LXL04_004867 | RubberDandelionOmics

Gene overview

LXL04_004867

Reference: OH-1004 Chr: Chr01 Coordinates: 149116360-149117971 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1521 bp · LXL04_004867|LXL04_004867|OH1004|cDNA

ATGTTTGGGTGCAGAAGTTTGCTAAAGCAAATTAGAAAGAGGAAGAGAAGAATACACCACAAACGTATTCCCAAAAACACCAAACAAAACCCTCGTTTAACAGAACAACAACAGCAAGATTTCGCTACAGATGAAGGTTTCAGCTTAAAGGGATCTTCCCCATCACAGAATTACGGAGTCCAACCATTGGGGAACTTTTACCTCAGCTCATCTCCTCACAACTCAAGAAACACAGGCTTAGGTAACATCCAAACCCTAAC...

CDS

Download CDS FASTA

1521 bp · LXL04_004867|LXL04_004867|OH1004|CDS

ATGTTTGGGTGCAGAAGTTTGCTAAAGCAAATTAGAAAGAGGAAGAGAAGAATACACCACAAACGTATTCCCAAAAACACCAAACAAAACCCTCGTTTAACAGAACAACAACAGCAAGATTTCGCTACAGATGAAGGTTTCAGCTTAAAGGGATCTTCCCCATCACAGAATTACGGAGTCCAACCATTGGGGAACTTTTACCTCAGCTCATCTCCTCACAACTCAAGAAACACAGGCTTAGGTAACATCCAAACCCTAAC...

Protein

Download Protein FASTA

506 aa · LXL04_004867|LXL04_004867|OH1004|PROTEIN

MFGCRSLLKQIRKRKRRIHHKRIPKNTKQNPRLTEQQQQDFATDEGFSLKGSSPSQNYGVQPLGNFYLSSSPHNSRNTGLGNIQTLTDELVLDILGFLRGTDLGILSTVSKSFYVFSNHEPLWRNLVLDNCGIDNGFLFKGSWKSTFVAAHHPSFDVSKIGSLGFKVKDFYSDYLFQSWLCANLELKHEWLSRDNIIRRKGISIEEFVTNFEEPNKPVLLEGCLDNWPAIKKWDKDYLIKTCNNTQFSIGPVQMNLQDYF...

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_004867`
TK1151 ID	TkA01G100770
OH-1004 ID	LXL04_004867
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.800
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_004867

Location Chr01:149116360-149117971 (-)

Description Similar to At5g06550: F-box protein At5g06550

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g06550`	Histone demethylase that demethylates 'Arg-3' (H4R3me) of histone H4 with a specific activity for H4R3me2.	No verified direct reference in this release
`At1g78280`	May function as histone H3 lysine demethylase and be involved in regulation of gene expression.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004867 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006909 phagocytosis Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0010030 positive regulation of seed germination Biological Process

GO:0010099 regulation of photomorphogenesis Biological Process

GO:0010114 response to red light Biological Process

GO:0010476 gibberellin mediated signaling pathway Biological Process

GO:0018395 peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine Biological Process

GO:0030154 cell differentiation Biological Process

GO:0035212 cell competition in a multicellular organism Biological Process

KEGG gene cross-reference

ath:AT1G78280

ath:AT5G06550

dme:Dmel_CG5383

dre:266962

hmg:100209631

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.

Nucleus0.804

Rank 1 · LXL04_004867 · OH-1004

Cytoplasm0.272

Rank 2 · LXL04_004867 · OH-1004

Mitochondrion0.031

Rank 3 · LXL04_004867 · OH-1004

Cell membrane0.027

Rank 4 · LXL04_004867 · OH-1004

Endoplasmic reticulum0.021

Rank 5 · LXL04_004867 · 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.

PF12937.13F-box-like88-128 aa

PF13621.13Cupin_8206-424 aa

PF02373.29JmjC313-424 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004867	`PF12937.13`	F-box-like	88	128	4.2e-07	30.3
LXL04_004867	`PF13621.13`	Cupin_8	206	424	8.4e-27	95.4
LXL04_004867	`PF02373.29`	JmjC	313	424	9.8e-16	58.9

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
`Q67XX3`	Arabidopsis thaliana	Arginine-specific demethylase JMJ22	69.264%	Swiss-Prot	strong database homology
`Q9M9E8`	Arabidopsis thaliana	Lysine-specific demethylase JMJ21	36.885%	Swiss-Prot	moderate database homology

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