LXL04_030308 | RubberDandelionOmics

Gene overview

LXL04_030308

Reference: OH-1004 Chr: Chr06 Coordinates: 113960523-113961122 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

600 bp · LXL04_030308|LXL04_030308|OH1004|cDNA

ATGAAGAGATCAATATCTAAATCCGAAGATCCTATCAACGGCACCGTTGATGTTAACAATAGCAAGACGAAGAAGATCAAATTATCGGAAGATCAGGCTCCGGTGACCGACTCAGTTCCGGAGGAGACGTCTGCGTCTGTTCTTTCGGACGAAAACTTGCTCTACGAGGTTCTGAAGCACGTCGATGCGCGGACGTTAGGTGCGGCGGGTTGCGTGAGCAAGCAGTGGCATCGGACTTCTCAGGATGAGCGGCTATGGGA...

CDS

Download CDS FASTA

600 bp · LXL04_030308|LXL04_030308|OH1004|CDS

ATGAAGAGATCAATATCTAAATCCGAAGATCCTATCAACGGCACCGTTGATGTTAACAATAGCAAGACGAAGAAGATCAAATTATCGGAAGATCAGGCTCCGGTGACCGACTCAGTTCCGGAGGAGACGTCTGCGTCTGTTCTTTCGGACGAAAACTTGCTCTACGAGGTTCTGAAGCACGTCGATGCGCGGACGTTAGGTGCGGCGGGTTGCGTGAGCAAGCAGTGGCATCGGACTTCTCAGGATGAGCGGCTATGGGA...

Protein

Download Protein FASTA

199 aa · LXL04_030308|LXL04_030308|OH1004|PROTEIN

MKRSISKSEDPINGTVDVNNSKTKKIKLSEDQAPVTDSVPEETSASVLSDENLLYEVLKHVDARTLGAAGCVSKQWHRTSQDERLWELICTKHWTNMGCGNNQLRSVVLALGGFRRLHAHYLWPLSKPPTSTITSSSSSTIAAVTSSSSVWPCLPSPRTIALSKPTSPKTHWGKDEVQLSISLLSIRYYEKMNYKNRTK

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_030308`
TK1151 ID	TkA07G396250
OH-1004 ID	LXL04_030308
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.000
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_030308

Location Chr06:113960523-113961122 (+)

Description Similar to GID2: F-box protein GID2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g24210`	Essential component of the SCF-type E3 ligase complex, SCF(GID2), a complex that positively regulates the gibberellin signaling pathway.	No verified direct reference in this release
`At5g48170`	Essential component of a SCF-type E3 ligase complex that positively regulates the gibberellin signaling pathway.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0580300`	Essential component of some SCF-type E3 ligase complex that positively regulates the gibberellin signaling pathway.	Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant.2003 · DOI: 10.1126/science.1081077 GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice.2004 · DOI: 10.1111/j.1365-313x.2003.01990.x

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030308 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009845 seed germination Biological Process

GO:0009937 regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0009939 positive regulation of gibberellic acid mediated signaling pathway Biological Process

GO:0010162 seed dormancy process Biological Process

GO:0010265 SCF complex assembly Biological Process

GO:0016567 protein ubiquitination Biological Process

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

GO:0048831 regulation of shoot system development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0019005 SCF ubiquitin ligase complex Cellular Component

KEGG gene cross-reference

ath:AT4G24210

ath:AT5G48170

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.

Nucleus0.913

Rank 1 · LXL04_030308 · OH-1004

Cytoplasm0.137

Rank 2 · LXL04_030308 · OH-1004

Cell membrane0.046

Rank 3 · LXL04_030308 · OH-1004

Endoplasmic reticulum0.038

Rank 4 · LXL04_030308 · OH-1004

Plastid0.019

Rank 5 · LXL04_030308 · 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-box52-87 aa

PF12937.13F-box-like53-91 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030308	`PF00646.39`	F-box	52	87	4.8e-06	27.0
LXL04_030308	`PF12937.13`	F-box-like	53	91	4.1e-07	30.4

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
`Q9STX3`	Arabidopsis thaliana	F-box protein GID2	50.254%	Swiss-Prot	strong database homology
`Q9LUB6`	Arabidopsis thaliana	F-box protein SNE	25.140%	Swiss-Prot	weak database homology
`Q7XAK4`	Oryza sativa subsp. japonica	F-box protein GID2	40.845%	Swiss-Prot	moderate database homology

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