LXL04_027000 | RubberDandelionOmics

Gene overview

LXL04_027000

Reference: OH-1004 Chr: Chr06 Coordinates: 6713443-6713919 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

477 bp · LXL04_027000|LXL04_027000|OH1004|cDNA

ATGAGTTGGACTATTCTCAAGTACGAAAGAAACACTAGTCAACCGAAGATAAAGGAGGCGTTATCATTGTTGGTGAGTAGGCATTTCGATTATGGCTTAATGAATTATTGTTTATCTGATAAGTCAGAAACACACACTGGGTTTTACATCGCCGTCTTAGAAACAAACAGAGGTATGGTCACCACTTGTGCTGTAAGCATCCATGATAATGAGTTGGCAGAAGTTCCTTATGTAGCCACAAAAGAAATGTACGAGAATAA...

CDS

Download CDS FASTA

477 bp · LXL04_027000|LXL04_027000|OH1004|CDS

ATGAGTTGGACTATTCTCAAGTACGAAAGAAACACTAGTCAACCGAAGATAAAGGAGGCGTTATCATTGTTGGTGAGTAGGCATTTCGATTATGGCTTAATGAATTATTGTTTATCTGATAAGTCAGAAACACACACTGGGTTTTACATCGCCGTCTTAGAAACAAACAGAGGTATGGTCACCACTTGTGCTGTAAGCATCCATGATAATGAGTTGGCAGAAGTTCCTTATGTAGCCACAAAAGAAATGTACGAGAATAA...

Protein

Download Protein FASTA

158 aa · LXL04_027000|LXL04_027000|OH1004|PROTEIN

MSWTILKYERNTSQPKIKEALSLLVSRHFDYGLMNYCLSDKSETHTGFYIAVLETNRGMVTTCAVSIHDNELAEVPYVATKEMYENKGFCKILMAQVEEKLKELNVKKIVLHSKLINRLGVVWNSLGFSPMTESAEKLVQGKYKLVPFDDVILWQKVL

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_027000`
TK1151 ID	TkA07G023750
OH-1004 ID	LXL04_027000
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_027000

Location Chr06:6713443-6713919 (+)

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_027000 · 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.

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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.

Cytoplasm0.658

Rank 1 · LXL04_027000 · OH-1004

Nucleus0.450

Rank 2 · LXL04_027000 · OH-1004

Mitochondrion0.055

Rank 3 · LXL04_027000 · OH-1004

Endoplasmic reticulum0.047

Rank 4 · LXL04_027000 · OH-1004

Cell membrane0.041

Rank 5 · LXL04_027000 · 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.

PF23209.2IDM1_C41-156 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027000	`PF23209.2`	IDM1_C	41	156	3.6e-25	89.4

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
`F4IXE7`	Arabidopsis thaliana	Increased DNA methylation 1	33.628%	Swiss-Prot	moderate database homology

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