LXL04_017901 | RubberDandelionOmics

Gene overview

LXL04_017901

Reference: OH-1004 Chr: Chr04 Coordinates: 3203058-3207934 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3420 bp · LXL04_017901|LXL04_017901|OH1004|cDNA

ATGGCGGAGGACATTGAAGCGGCGGGACTGATTTCTGAGCGATCAAGAAAACGCAAGAGACGCCACCCAATTCATAAGCTTCTTCCAAACCAAAAAGTTGAAGTAAGGAGTATTGAAGAAGGATTTGGGGGCTCATGGCACTGTGCAACTGTAATCACTTGTAAAAACCAAATTCATGTGGTCAAATATGATCATATTACATGCGATGATGGTTCTGATAACCTTACTGACTCCATTACAGCTTCATTTACATCAAAGTT...

CDS

Download CDS FASTA

3420 bp · LXL04_017901|LXL04_017901|OH1004|CDS

ATGGCGGAGGACATTGAAGCGGCGGGACTGATTTCTGAGCGATCAAGAAAACGCAAGAGACGCCACCCAATTCATAAGCTTCTTCCAAACCAAAAAGTTGAAGTAAGGAGTATTGAAGAAGGATTTGGGGGCTCATGGCACTGTGCAACTGTAATCACTTGTAAAAACCAAATTCATGTGGTCAAATATGATCATATTACATGCGATGATGGTTCTGATAACCTTACTGACTCCATTACAGCTTCATTTACATCAAAGTT...

Protein

Download Protein FASTA

1139 aa · LXL04_017901|LXL04_017901|OH1004|PROTEIN

MAEDIEAAGLISERSRKRKRRHPIHKLLPNQKVEVRSIEEGFGGSWHCATVITCKNQIHVVKYDHITCDDGSDNLTDSITASFTSKFHNNRGRIRPVAPQFNSNLKSLHYGLCVDVFHEDAWWEGVVFDYDDGCDERLVFFPDIGDELMAKIENLRFTRDWNPDSDKWKVRGNWVFLEVLEELELEWPILVSVRQIWYELRMKKMFLKEIKEWTCQIREVWKETVKEVIVDNLKLTMVEFFNRFQCEGHESLDINTKILD...

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_017901`
TK1151 ID	TkA08G041910
OH-1004 ID	LXL04_017901
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.400
Protein coverage (%)	TK1151 90.833 / OH-1004 28.709 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_017901

Location Chr04:3203058-3207934 (+)

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_017901 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II 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:0006366 transcription by RNA polymerase II Biological Process

GO:0007064 mitotic sister chromatid cohesion Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0030261 chromosome condensation Biological Process

GO:0034728 nucleosome organization Biological Process

GO:0035092 sperm DNA condensation Biological Process

GO:0045595 regulation of cell differentiation Biological Process

KEGG gene cross-reference

ath:AT3G14980

dme:Dmel_CG8103

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.

Nucleus0.945

Rank 1 · LXL04_017901 · OH-1004

Cytoplasm0.094

Rank 2 · LXL04_017901 · OH-1004

Cell membrane0.036

Rank 3 · LXL04_017901 · OH-1004

Endoplasmic reticulum0.020

Rank 4 · LXL04_017901 · OH-1004

Plastid0.016

Rank 5 · LXL04_017901 · 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.

PF05641.19Agenet31-99 aa

PF22970.3DUF7028348-427 aa

PF22970.3DUF7028447-529 aa

PF16135.11TDBD652-702 aa

PF23011.3PHD-1st_NSD730-773 aa

PF00628.36PHD734-773 aa

PF23209.2IDM1_C892-1030 aa

PF00583.32Acetyltransf_1910-987 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017901	`PF05641.19`	Agenet	31	99	2.2e-14	54.3
LXL04_017901	`PF22970.3`	DUF7028	348	427	1.5e-43	147.3
LXL04_017901	`PF22970.3`	DUF7028	447	529	1.5e-43	147.3
LXL04_017901	`PF16135.11`	TDBD	652	702	1.7e-23	83.1
LXL04_017901	`PF23011.3`	PHD-1st_NSD	730	773	7.7e-08	33.1
LXL04_017901	`PF00628.36`	PHD	734	773	6.2e-12	46.1
LXL04_017901	`PF23209.2`	IDM1_C	892	1030	2.1e-55	187.3
LXL04_017901	`PF00583.32`	Acetyltransf_1	910	987	2.3e-06	28.6

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	37.238%	Swiss-Prot	weak database homology

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