LXL04_012605 | RubberDandelionOmics

Gene overview

LXL04_012605

Reference: OH-1004 Chr: Chr03 Coordinates: 15453861-15458763 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3645 bp · LXL04_012605|LXL04_012605|OH1004|cDNA

ATGGGAGAAGGTGAGGTATGTGTGGCTGTGCTGACCAATGTTGGGGAAAtggaaaatgagaaaattcagCAAAAGCGTGACCATCAATGGCTAACTGTTGGTTCTGAGATGGAGCCTTTGCCCAAAAAACAGGCCAAAGAGGGTTCACTTGATGATGAAGTGGATTCTTGTGCTATTAGTCATTCAGATGTGGCCCTAGTATCTGTTGAACAAGAGCCATGTGCTAAAACACCTCCCACAGATGGTTTAAATATTATTAA...

CDS

Download CDS FASTA

3645 bp · LXL04_012605|LXL04_012605|OH1004|CDS

ATGGGAGAAGGTGAGGTATGTGTGGCTGTGCTGACCAATGTTGGGGAAATGGAAAATGAGAAAATTCAGCAAAAGCGTGACCATCAATGGCTAACTGTTGGTTCTGAGATGGAGCCTTTGCCCAAAAAACAGGCCAAAGAGGGTTCACTTGATGATGAAGTGGATTCTTGTGCTATTAGTCATTCAGATGTGGCCCTAGTATCTGTTGAACAAGAGCCATGTGCTAAAACACCTCCCACAGATGGTTTAAATATTATTAA...

Protein

Download Protein FASTA

1214 aa · LXL04_012605|LXL04_012605|OH1004|PROTEIN

MGEGEVCVAVLTNVGEMENEKIQQKRDHQWLTVGSEMEPLPKKQAKEGSLDDEVDSCAISHSDVALVSVEQEPCAKTPPTDGLNIIKPEPSIEQVIKECSDGLDLGQTTEALNGTMPDASGEELVQEWLKVTEQQICESKQAKESLNYNGVNSSVEQPVTEGLDNMELDPCGEKHSLEVSNDMEIEHIVEQPVKECLNEMVPEPIVEQPVKECLNEMVPEPIVEQPVKECLNEMVPEPIVEQPVKECLNEMVQESIVEQP...

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_012605`
TK1151 ID	TkA02G550460
OH-1004 ID	LXL04_012605
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.800
Protein coverage (%)	TK1151 99.053 / OH-1004 94.316 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_012605

Location Chr03:15453861-15458763 (+)

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_012605 · 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:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

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

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0007051 spindle organization Biological Process

GO:0007098 centrosome cycle Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0015671 oxygen transport Biological Process

KEGG gene cross-reference

ath:AT3G14980

hsa:1107

hsa:1108

mmu:107932

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.

Nucleus0.835

Rank 1 · LXL04_012605 · OH-1004

Cytoplasm0.165

Rank 2 · LXL04_012605 · OH-1004

Cell membrane0.067

Rank 3 · LXL04_012605 · OH-1004

Endoplasmic reticulum0.030

Rank 4 · LXL04_012605 · OH-1004

Golgi apparatus0.018

Rank 5 · LXL04_012605 · 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.

PF16135.11TDBD603-656 aa

PF16135.11TDBD812-857 aa

PF00628.36PHD876-915 aa

PF23209.2IDM1_C1071-1208 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012605	`PF16135.11`	TDBD	603	656	2.1e-25	89.2
LXL04_012605	`PF16135.11`	TDBD	812	857	2.1e-25	89.2
LXL04_012605	`PF00628.36`	PHD	876	915	1.4e-09	38.6
LXL04_012605	`PF23209.2`	IDM1_C	1071	1208	3.5e-49	167.2

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	28.205%	Swiss-Prot	weak database homology

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