LXL04_038884 | RubberDandelionOmics

Gene overview

LXL04_038884

Reference: OH-1004 Chr: Chr09 Coordinates: 52471037-52472074 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

840 bp · LXL04_038884|LXL04_038884|OH1004|cDNA

ATGGCGACAAGATTGAACATGCTGCCAGAAGACTGTCTCTCAACTATTGTATCTCTCACTTCTGCCGCAGATGCAAGTAGACTAATGGTTGCGTCTTCTTCTTTGAAATCGGCTGCAGAATCCGACATGGTTTGGAGCACCTTCTTGCCATCTGATTACTCTTCTATTCTCTCAAGAACACACTCTCAAATCAACTTCTCTTCAAAGAAAGATTTATATTTCCAGTTGTGTGATTCCCTTCTCATCGATGGTGGAATCAG...

CDS

Download CDS FASTA

840 bp · LXL04_038884|LXL04_038884|OH1004|CDS

ATGGCGACAAGATTGAACATGCTGCCAGAAGACTGTCTCTCAACTATTGTATCTCTCACTTCTGCCGCAGATGCAAGTAGACTAATGGTTGCGTCTTCTTCTTTGAAATCGGCTGCAGAATCCGACATGGTTTGGAGCACCTTCTTGCCATCTGATTACTCTTCTATTCTCTCAAGAACACACTCTCAAATCAACTTCTCTTCAAAGAAAGATTTATATTTCCAGTTGTGTGATTCCCTTCTCATCGATGGTGGAATCAG...

Protein

Download Protein FASTA

279 aa · LXL04_038884|LXL04_038884|OH1004|PROTEIN

MATRLNMLPEDCLSTIVSLTSAADASRLMVASSSLKSAAESDMVWSTFLPSDYSSILSRTHSQINFSSKKDLYFQLCDSLLIDGGIRSFSLNKISGKKCFVLSARALSISLSEDANHWTWTTHSRSRFSEVIELKSIPSIEIEGSLNTQELSPNTTYGVYLMIQVTDRAFGLDSIASEISVSKDECSVSNTAYLCPVNERKQQLESLLFMNRRRMMEKLVVEGEGRRPIKRDDGWMEIELGEFFVGEKSEDVKMNLMEVK...

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_038884`
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_038884

Location Chr09:52471037-52472074 (+)

Description Similar to VBF: F-box protein VBF

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g56250`	Component of SCF(VBF) E3 ubiquitin ligase complexes, which mediate the ubiquitination and subsequent proteasomal degradation of target proteins such as VIP1 and Agrobacterium virE2, after their implication in T-DNA translocation to the host nucleus (can functionally replace Agrobacterium VirF).	No verified direct reference in this release
`At1g56240`	F-box protein PP2-B13.	No verified direct reference in this release
`At1g09155`	F-box protein PP2-B15.	No verified direct reference in this release
`At2g02250`	Putative F-box protein PP2-B2.	No verified direct reference in this release
`At2g02240`	F-box protein At2g02240.	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_038884 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009617 response to bacterium Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0030246 carbohydrate binding Molecular Function

KEGG gene cross-reference

ath:AT1G09155

ath:AT1G56240

ath:AT1G56250

ath:AT2G02240

ath:AT2G02250

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.

Nucleus0.695

Rank 1 · LXL04_038884 · OH-1004

Cytoplasm0.447

Rank 2 · LXL04_038884 · OH-1004

Endoplasmic reticulum0.050

Rank 3 · LXL04_038884 · OH-1004

Cell membrane0.046

Rank 4 · LXL04_038884 · OH-1004

Lysosome / Vacuole0.020

Rank 5 · LXL04_038884 · 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.

PF14299.14PP297-277 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038884	`PF14299.14`	PP2	97	277	7e-48	163.1

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
`Q9C7K0`	Arabidopsis thaliana	F-box protein VBF	50.538%	Swiss-Prot	strong database homology
`Q9C7J9`	Arabidopsis thaliana	F-box protein PP2-B13	50.538%	Swiss-Prot	strong database homology
`O80494`	Arabidopsis thaliana	F-box protein PP2-B15	47.500%	Swiss-Prot	moderate database homology
`Q9ZVR5`	Arabidopsis thaliana	Putative F-box protein PP2-B2	37.906%	Swiss-Prot	moderate database homology
`Q3E6P4`	Arabidopsis thaliana	F-box protein At2g02240	36.232%	Swiss-Prot	moderate database homology

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