LXL04_002500 | RubberDandelionOmics

Gene overview

LXL04_002500

Reference: OH-1004 Chr: Chr01 Coordinates: 50084145-50085267 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

613 bp · LXL04_002500|LXL04_002500|OH1004|cDNA

TTATTTTACTCCTGGTACATACGCAAACAAAGATTCAGCAGTTGCAGCCAAGCTGGCAGCAGGGTTGTGTGCTGATCTGGCTTTAGCAATATATACCGGACGTGCTAAAAATGGGTTTGCACTGGTGCGTCCTCCTGGTCATCATGCTGGTGTGAAACAGGAAATGGGGTTCTGCCTTCACAACAATGCAGCAATTGCTGCATTTGCAGCACAAGCTGTAGGAGCAATTGGGGGTATCTTTGGTTTTGGCAAGGGCTCTG...

CDS

Download CDS FASTA

561 bp · LXL04_002500|LXL04_002500|OH1004|CDS

CTGGCAGCAGGGTTGTGTGCTGATCTGGCTTTAGCAATATATACCGGACGTGCTAAAAATGGGTTTGCACTGGTGCGTCCTCCTGGTCATCATGCTGGTGTGAAACAGGAAATGGGGTTCTGCCTTCACAACAATGCAGCAATTGCTGCATTTGCAGCACAAGCTGTAGGAGCAATTGGGGGTATCTTTGGTTTTGGCAAGGGCTCTGCCAGTGTTCCTTTTCTTTGGCTTCTACTGTGGATTACTGATGTCATTTGGTA...

Protein

Download Protein FASTA

186 aa · LXL04_002500|LXL04_002500|OH1004|PROTEIN

MAAGLCADLALAIYTGRAKNGFALVRPPGHHAGVKQEMGFCLHNNAAIAAFAAQAVGAIGGIFGFGKGSASVPFLWLLLWITDVIWYMWSLRPILKRVLYGGGKLAAFWLFSNFFTWLPKCVKMLTSEPNDQHQILAFNWFVAVIVPNSCNKTMLVLFNILIFFHYLFTYKLNGGEPALQKLQFRV

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_002500`
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_002500

Location Chr01:50084145-50085267 (+)

Description No functional description available

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18520`	Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4).	PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings.2013 · DOI: 10.1105/tpc.113.109710 MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis.2019 · DOI: 10.1038/s41467-019-09417-1 HY5 Interacts with the Histone Deacetylase HDA15 to Repress Hypocotyl Cell Elongation in Photomorphogenesis.2019 · DOI: 10.1104/pp.19.00055 Arabidopsis histone deacetylase HDA15 directly represses plant response to elevated ambient temperature.2019 · DOI: 10.1111/tpj.14492

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002500 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0007165 signal transduction Biological Process

GO:0007168 receptor guanylyl cyclase signaling pathway Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009408 response to heat Biological Process

GO:0009410 response to xenobiotic stimulus Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009789 positive regulation of abscisic acid-activated signaling pathway Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0033555 multicellular organismal response to stress Biological Process

KEGG gene cross-reference

ath:AT3G18520

cbr:CBG_16328

cel:CELE_C10E2.3

cge:100689350

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.

Endoplasmic reticulum0.399

Rank 1 · LXL04_002500 · OH-1004

Golgi apparatus0.235

Rank 2 · LXL04_002500 · OH-1004

Cytoplasm0.140

Rank 3 · LXL04_002500 · OH-1004

Nucleus0.109

Rank 4 · LXL04_002500 · OH-1004

Mitochondrion0.101

Rank 5 · LXL04_002500 · 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.

PF00850.25Hist_deacetyl2-55 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002500	`PF00850.25`	Hist_deacetyl	2	55	8.6e-13	49.0

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
`Q8GXJ1`	Arabidopsis thaliana	Histone deacetylase 15	82.500%	Swiss-Prot	weak database homology

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