LXL04_022248 | RubberDandelionOmics

Gene overview

LXL04_022248

Reference: OH-1004 Chr: Chr04 Coordinates: 146787289-146787958 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

525 bp · LXL04_022248|LXL04_022248|OH1004|cDNA

ATGGTGTTGAAGAAGTTTCAAGAAACATCACCATCAAATGAAAACGGAAATTCATCTACTTTTATCGAAGAAATTTCGAATAAAAAGCAACGAATCGATGGCCCTTTTGTCATGCCCCTATTATCAATCCCTAAACTGGAAGAAGAAAGTTCAAAGGCATCAATTATCTTATCTGGAACCGCTAAAAAAGGCAAACTGGGCCCACCTTTAGGATCCGTAGACATCGGTGTTAGCAAAACCGCGTATTTTTTTCAAGTTGC...

CDS

Download CDS FASTA

525 bp · LXL04_022248|LXL04_022248|OH1004|CDS

ATGGTGTTGAAGAAGTTTCAAGAAACATCACCATCAAATGAAAACGGAAATTCATCTACTTTTATCGAAGAAATTTCGAATAAAAAGCAACGAATCGATGGCCCTTTTGTCATGCCCCTATTATCAATCCCTAAACTGGAAGAAGAAAGTTCAAAGGCATCAATTATCTTATCTGGAACCGCTAAAAAAGGCAAACTGGGCCCACCTTTAGGATCCGTAGACATCGGTGTTAGCAAAACCGCGTATTTTTTTCAAGTTGC...

Protein

Download Protein FASTA

174 aa · LXL04_022248|LXL04_022248|OH1004|PROTEIN

MVLKKFQETSPSNENGNSSTFIEEISNKKQRIDGPFVMPLLSIPKLEEESSKASIILSGTAKKGKLGPPLGSVDIGVSKTAYFFQVALPGVKKDPGQFSCEIEQSGMVHVKGETSTGGKSVTRHSRVFEMKFQQQSPPGQFTLSFSLPGRVDPRLFYPNFRSDGIFEAIVMKCE

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_022248`
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_022248

Location Chr04:146787289-146787958 (-)

Description Similar to IDM3: Increased DNA methylation 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20870`	Acts as an anti-silencing factor that prevents DNA hypermethylation and gene repression.	The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing.2015 · DOI: 10.1016/j.molcel.2015.01.009
`At1g54850`	Alpha-crystallin domain-containing protein 22.3.	No verified direct reference in this release
`At1g54840`	Prevents DNA hypermethylation and transcriptional silencing of transgenes and of some endogenous genes.	REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis.2014 · DOI: 10.1105/tpc.114.126730 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_022248 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G20870

ath:AT1G54840

ath:AT1G54850

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.

Nucleus0.510

Rank 1 · LXL04_022248 · OH-1004

Cytoplasm0.440

Rank 2 · LXL04_022248 · OH-1004

Cell membrane0.143

Rank 3 · LXL04_022248 · OH-1004

Endoplasmic reticulum0.060

Rank 4 · LXL04_022248 · OH-1004

Mitochondrion0.034

Rank 5 · LXL04_022248 · 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.

PF31004.1IDM_C57-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022248	`PF31004.1`	IDM_C	57	172	1.2e-52	177.3

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
`Q9SYQ0`	Arabidopsis thaliana	Increased DNA methylation 3	49.704%	Swiss-Prot	moderate database homology
`Q84K79`	Arabidopsis thaliana	Alpha-crystallin domain-containing protein 22.3	46.721%	Swiss-Prot	moderate database homology
`Q8RWL4`	Arabidopsis thaliana	Increased DNA methylation 2	53.774%	Swiss-Prot	moderate database homology

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