LXL04_027572 | RubberDandelionOmics

Gene overview

LXL04_027572

Reference: OH-1004 Chr: Chr06 Coordinates: 19269122-19270164 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

906 bp · LXL04_027572|LXL04_027572|OH1004|cDNA

ATGGCGTCGATCGATCTCCACCGCGTAAAGCGGTTGTCTGCAGTGGAGAAATCACCAAATTGGCTCGAAATGTCTCATGAACTGATGTCAAATATACTTGAAAGATTGGATGATGTAGAAATACTCAACAGCGCAATGAAGGTTTGCACCACATGGCGGAGAATGGGTAGGGATCCTGCGATGTGGAAGGTCATTAATATGCACAAACCGGCTAGGGCTCGGAATACTAATTACGATCTTGAGGCTCTGACTAAGCAGGC...

CDS

Download CDS FASTA

906 bp · LXL04_027572|LXL04_027572|OH1004|CDS

ATGGCGTCGATCGATCTCCACCGCGTAAAGCGGTTGTCTGCAGTGGAGAAATCACCAAATTGGCTCGAAATGTCTCATGAACTGATGTCAAATATACTTGAAAGATTGGATGATGTAGAAATACTCAACAGCGCAATGAAGGTTTGCACCACATGGCGGAGAATGGGTAGGGATCCTGCGATGTGGAAGGTCATTAATATGCACAAACCGGCTAGGGCTCGGAATACTAATTACGATCTTGAGGCTCTGACTAAGCAGGC...

Protein

Download Protein FASTA

301 aa · LXL04_027572|LXL04_027572|OH1004|PROTEIN

MASIDLHRVKRLSAVEKSPNWLEMSHELMSNILERLDDVEILNSAMKVCTTWRRMGRDPAMWKVINMHKPARARNTNYDLEALTKQAIHLSSGELIDISLEGFGTDDLLHHIVSGSSKLNSVCLTNCYNITSKRLNHALKMVPQLEKLHISYTMNKFHEVIVPNCPHLKSFKMDIARVYVDIIRDIDAFAIAKNMPELRQLQLYGNAMSDIGLKAILDGCPHLESLDIRTCYNVDIHAKELKLSMERLKNFKGPNDSIEN...

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_027572`
TK1151 ID	TkA07G073800
OH-1004 ID	LXL04_027572
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.700
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_027572

Location Chr06:19269122-19270164 (-)

Description Similar to SKIP19: F-box protein SKIP19

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g05460`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.	No verified direct reference in this release
`At4g05500`	Putative F-box/LRR-repeat protein 23.	No verified direct reference in this release
`At4g05475`	Putative F-box protein At4g05475.	No verified direct reference in this release
`At4g05470`	Putative F-box/LRR-repeat protein 21.	No verified direct reference in this release
`At4g05497`	Putative F-box/LRR-repeat protein 9.	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_027572 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:1905761 SCF ubiquitin ligase complex binding Molecular Function

KEGG gene cross-reference

ath:AT4G05460

ath:AT4G05475

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.

Nucleus0.557

Rank 1 · LXL04_027572 · OH-1004

Cytoplasm0.535

Rank 2 · LXL04_027572 · OH-1004

Endoplasmic reticulum0.062

Rank 3 · LXL04_027572 · OH-1004

Cell membrane0.057

Rank 4 · LXL04_027572 · OH-1004

Plastid0.026

Rank 5 · LXL04_027572 · 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.

PF00646.39F-box21-62 aa

PF12937.13F-box-like26-65 aa

PF29594.1LRR_SKP286-157 aa

PF24758.2LRR_At5g56370178-242 aa

PF12799.14LRR_4196-231 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027572	`PF00646.39`	F-box	21	62	1.6e-06	28.5
LXL04_027572	`PF12937.13`	F-box-like	26	65	1.1e-06	29.0
LXL04_027572	`PF29594.1`	LRR_SKP2	86	157	3.3e-08	33.8
LXL04_027572	`PF24758.2`	LRR_At5g56370	178	242	3.7e-11	43.8
LXL04_027572	`PF12799.14`	LRR_4	196	231	7.9e-07	29.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9M0U9`	Arabidopsis thaliana	F-box protein SKIP19	39.446%	Swiss-Prot	moderate database homology
`Q9S9V9`	Arabidopsis thaliana	Putative F-box/LRR-repeat protein 23	40.741%	Swiss-Prot	moderate database homology
`Q9M0U7`	Arabidopsis thaliana	Putative F-box protein At4g05475	37.643%	Swiss-Prot	moderate database homology
`Q9M0U8`	Arabidopsis thaliana	Putative F-box/LRR-repeat protein 21	34.470%	Swiss-Prot	moderate database homology
`Q9S9V8`	Arabidopsis thaliana	Putative F-box/LRR-repeat protein 9	36.607%	Swiss-Prot	moderate database homology

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