LXL04_038886 | RubberDandelionOmics

Gene overview

LXL04_038886

Reference: OH-1004 Chr: Chr09 Coordinates: 52573633-52575468 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

846 bp · LXL04_038886|LXL04_038886|OH1004|cDNA

ATGGCCACCAAATTGAACATGTTGCCAGAAGACTGTGTCTCAACTATTGTATCTCTCACTTCTGCCGCAGATGCAAGTAGACTAATGGTTGCGTCTTCTTCTTTGAAATCGGCTGCAGAATCCGACATGGTTTGGAGCACCTTCTTGCCATCTGATTACTCTTCTATTCTCTCAAGAACACACTCTCAAATCAACTTCTCTTCAAAGAAAGATTTATATTTCCAGTTGTGTGATTCCCTTCTCATCGATGGTGGAATCAG...

CDS

Download CDS FASTA

846 bp · LXL04_038886|LXL04_038886|OH1004|CDS

ATGGCCACCAAATTGAACATGTTGCCAGAAGACTGTGTCTCAACTATTGTATCTCTCACTTCTGCCGCAGATGCAAGTAGACTAATGGTTGCGTCTTCTTCTTTGAAATCGGCTGCAGAATCCGACATGGTTTGGAGCACCTTCTTGCCATCTGATTACTCTTCTATTCTCTCAAGAACACACTCTCAAATCAACTTCTCTTCAAAGAAAGATTTATATTTCCAGTTGTGTGATTCCCTTCTCATCGATGGTGGAATCAG...

Protein

Download Protein FASTA

281 aa · LXL04_038886|LXL04_038886|OH1004|PROTEIN

MATKLNMLPEDCVSTIVSLTSAADASRLMVASSSLKSAAESDMVWSTFLPSDYSSILSRTHSQINFSSKKDLYFQLCDSLLIDGGIRSFSMNKISGKKCFVLSARALSISLSDEANHWTWTTHSTSRFSEVIELKSIPSIEIEGSLNTQDLSPNTTYGAYLMIQVTDRAFGLDSIASEISVSKNECSVFNTAYLSPVNERKQQLESLLFMNRRRMMEKLVVEGEGRRPIKRDDGWMEIELGEFFVGEKSENVKMNLMEVK...

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_038886`
TK1151 ID	TkA04G474560
OH-1004 ID	LXL04_038886
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.200
Protein coverage (%)	TK1151 94.488 / OH-1004 42.705 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_038886

Location Chr09:52573633-52575468 (-)

Description Similar to PP2B13: F-box protein PP2-B13

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g56240`	F-box protein PP2-B13.	No verified direct reference in this release
`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
`At1g09155`	F-box protein PP2-B15.	No verified direct reference in this release
`At5g24560`	Putative F-box protein PP2-B12.	No verified direct reference in this release
`At2g02250`	Putative F-box protein PP2-B2.	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_038886 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009617 response to bacterium 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: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_038886 · OH-1004

Cytoplasm0.445

Rank 2 · LXL04_038886 · OH-1004

Endoplasmic reticulum0.048

Rank 3 · LXL04_038886 · OH-1004

Cell membrane0.045

Rank 4 · LXL04_038886 · OH-1004

Lysosome / Vacuole0.020

Rank 5 · LXL04_038886 · 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_038886	`PF14299.14`	PP2	97	277	7.4e-48	163.0

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
`Q9C7J9`	Arabidopsis thaliana	F-box protein PP2-B13	50.355%	Swiss-Prot	strong database homology
`Q9C7K0`	Arabidopsis thaliana	F-box protein VBF	50.357%	Swiss-Prot	strong database homology
`O80494`	Arabidopsis thaliana	F-box protein PP2-B15	48.043%	Swiss-Prot	moderate database homology
`Q9FLU7`	Arabidopsis thaliana	Putative F-box protein PP2-B12	38.909%	Swiss-Prot	moderate database homology
`Q9ZVR5`	Arabidopsis thaliana	Putative F-box protein PP2-B2	38.434%	Swiss-Prot	moderate database homology

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