LXL04_001298 | RubberDandelionOmics

Gene overview

LXL04_001298

Reference: OH-1004 Chr: Chr01 Coordinates: 23596964-23598308 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1155 bp · LXL04_001298|LXL04_001298|OH1004|cDNA

ATGTCGGATGTTCCGATGCCGCCGGATCTCCTCGCCCAAATCCTGGCATGGTTGCCGGTAGCCTCGCTTCTGCGATTCAGGTCTGTTTCCAAAACCTTTCGTGCCCTAATTGATAGCGACTATGTGATTAAGCTCCATCTCAATCACTCAGTCGAAACCAACACCAATCTCAATATCATTTTCGGCGGCGATAGAACGCTTTGCTATCTTAACTTAGATTCGTCTCCCAAAGTTGTCAACAAAATAGATAACCCTCTGTA...

CDS

Download CDS FASTA

1155 bp · LXL04_001298|LXL04_001298|OH1004|CDS

ATGTCGGATGTTCCGATGCCGCCGGATCTCCTCGCCCAAATCCTGGCATGGTTGCCGGTAGCCTCGCTTCTGCGATTCAGGTCTGTTTCCAAAACCTTTCGTGCCCTAATTGATAGCGACTATGTGATTAAGCTCCATCTCAATCACTCAGTCGAAACCAACACCAATCTCAATATCATTTTCGGCGGCGATAGAACGCTTTGCTATCTTAACTTAGATTCGTCTCCCAAAGTTGTCAACAAAATAGATAACCCTCTGTA...

Protein

Download Protein FASTA

384 aa · LXL04_001298|LXL04_001298|OH1004|PROTEIN

MSDVPMPPDLLAQILAWLPVASLLRFRSVSKTFRALIDSDYVIKLHLNHSVETNTNLNIIFGGDRTLCYLNLDSSPKVVNKIDNPLYFAIFETVILGSCNGVVCLCTTEPDNEIAFWNPLVRKFKKIRLAPAKCAEGLGRGVCIKGFGYDDVNNDHKVVRLVQYCSLHNELAHSKIDVFSSKTDAWREVGDFPYYLCYRRNFNTFTKGALHWLVSRKPEKRLDFLICAFDLTNDELRIVPQPDFSNEKFHVNLAVLGGCL...

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_001298`
TK1151 ID	TkA01G549020
OH-1004 ID	LXL04_001298
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.500
Protein coverage (%)	TK1151 99.487 / OH-1004 93.229 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_001298

Location Chr01:23596964-23598308 (-)

Description Similar to CPR1: F-box protein CPR1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At4g22390`	F-box protein At4g22390.	No verified direct reference in this release
`At3g23880`	F-box/kelch-repeat protein At3g23880.	No verified direct reference in this release
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001298 · 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: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

KEGG gene cross-reference

ath:AT3G06240

ath:AT3G07870

ath:AT3G23880

ath:AT4G12560

ath:AT4G22390

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.

Cytoplasm0.706

Rank 1 · LXL04_001298 · OH-1004

Nucleus0.366

Rank 2 · LXL04_001298 · OH-1004

Cell membrane0.074

Rank 3 · LXL04_001298 · OH-1004

Endoplasmic reticulum0.067

Rank 4 · LXL04_001298 · OH-1004

Lysosome / Vacuole0.038

Rank 5 · LXL04_001298 · 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-box6-42 aa

PF12937.13F-box-like7-41 aa

PF07734.19FBA_172-324 aa

PF24750.2b-prop_At3g26010-like90-336 aa

PF08268.18FBA_394-325 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001298	`PF00646.39`	F-box	6	42	2.9e-10	40.3
LXL04_001298	`PF12937.13`	F-box-like	7	41	1.4e-06	28.7
LXL04_001298	`PF07734.19`	FBA_1	72	324	2.8e-27	96.3
LXL04_001298	`PF24750.2`	b-prop_At3g26010-like	90	336	2.1e-11	44.2
LXL04_001298	`PF08268.18`	FBA_3	94	325	1.3e-18	67.8

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
`Q9SU30`	Arabidopsis thaliana	F-box protein CPR1	30.695%	Swiss-Prot	moderate database homology
`Q9SUY0`	Arabidopsis thaliana	F-box protein At4g22390	30.673%	Swiss-Prot	moderate database homology
`Q9LIR8`	Arabidopsis thaliana	F-box/kelch-repeat protein At3g23880	29.118%	Swiss-Prot	weak database homology
`Q9SFC7`	Arabidopsis thaliana	F-box protein At3g07870	25.982%	Swiss-Prot	weak database homology
`Q8GXC7`	Arabidopsis thaliana	F-box/kelch-repeat protein At3g06240	27.717%	Swiss-Prot	weak database homology

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