LXL04_003004 | RubberDandelionOmics

Gene overview

LXL04_003004

Reference: OH-1004 Chr: Chr01 Coordinates: 64623456-64627699 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1647 bp · LXL04_003004|LXL04_003004|OH1004|cDNA

ATGTTTAGAAGCAACAATTTAACAGCAAGGATTTTTGAGCGTCAGATTCGAACTCCTTCTCCTGGTACCACTATTCACCGTGCGAGGAGATTTTATGAGAATATAGTTCCCGGATCAACAATATACGATGTTGAATGTCCGGACCATTCATTCCGCAAGTTCACAGAAGATGGGAAATACCTGATAAGTTTTAGTAGAAACCATCAAGACTTGATTGTGTATCGGCCCACATGGCTTTCGTTTTCATGCAAAAATGAAGA...

CDS

Download CDS FASTA

1647 bp · LXL04_003004|LXL04_003004|OH1004|CDS

ATGTTTAGAAGCAACAATTTAACAGCAAGGATTTTTGAGCGTCAGATTCGAACTCCTTCTCCTGGTACCACTATTCACCGTGCGAGGAGATTTTATGAGAATATAGTTCCCGGATCAACAATATACGATGTTGAATGTCCGGACCATTCATTCCGCAAGTTCACAGAAGATGGGAAATACCTGATAAGTTTTAGTAGAAACCATCAAGACTTGATTGTGTATCGGCCCACATGGCTTTCGTTTTCATGCAAAAATGAAGA...

Protein

Download Protein FASTA

548 aa · LXL04_003004|LXL04_003004|OH1004|PROTEIN

MFRSNNLTARIFERQIRTPSPGTTIHRARRFYENIVPGSTIYDVECPDHSFRKFTEDGKYLISFSRNHQDLIVYRPTWLSFSCKNEDCYAQHLPPKANKFESFFTQLYSVPLASASELICKDFFLYAESNQFGLFATSTAQIYDAPPTGGAIQGVPSIEKITFHLLRLEDGVVLDERVFCNDYINLAHSMGVFLYDDLLAIVSLRYQHIHILQIRDSGTLVDVRAIGDFCREDDQLFLNSSSQAKMFLRKHMTKISFNGM...

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_003004`
TK1151 ID	TkA01G410650
OH-1004 ID	LXL04_003004
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.000
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_003004

Location Chr01:64623456-64627699 (-)

Description Similar to DET1: Light-mediated development protein DET1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g10180`	Component of light signal transduction machinery.	Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes.2004 · DOI: 10.1101/gad.1229504 DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis.2018 · DOI: 10.7554/elife.37892 DET1 represses a chloroplast blue light-responsive promoter in a developmental and tissue-specific manner in Arabidopsis thaliana.1998 · DOI: 10.1046/j.1365-313x.1998.00078.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_003004 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005975 carbohydrate metabolic process Biological Process

GO:0006281 DNA repair Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0065003 protein-containing complex assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0031461 cullin-RING ubiquitin ligase complex Cellular Component

GO:0031464 Cul4A-RING E3 ubiquitin ligase complex Cellular Component

GO:0080008 Cul4-RING E3 ubiquitin ligase complex Cellular Component

GO:0031625 ubiquitin protein ligase binding Molecular Function

KEGG gene cross-reference

ath:AT4G10180

hsa:55070

mmu:76375

sly:778329

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.

Cytoplasm0.559

Rank 1 · LXL04_003004 · OH-1004

Nucleus0.270

Rank 2 · LXL04_003004 · OH-1004

Cell membrane0.105

Rank 3 · LXL04_003004 · OH-1004

Lysosome / Vacuole0.095

Rank 4 · LXL04_003004 · OH-1004

Golgi apparatus0.084

Rank 5 · LXL04_003004 · 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.

PF09737.15Det1121-548 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003004	`PF09737.15`	Det1	121	548	4.2e-142	474.8

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
`P48732`	Arabidopsis thaliana	Light-mediated development protein DET1	69.189%	Swiss-Prot	strong database homology

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