LXL04_027771 | RubberDandelionOmics

Gene overview

LXL04_027771

Reference: OH-1004 Chr: Chr06 Coordinates: 23738085-23744007 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2886 bp · LXL04_027771|LXL04_027771|OH1004|cDNA

ATGGATCCAAAGCCTTCCCCCAGATCGGGAAGGGTCGCCCCTATTCGACATAATTCTTCCCCTACCTCCTTGTTAGCGAAAACACTTTCCGATGCAAGTACCCAAAACTTATCCTCCATCCTCAACAATCCACATGTCTCCGATGGCTCCTGGGCTGGTTGGTGGTCCTCTTCAACTGCTGTACAAGTCGCTGAATTTGCTCCTCCTTCCGCCAACAAAACCCCTGGTTTAGAAATAACTAGATCCGATTTCACATCATA...

CDS

Download CDS FASTA

2886 bp · LXL04_027771|LXL04_027771|OH1004|CDS

ATGGATCCAAAGCCTTCCCCCAGATCGGGAAGGGTCGCCCCTATTCGACATAATTCTTCCCCTACCTCCTTGTTAGCGAAAACACTTTCCGATGCAAGTACCCAAAACTTATCCTCCATCCTCAACAATCCACATGTCTCCGATGGCTCCTGGGCTGGTTGGTGGTCCTCTTCAACTGCTGTACAAGTCGCTGAATTTGCTCCTCCTTCCGCCAACAAAACCCCTGGTTTAGAAATAACTAGATCCGATTTCACATCATA...

Protein

Download Protein FASTA

961 aa · LXL04_027771|LXL04_027771|OH1004|PROTEIN

MDPKPSPRSGRVAPIRHNSSPTSLLAKTLSDASTQNLSSILNNPHVSDGSWAGWWSSSTAVQVAEFAPPSANKTPGLEITRSDFTSYLSSISDHHSRFEDIRNHSNKESKDEDAIDHHERAGEALVACLREVPSLYFKEDFALEDGATFRAASPFSTVAENTVLQEKLSQYLDVVELHLVKEISLRSNSFFEAQGQLEDLNLKIVEGCSRIRQLKETIRLLDVDLVDSARQIQDLNHTRSAMLALQEKLRLILYVNQSLA...

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_027771`
TK1151 ID	TkA07G093310
OH-1004 ID	LXL04_027771
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
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_027771

Location Chr06:23738085-23744007 (+)

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_027771 · 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.

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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.

Cytoplasm0.504

Rank 1 · LXL04_027771 · OH-1004

Golgi apparatus0.473

Rank 2 · LXL04_027771 · OH-1004

Cell membrane0.137

Rank 3 · LXL04_027771 · OH-1004

Endoplasmic reticulum0.115

Rank 4 · LXL04_027771 · OH-1004

Nucleus0.113

Rank 5 · LXL04_027771 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF07928.18Vps54704-834 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027771	`PF07928.18`	Vps54	704	834	1.8e-46	158.5

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
`F4JT76`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 54, chloroplastic	60.256%	Swiss-Prot	strong database homology

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