LXL04_013354 | RubberDandelionOmics

Gene overview

LXL04_013354

Reference: OH-1004 Chr: Chr03 Coordinates: 28297522-28298387 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

573 bp · LXL04_013354|LXL04_013354|OH1004|cDNA

ATGGTTTTGGTATTGGCGATCGGGGATTTACATATCCCACATAGAGCACCTGATCTACCTGCCAAGTTCAAATCTATGCTTGTTCCTGGCAAGATTCAACACATTATTTGCACCGGTAATCTCTGTATCAAAGAAGTTCATGATTATTTGAAAAGTCTGTGCCCAAGTTTACACATCACTCGAGGTGAATATGATGAAGATGCTCGTTACCCAGAGACCAAAACAATCACCATTGGCCAATTCAAACTTGGATTATGTCA...

CDS

Download CDS FASTA

573 bp · LXL04_013354|LXL04_013354|OH1004|CDS

ATGGTTTTGGTATTGGCGATCGGGGATTTACATATCCCACATAGAGCACCTGATCTACCTGCCAAGTTCAAATCTATGCTTGTTCCTGGCAAGATTCAACACATTATTTGCACCGGTAATCTCTGTATCAAAGAAGTTCATGATTATTTGAAAAGTCTGTGCCCAAGTTTACACATCACTCGAGGTGAATATGATGAAGATGCTCGTTACCCAGAGACCAAAACAATCACCATTGGCCAATTCAAACTTGGATTATGTCA...

Protein

Download Protein FASTA

190 aa · LXL04_013354|LXL04_013354|OH1004|PROTEIN

MVLVLAIGDLHIPHRAPDLPAKFKSMLVPGKIQHIICTGNLCIKEVHDYLKSLCPSLHITRGEYDEDARYPETKTITIGQFKLGLCHGHQVVPWGDLDSLAMLQRQLDVDILVSGHTHQFKAYKHEAGVVINPGSATGAYSSITYDVNPSFVLMDIDGLRVVVYVYELIDGEVKVDKIDFKKTSTATTTI

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_013354`
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_013354

Location Chr03:28297522-28298387 (-)

Description Similar to VPS29: Vacuolar protein sorting-associated protein 29

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g47810`	Plays a role in vesicular protein sorting.	The retromer protein VPS29 links cell polarity and organ initiation in plants.2007 · DOI: 10.1016/j.cell.2007.08.040 Differential degradation of PIN2 auxin efflux carrier by retromer-dependent vacuolar targeting.2008 · DOI: 10.1073/pnas.0808073105 The Arabidopsis USL1 controls multiple aspects of development by affecting late endosome morphology.2018 · DOI: 10.1111/nph.15249

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013354 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001881 receptor recycling Biological Process

GO:0006623 protein targeting to vacuole Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006896 Golgi to vacuole transport Biological Process

GO:0007034 vacuolar transport Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0015031 protein transport Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:2000012 regulation of auxin polar transport Biological Process

GO:0005768 endosome Cellular Component

GO:0005769 early endosome Cellular Component

KEGG gene cross-reference

ath:AT3G47810

bta:513840

dre:573437

mmu:56433

pon:100190862

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.

Cytoplasm0.578

Rank 1 · LXL04_013354 · OH-1004

Nucleus0.253

Rank 2 · LXL04_013354 · OH-1004

Mitochondrion0.104

Rank 3 · LXL04_013354 · OH-1004

Peroxisome0.084

Rank 4 · LXL04_013354 · OH-1004

Endoplasmic reticulum0.074

Rank 5 · LXL04_013354 · 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.

PF12850.13Metallophos_24-157 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013354	`PF12850.13`	Metallophos_2	4	157	7e-22	78.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9STT2`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 29	85.638%	Swiss-Prot	strong database homology

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