LXL04_011743 | RubberDandelionOmics

Gene overview

LXL04_011743

Reference: OH-1004 Chr: Chr02 Coordinates: 170742088-170743268 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

702 bp · LXL04_011743|LXL04_011743|OH1004|cDNA

ATGCAGGCACACTTAGTTAGAGCAGCTGAAGTTAAAAAAACAATCGAGTGGATAATGTCGAATCTTGATGGCCATTATGCTGCTGACTCAGTTGCTGCTGCCATTGCTCATGGTGCTTTAACTTCTTCCGAAAATGTAATTAATCTGTCTCAGGTTAATAATGCTAAAACAAAGAATGAAAAATCTGGTACTCATATGATATTCTTCAGAGGTGTTGGGTACCACATGGTAAACTGTGGTTTAATCTTGGTGAAGATGTT...

CDS

Download CDS FASTA

702 bp · LXL04_011743|LXL04_011743|OH1004|CDS

ATGCAGGCACACTTAGTTAGAGCAGCTGAAGTTAAAAAAACAATCGAGTGGATAATGTCGAATCTTGATGGCCATTATGCTGCTGACTCAGTTGCTGCTGCCATTGCTCATGGTGCTTTAACTTCTTCCGAAAATGTAATTAATCTGTCTCAGGTTAATAATGCTAAAACAAAGAATGAAAAATCTGGTACTCATATGATATTCTTCAGAGGTGTTGGGTACCACATGGTAAACTGTGGTTTAATCTTGGTGAAGATGTT...

Protein

Download Protein FASTA

233 aa · LXL04_011743|LXL04_011743|OH1004|PROTEIN

MQAHLVRAAEVKKTIEWIMSNLDGHYAADSVAAAIAHGALTSSENVINLSQVNNAKTKNEKSGTHMIFFRGVGYHMVNCGLILVKMLSEYIDMNAVLPALSSEVIHRVLEMLKFFNTRACQLVLGAGAMQVSGLKSITSKHLALASQVVSFVHAIIPEIRRILFLKVPETQKVLLLSEIKRVSQDYKVHRDEIHTKLVQIMRERLLVHLRGLPQIIETWNRTDESVNTTQSVC

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_011743`
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_011743

Location Chr02:170742088-170743268 (-)

Description Similar to VPS54: Vacuolar protein sorting-associated protein 54, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g19490`	Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN).	The POK/AtVPS52 protein localizes to several distinct post-Golgi compartments in sporophytic and gametophytic cells.2008 · DOI: 10.1093/jxb/ern162

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011743 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006622 protein targeting to lysosome Biological Process

GO:0006623 protein targeting to vacuole Biological Process

GO:0006874 intracellular calcium ion homeostasis Biological Process

GO:0006896 Golgi to vacuole transport Biological Process

GO:0006941 striated muscle contraction Biological Process

GO:0007005 mitochondrion organization Biological Process

GO:0007033 vacuole organization Biological Process

GO:0007041 lysosomal transport Biological Process

GO:0008104 intracellular protein localization Biological Process

GO:0010467 gene expression Biological Process

GO:0010992 ubiquitin recycling Biological Process

GO:0015031 protein transport Biological Process

KEGG gene cross-reference

ath:AT4G19490

hsa:51542

mmu:245944

rno:286932

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.

Cytoplasm0.569

Rank 1 · LXL04_011743 · OH-1004

Golgi apparatus0.433

Rank 2 · LXL04_011743 · OH-1004

Nucleus0.118

Rank 3 · LXL04_011743 · OH-1004

Cell membrane0.110

Rank 4 · LXL04_011743 · OH-1004

Lysosome / Vacuole0.091

Rank 5 · LXL04_011743 · 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.

PF07928.18Vps5473-204 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011743	`PF07928.18`	Vps54	73	204	2.8e-47	161.2

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
`F4JT76`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 54, chloroplastic	65.934%	Swiss-Prot	strong database homology

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