LXL04_016515 | RubberDandelionOmics

Gene overview

LXL04_016515

Reference: OH-1004 Chr: Chr03 Coordinates: 125265647-125266777 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1131 bp · LXL04_016515|LXL04_016515|OH1004|cDNA

ATGTCTCTTCTCGATCCCTCCATCGAAGACTTACCAGTACCTATCATGGCTGATGTCCTTTCAAGACTTCCTGTCAAGAAAATCATCCACTGCAAGTGCGTATGCAAGCAATTTCAAAATATTGTTTTGGACTCATCCTTTTCTCATCTTCACTTCTCGCGATCACCTACAGGCTTCATGATTCTTCACGTTTCTGGATTTAGTTCTGAAATCTTACCAGGGATTTTAAAGTGGGTTGAGGTCGATAACCAAGTCGATCA...

CDS

Download CDS FASTA

1131 bp · LXL04_016515|LXL04_016515|OH1004|CDS

ATGTCTCTTCTCGATCCCTCCATCGAAGACTTACCAGTACCTATCATGGCTGATGTCCTTTCAAGACTTCCTGTCAAGAAAATCATCCACTGCAAGTGCGTATGCAAGCAATTTCAAAATATTGTTTTGGACTCATCCTTTTCTCATCTTCACTTCTCGCGATCACCTACAGGCTTCATGATTCTTCACGTTTCTGGATTTAGTTCTGAAATCTTACCAGGGATTTTAAAGTGGGTTGAGGTCGATAACCAAGTCGATCA...

Protein

Download Protein FASTA

376 aa · LXL04_016515|LXL04_016515|OH1004|PROTEIN

MSLLDPSIEDLPVPIMADVLSRLPVKKIIHCKCVCKQFQNIVLDSSFSHLHFSRSPTGFMILHVSGFSSEILPGILKWVEVDNQVDHHRFLHDPFMNLDLNLSPNFQNSQLFPIGSVNGLICLSQFGLETDNIYICNPITREYMILPTQKYHKENYENIVYSFGVGSLTHEYKVIRIFQIDITSKAEIYTLGTGQWRSIGHVPYRLTESYPPFLNGHAHWITCTKNYPKKICVFNFDNETFELFPSPPSIDKGQIHLRRL...

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_016515`
TK1151 ID	TkA02G130850
OH-1004 ID	LXL04_016515
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_016515

Location Chr03:125265647-125266777 (+)

Description Similar to At3g07870: F-box protein At3g07870

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g07870`	F-box protein At3g07870.	No verified direct reference in this release
`At3g06240`	F-box/kelch-repeat protein At3g06240.	No verified direct reference in this release
`At4g12560`	Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins (By similarity).	An F-box gene, CPR30, functions as a negative regulator of the defense response in Arabidopsis.2009 · DOI: 10.1111/j.1365-313x.2009.03995.x
`At1g12855`	Putative F-box protein At1g12855.	No verified direct reference in this release
`At1g13200`	Putative F-box/kelch-repeat protein At1g13200.	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_016515 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009626 plant-type hypersensitive response Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Biological Process

GO:0031348 negative regulation of defense response Biological Process

GO:0042177 negative regulation of protein catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

KEGG gene cross-reference

ath:AT1G12855

ath:AT1G13200

ath:AT3G06240

ath:AT3G07870

ath:AT4G12560

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.

Cytoplasm0.671

Rank 1 · LXL04_016515 · OH-1004

Nucleus0.425

Rank 2 · LXL04_016515 · OH-1004

Cell membrane0.077

Rank 3 · LXL04_016515 · OH-1004

Endoplasmic reticulum0.067

Rank 4 · LXL04_016515 · OH-1004

Lysosome / Vacuole0.040

Rank 5 · LXL04_016515 · 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-like8-46 aa

PF00646.39F-box8-47 aa

PF07734.19FBA_1102-342 aa

PF08268.18FBA_3105-332 aa

PF24750.2b-prop_At3g26010-like106-282 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016515	`PF12937.13`	F-box-like	8	46	2.8e-07	30.9
LXL04_016515	`PF00646.39`	F-box	8	47	3e-07	30.8
LXL04_016515	`PF07734.19`	FBA_1	102	342	1.7e-20	74.0
LXL04_016515	`PF08268.18`	FBA_3	105	332	1.5e-23	84.0
LXL04_016515	`PF24750.2`	b-prop_At3g26010-like	106	282	1.2e-07	31.8

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
`Q9SFC7`	Arabidopsis thaliana	F-box protein At3g07870	27.865%	Swiss-Prot	weak database homology
`Q8GXC7`	Arabidopsis thaliana	F-box/kelch-repeat protein At3g06240	27.217%	Swiss-Prot	weak database homology
`Q9SU30`	Arabidopsis thaliana	F-box protein CPR1	25.076%	Swiss-Prot	weak database homology
`Q9LPW4`	Arabidopsis thaliana	Putative F-box protein At1g12855	22.764%	Swiss-Prot	weak database homology
`Q9SAF4`	Arabidopsis thaliana	Putative F-box/kelch-repeat protein At1g13200	22.835%	Swiss-Prot	weak database homology

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