LXL04_014701 | RubberDandelionOmics

Gene overview

LXL04_014701

Reference: OH-1004 Chr: Chr03 Coordinates: 55094137-55097763 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1659 bp · LXL04_014701|LXL04_014701|OH1004|cDNA

atgattaaacactgtggtggtccggcggtggtacagcggtggtccggcggtggtgcatcagtggtccaatgtgccgatgggtgcaggtggtgcaccgacggtggtccggcggtggtccggtggtgggtgcagATTCCATTCATGAATTCTATTTCTTTTGAACCAAACTTAGAAATCTTGTGTTACACCGAGAACAAATACGACATGAACATCAATGCCAAAAATCAAAACCCATCACTTTTTGCGTACTTCAAATCTAG...

CDS

Download CDS FASTA

1659 bp · LXL04_014701|LXL04_014701|OH1004|CDS

ATGATTAAACACTGTGGTGGTCCGGCGGTGGTACAGCGGTGGTCCGGCGGTGGTGCATCAGTGGTCCAATGTGCCGATGGGTGCAGGTGGTGCACCGACGGTGGTCCGGCGGTGGTCCGGTGGTGGGTGCAGATTCCATTCATGAATTCTATTTCTTTTGAACCAAACTTAGAAATCTTGTGTTACACCGAGAACAAATACGACATGAACATCAATGCCAAAAATCAAAACCCATCACTTTTTGCGTACTTCAAATCTAG...

Protein

Download Protein FASTA

552 aa · LXL04_014701|LXL04_014701|OH1004|PROTEIN

MIKHCGGPAVVQRWSGGGASVVQCADGCRWCTDGGPAVVRWWVQIPFMNSISFEPNLEILCYTENKYDMNINAKNQNPSLFAYFKSRNTFMVLVFIFETPKFGDHIQKTLDSGIHIHRKTQKVGHGSNLFCKHYSTRLSDTPARSSSLSVDVTMSDQQCEGPPLQHSSSSSSSSSPRNGIDVFWDDCMLDHDTGAGVFDTGMDPGFLDVLEKHPENSDRIRNMLSILKRGPISPFISWHPSRPALVSELLSFHSREYIDS...

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_014701`
TK1151 ID	TkA02G404340
OH-1004 ID	LXL04_014701
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	93.000
Protein coverage (%)	TK1151 100.000 / OH-1004 72.283 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_014701

Location Chr03:55094137-55097763 (-)

Description Similar to HDA8: Histone deacetylase 8

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08460`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os12g0182700`	Involved in the regulation of melatonin biosynthesis by catalyzing the deacetylation of N-acetylserotonin to produce serotonin.	Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes encode N-acetylserotonin deacetylase, which catalyzes conversion of N-acetylserotonin into serotonin, a reverse reaction for melatonin biosynthesis in plants.2018 · DOI: 10.1111/jpi.12460

Functional annotation source

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Functional annotation source: OH1004 · LXL04_014701 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0030186 melatonin metabolic process Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0000118 histone deacetylase complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0004407 histone deacetylase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0016787 hydrolase activity Molecular Function

GO:0019213 deacetylase activity Molecular Function

KEGG gene cross-reference

afu:AF_0130

ath:AT1G08460

dosa:Os12g0182700

osa:4351682

pae:PA3774

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.

Cytoplasm0.526

Rank 1 · LXL04_014701 · OH-1004

Nucleus0.397

Rank 2 · LXL04_014701 · OH-1004

Mitochondrion0.082

Rank 3 · LXL04_014701 · OH-1004

Cell membrane0.079

Rank 4 · LXL04_014701 · OH-1004

Endoplasmic reticulum0.076

Rank 5 · LXL04_014701 · 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.

PF00850.25Hist_deacetyl213-504 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014701	`PF00850.25`	Hist_deacetyl	213	504	1.3e-84	284.7

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
`Q94EJ2`	Arabidopsis thaliana	Histone deacetylase 8	70.161%	Swiss-Prot	moderate database homology
`Q2QWU2`	Oryza sativa subsp. japonica	Histone deacetylase 10, chloroplastic	31.124%	Swiss-Prot	moderate database homology

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