LXL04_039100 | RubberDandelionOmics

Gene overview

LXL04_039100

Reference: OH-1004 Chr: Chr09 Coordinates: 59302612-59306699 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2616 bp · LXL04_039100|LXL04_039100|OH1004|cDNA

ATGAAAGAGGCGGACAGATCTAAGCAGTCGAGAACTGTGGTAAAGAAGAAAAACTCCTCAAAGGAGAAAAAGAGACGTCGAGTTGTTGAGAGTGATTGTGAGTCCAGTGATCACTCCTCAGAAACTAGTCGCCAGAAAGCCGATAAACACGATACACCTTCAGCTGTTTACAAAGGGGCTTATTCAGAAACGAAAGAATTTGAGACGGAGAAAAGGGCAAGTAGTGGATTAGATGTATTTGAGTTTGACGAATACGATGG...

CDS

Download CDS FASTA

2616 bp · LXL04_039100|LXL04_039100|OH1004|CDS

ATGAAAGAGGCGGACAGATCTAAGCAGTCGAGAACTGTGGTAAAGAAGAAAAACTCCTCAAAGGAGAAAAAGAGACGTCGAGTTGTTGAGAGTGATTGTGAGTCCAGTGATCACTCCTCAGAAACTAGTCGCCAGAAAGCCGATAAACACGATACACCTTCAGCTGTTTACAAAGGGGCTTATTCAGAAACGAAAGAATTTGAGACGGAGAAAAGGGCAAGTAGTGGATTAGATGTATTTGAGTTTGACGAATACGATGG...

Protein

Download Protein FASTA

871 aa · LXL04_039100|LXL04_039100|OH1004|PROTEIN

MKEADRSKQSRTVVKKKNSSKEKKRRRVVESDCESSDHSSETSRQKADKHDTPSAVYKGAYSETKEFETEKRASSGLDVFEFDEYDGFDDIKSTKFANSRKHRWSSYRQSGDQMESGNGGKSRLEIEDDDFDLPLSAFTNKYRSFSNQPIRLQHDGEGQTSKSPKPMAEKTTKKSNSKVESAKIKPIENVKKDKEITVNNGGTEKQILREKIKNMLLDAGWSIGYRPRKNKNYLDAIYTNPSGTAYWSIIKAYETLEKGD...

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_039100`
TK1151 ID	TkA04G504440
OH-1004 ID	LXL04_039100
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	98.700
Protein coverage (%)	TK1151 95.567 / OH-1004 44.546 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_039100

Location Chr09:59302612-59306699 (+)

Description Similar to IDM1: Increased DNA methylation 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_039100 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0000724 double-strand break repair via homologous recombination Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0007064 mitotic sister chromatid cohesion Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0015671 oxygen transport Biological Process

GO:0030261 chromosome condensation Biological Process

GO:0034728 nucleosome organization Biological Process

KEGG gene cross-reference

ath:AT3G14980

dme:Dmel_CG8103

dme:Dmel_CG9594

mmu:107932

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.

Nucleus0.946

Rank 1 · LXL04_039100 · OH-1004

Cytoplasm0.096

Rank 2 · LXL04_039100 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_039100 · OH-1004

Endoplasmic reticulum0.019

Rank 4 · LXL04_039100 · OH-1004

Plastid0.014

Rank 5 · LXL04_039100 · 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.

PF22970.3DUF7028195-258 aa

PF16135.11TDBD352-403 aa

PF00628.36PHD431-470 aa

PF23209.2IDM1_C570-709 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039100	`PF22970.3`	DUF7028	195	258	2.5e-14	53.7
LXL04_039100	`PF16135.11`	TDBD	352	403	1.2e-18	67.6
LXL04_039100	`PF00628.36`	PHD	431	470	4.8e-11	43.2
LXL04_039100	`PF23209.2`	IDM1_C	570	709	1.1e-57	194.7

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4IXE7`	Arabidopsis thaliana	Increased DNA methylation 1	38.793%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card