TkA03G536510 | RubberDandelionOmics

Gene overview

TkA03G536510

Reference: TK1151 Chr: Chr03 Coordinates: 135014364-135018769 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3450 bp · TkA03G536510|TK1151|cDNA

GTGATTTTTTATAAAGGAGGATTTTTTTCACATTACTTTGGAATAAGTTGGGAATTTTGTAGTCGTTGGTAAACTGAATCGCATCGCTAGAACTCACCGTCAGTCCATCGTCTTCTTCATCTTGCTCTACATCATCATGGCGGAAATTTCGAAGCTTTAAACCAAAAAACTCGTCTGCCATGGCTAAACCCCTGTTGAAATCACGCACGATCCTCGAACCTTTTGCACAATTCAACGCATCTTCATCATCAATTCGATCT...

CDS

Download CDS FASTA

1179 bp · TkA03G536510|TK1151|CDS

ATGAGCTCCAAAGCTCTTGCCATATGGAGAATATTGGCAAGAAACTATTCATCCGGATTTTGGAAGGACCAAACACGGATAAATGAGACAAGAGGGGAAGAAAGTGTAAATATTGTTATATCCGGTAAAGAGACTGAGCAAGAATTCAAGATTCTCAGGATTCTTGAGGAATTATCTGATAAAGATCTCATACTGCAACATCTTGGATGGATTGCAGATATTAACCAGGTGCTTTCTGTTCGCGTATTAACATCTGAAAA...

Protein

Download Protein FASTA

392 aa · TkA03G536510|TK1151|PROTEIN

MSSKALAIWRILARNYSSGFWKDQTRINETRGEESVNIVISGKETEQEFKILRILEELSDKDLILQHLGWIADINQVLSVRVLTSEKRSHQLPPNDVITAIDTKKTEILQRYLQWLIEEQDSDDPQFHTSYANLLTKSVLETYETESLPSESETGKQSIFQNPVRERLQFFLQSSDLYDPEEVLDLIQDSELWLEKAILYRKLGQETLVLQILAVKLEDSDAAEHYCAEIGRPDAYMQLLDIYLNPTEGKKPMFKAAVRL...

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	`TkA03G536510`
TK1151 ID	TkA03G536510
OH-1004 ID	LXL04_010596
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	98.200
Protein coverage (%)	TK1151 100.000 / OH-1004 39.139 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

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Basic Information and Functional Annotation

Gene ID TkA03G536510

Location Chr03:135014364-135018769 (-)

Description Similar to VPS3: Vacuolar sorting protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g22860`	Essential protein required during embryogenesis.	Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases mediate membrane fusion at the vacuole in Arabidopsis.2018 · DOI: 10.1073/pnas.1717839115

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010596 · 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:0006355 regulation of DNA-templated transcription Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0007165 signal transduction Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0034058 endosomal vesicle fusion Biological Process

GO:0035542 regulation of SNARE complex assembly Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005769 early endosome Cellular Component

GO:0010008 endosome membrane Cellular Component

KEGG gene cross-reference

ath:AT1G22860

bta:514660

dre:565026

hsa:9392

mmu:73122

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.

Cytoplasm0.551

Rank 1 · TkA03G536510 · TK1151

Nucleus0.319

Rank 2 · TkA03G536510 · TK1151

Lysosome / Vacuole0.154

Rank 3 · TkA03G536510 · TK1151

Golgi apparatus0.144

Rank 4 · TkA03G536510 · TK1151

Cell membrane0.111

Rank 5 · TkA03G536510 · 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.

PF28737VPS18_solenoid_2nd50-139 aa

PF23556TPR_Vps4161-274 aa

PF00637Clathrin102-245 aa

PF13431TPR_17119-136 aa

PF13431TPR_17189-206 aa

PF28737VPS18_solenoid_2nd256-310 aa

PF10367zf-Vps39_C327-367 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G536510	`PF28737`	VPS18_solenoid_2nd	50	139	0.016	15.8
TkA03G536510	`PF23556`	TPR_Vps41	61	274	0.00013	22.0
TkA03G536510	`PF00637`	Clathrin	102	245	9.3e-09	35.9
TkA03G536510	`PF13431`	TPR_17	119	136	0.079	14.0
TkA03G536510	`PF13431`	TPR_17	189	206	0.079	14.0
TkA03G536510	`PF28737`	VPS18_solenoid_2nd	256	310	0.016	15.8
TkA03G536510	`PF10367`	zf-Vps39_C	327	367	2.5e-17	62.9

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
`F4I312`	Arabidopsis thaliana	sp\|F4I312\|VPS3_ARATH Vacuolar sorting protein 3	60.100%	Swiss-Prot	High

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