 aa

PF00628.36PHD177-216 aa

PF23209.2IDM1_C328-466 aa

PF00583.32Acetyltransf_1356-439 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029823	`PF16135.11`	TDBD	89	128	3.3e-08	34.1
LXL04_029823	`PF00628.36`	PHD	177	216	4.1e-06	27.4
LXL04_029823	`PF23209.2`	IDM1_C	328	466	2e-46	158.3
LXL04_029823	`PF00583.32`	Acetyltransf_1	356	439	8.7e-06	26.7

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
`F4IXE7`	Arabidopsis thaliana	Increased DNA methylation 1	32.151%	Swiss-Prot	moderate database homology

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