LXL04_039108 | RubberDandelionOmics

Gene overview

LXL04_039108

Reference: OH-1004 Chr: Chr09 Coordinates: 59395533-59400697 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2769 bp · LXL04_039108|LXL04_039108|OH1004|cDNA

ATGAGGTTATCAATGGAGGTCGACGGGGATTCGCAACCTCAAGTTGTTCCGAGAGATCGGAGACCTGATGCTCTTGGAGATTTTAACGTCCTTTCTGATGAAATTGTTTGTTCGATACTGACTCTTCTCTCACCTCGTGATGTCGCTCGTCTTGCTTGTGCTAGCAGTGTGATGTATATTCTATGCAATGAAGATCCTCTGTGGATGAACTTATGCCTTAATAACGAAAATCGTGAGCTTCAGTATAAAGGATCATGGAA...

CDS

Download CDS FASTA

2769 bp · LXL04_039108|LXL04_039108|OH1004|CDS

ATGAGGTTATCAATGGAGGTCGACGGGGATTCGCAACCTCAAGTTGTTCCGAGAGATCGGAGACCTGATGCTCTTGGAGATTTTAACGTCCTTTCTGATGAAATTGTTTGTTCGATACTGACTCTTCTCTCACCTCGTGATGTCGCTCGTCTTGCTTGTGCTAGCAGTGTGATGTATATTCTATGCAATGAAGATCCTCTGTGGATGAACTTATGCCTTAATAACGAAAATCGTGAGCTTCAGTATAAAGGATCATGGAA...

Protein

Download Protein FASTA

922 aa · LXL04_039108|LXL04_039108|OH1004|PROTEIN

MRLSMEVDGDSQPQVVPRDRRPDALGDFNVLSDEIVCSILTLLSPRDVARLACASSVMYILCNEDPLWMNLCLNNENRELQYKGSWKRTTLHRLQVLSKCEDPCKKPLHFDGFNSLFLYKRLYRCYTRLDGFAFDQGNVERKTNISQEEFLQQYDAHKPVLISGLADTWSARKTWTPEQLLDKYRDTPFRISQRSAKKLSMKFEDYVSYMQEQHDEDPLYIFDDKFGEVAPDLLKDYSVPHLFPDDYFDVLDSDQRPPYR...

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_039108`
TK1151 ID	TkA04G504600
OH-1004 ID	LXL04_039108
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
Protein coverage (%)	TK1151 99.892 / OH-1004 99.892 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_039108

Location Chr09:59395533-59400697 (-)

Description Similar to At1g78280: F-box protein At1g78280

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g78280`	May function as histone H3 lysine demethylase and be involved in regulation of gene expression.	No verified direct reference in this release
`At5g06550`	Histone demethylase that demethylates 'Arg-3' (H4R3me) of histone H4 with a specific activity for H4R3me2.	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_039108 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

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:0017185 peptidyl-lysine hydroxylation Biological Process

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

KEGG gene cross-reference

ath:AT1G78280

ath:AT5G06550

dre:266962

hsa:23210

pon:100173544

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.

Cytoplasm0.510

Rank 1 · LXL04_039108 · OH-1004

Nucleus0.359

Rank 2 · LXL04_039108 · OH-1004

Endoplasmic reticulum0.101

Rank 3 · LXL04_039108 · OH-1004

Cell membrane0.097

Rank 4 · LXL04_039108 · OH-1004

Mitochondrion0.092

Rank 5 · LXL04_039108 · 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-like33-73 aa

PF13621.13Cupin_8150-378 aa

PF02373.29JmjC261-373 aa

PF01636.30APH652-859 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_039108	`PF12937.13`	F-box-like	33	73	1.3e-06	28.8
LXL04_039108	`PF13621.13`	Cupin_8	150	378	1.3e-21	78.4
LXL04_039108	`PF02373.29`	JmjC	261	373	9.6e-14	52.5
LXL04_039108	`PF01636.30`	APH	652	859	2.2e-07	31.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9M9E8`	Arabidopsis thaliana	Lysine-specific demethylase JMJ21	58.395%	Swiss-Prot	strong database homology
`Q67XX3`	Arabidopsis thaliana	Arginine-specific demethylase JMJ22	37.293%	Swiss-Prot	weak database homology

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