TkA01G578790 | RubberDandelionOmics

Gene overview

TkA01G578790

Reference: TK1151 Chr: Chr01 Coordinates: 145544745-145545950 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

727 bp · TkA01G578790|TK1151|cDNA

ATGTCGAATCTTGATGGCCATTATGCTGATGACTCAGTTGCTGCTGCCATTGCTCATGGTGCTTTAACTTCTTCCGAAAATGTAATTAATCTGTCTCAGGTTAATAATGCTAAAACAAAGAATGAAAAATCTGGTACTCATATGATATTCTTCAGAGGTGTTGGGTACCACATGGTAAACTGTGGTTTAATCTTGGTGAAGATGTTATCAGAGTATATTGACATGAATGCTGTATTACCAGCACTTTCATCTGAAGTGAT...

CDS

Download CDS FASTA

648 bp · TkA01G578790|TK1151|CDS

ATGTCGAATCTTGATGGCCATTATGCTGATGACTCAGTTGCTGCTGCCATTGCTCATGGTGCTTTAACTTCTTCCGAAAATGTAATTAATCTGTCTCAGGTTAATAATGCTAAAACAAAGAATGAAAAATCTGGTACTCATATGATATTCTTCAGAGGTGTTGGGTACCACATGGTAAACTGTGGTTTAATCTTGGTGAAGATGTTATCAGAGTATATTGACATGAATGCTGTATTACCAGCACTTTCATCTGAAGTGAT...

Protein

Download Protein FASTA

215 aa · TkA01G578790|TK1151|PROTEIN

MSNLDGHYADDSVAAAIAHGALTSSENVINLSQVNNAKTKNEKSGTHMIFFRGVGYHMVNCGLILVKMLSEYIDMNAVLPALSSEVIHRVREMLNFFNTRACQLVLGAGAMQVSGLKSITSKHLALASQVVSFVHAIIPEIRRILFLKVPETQKVLLLSEIERVSQDYKVHRDEIHTKLVQIMREKLLVHLRGLPQIIETWNRTAESVNTTQSVC

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	`TkA01G578790`
TK1151 ID	TkA01G578790
OH-1004 ID	LXL04_011743
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.200
Protein coverage (%)	TK1151 100.000 / OH-1004 92.275 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G578790

Location Chr01:145544745-145545950 (-)

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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

Cytoplasm0.575

Rank 1 · TkA01G578790 · TK1151

Golgi apparatus0.419

Rank 2 · TkA01G578790 · TK1151

Nucleus0.120

Rank 3 · TkA01G578790 · TK1151

Cell membrane0.114

Rank 4 · TkA01G578790 · TK1151

Lysosome / Vacuole0.095

Rank 5 · TkA01G578790 · TK1151

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.

PF07928Vps5455-185 aa

PF25402PH_2868-132 aa

PF25402PH_28161-183 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G578790	`PF07928`	Vps54	55	185	4.7e-46	157.2
TkA01G578790	`PF25402`	PH_28	68	132	0.086	13.7
TkA01G578790	`PF25402`	PH_28	161	183	0.086	13.7

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	sp\|F4JT76\|VPS54_ARATH Vacuolar protein sorting-associated protein 54, chloroplastic	66.700%	Swiss-Prot	High

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