LXL04_016211 | RubberDandelionOmics

Gene overview

LXL04_016211

Reference: OH-1004 Chr: Chr03 Coordinates: 115236048-115237969 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1260 bp · LXL04_016211|LXL04_016211|OH1004|cDNA

ATGGGGAGCGAGAACGAACCAGCGAAGCTACTGTTACCTTACCTTCAACGAGCCGATGAATTGCAAAAGCACGAGCCTCTCGTCGCCTACTACTGTCGGTTATATGCGATGGAACGGGGTTTGAGGATTCCTCAGAGTGAACGAACCAAAACCACAAATTCCCTACTCATTTCCCTCATGAACCAACTTGAAAAGGATAAGAAGACAGTGCAGTTGCAACCTGATGACAATCTCCACGTAGAAGGTTTTGCTTCAAATGT...

CDS

Download CDS FASTA

1260 bp · LXL04_016211|LXL04_016211|OH1004|CDS

ATGGGGAGCGAGAACGAACCAGCGAAGCTACTGTTACCTTACCTTCAACGAGCCGATGAATTGCAAAAGCACGAGCCTCTCGTCGCCTACTACTGTCGGTTATATGCGATGGAACGGGGTTTGAGGATTCCTCAGAGTGAACGAACCAAAACCACAAATTCCCTACTCATTTCCCTCATGAACCAACTTGAAAAGGATAAGAAGACAGTGCAGTTGCAACCTGATGACAATCTCCACGTAGAAGGTTTTGCTTCAAATGT...

Protein

Download Protein FASTA

419 aa · LXL04_016211|LXL04_016211|OH1004|PROTEIN

MGSENEPAKLLLPYLQRADELQKHEPLVAYYCRLYAMERGLRIPQSERTKTTNSLLISLMNQLEKDKKTVQLQPDDNLHVEGFASNVFAKADKQDRAGRADLNTAKTFYAASIFFEILNQFGVLQPDLEQKQKYAAWKAADIRKAIKEGRKPVPGPPGGDLDKDPSDTSTTGYEDIEPSQPTTRHEPESHPSSRSFDRNDSQKFTNTFSSPSPPRDTPPPPPPPPHSTMPPPPSNTQPPPPSNFPPPSSSDDYPSNNFQQ...

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_016211`
TK1151 ID	TkA02G174600
OH-1004 ID	LXL04_016211
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.400
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_016211

Location Chr03:115236048-115237969 (-)

Description Similar to LIP5: Protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g26750`	Involved in the endosomal multivesicular bodies (MVB) pathway.	The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5.2007 · DOI: 10.1105/tpc.106.049346 Arabidopsis LIP5, a positive regulator of multivesicular body biogenesis, is a critical target of pathogen-responsive MAPK cascade in plant basal defense.2014 · DOI: 10.1371/journal.ppat.1004243

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016211 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009555 pollen development Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0016197 endosomal transport Biological Process

GO:0016236 macroautophagy Biological Process

GO:0032511 late endosome to vacuole transport via multivesicular body sorting pathway Biological Process

GO:0036258 multivesicular body assembly Biological Process

GO:0071985 multivesicular body sorting pathway Biological Process

GO:0080001 mucilage extrusion from seed coat Biological Process

GO:0098542 defense response to other organism Biological Process

GO:1900426 positive regulation of defense response to bacterium Biological Process

GO:1903335 regulation of vacuolar transport Biological Process

KEGG gene cross-reference

ath:AT4G26750

ddi:DDB_G0271488

hsa:51534

pon:100173666

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.

Cytoplasm0.672

Rank 1 · LXL04_016211 · OH-1004

Nucleus0.326

Rank 2 · LXL04_016211 · OH-1004

Golgi apparatus0.174

Rank 3 · LXL04_016211 · OH-1004

Endoplasmic reticulum0.099

Rank 4 · LXL04_016211 · OH-1004

Lysosome / Vacuole0.071

Rank 5 · LXL04_016211 · 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.

PF04652.22Vta112-148 aa

PF18097.7Vta1_C377-413 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016211	`PF04652.22`	Vta1	12	148	6.2e-47	160.0
LXL04_016211	`PF18097.7`	Vta1_C	377	413	8.4e-10	38.8

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
`Q9SZ15`	Arabidopsis thaliana	Protein HOMOLOG OF MAMMALIAN LYST-INTERACTING PROTEIN 5	54.628%	Swiss-Prot	strong database homology

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