TkA07G397540 | RubberDandelionOmics

Gene overview

TkA07G397540

Reference: TK1151 Chr: Chr07 Coordinates: 99882167-99887097 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2666 bp · TkA07G397540|TK1151|cDNA

GACAAATAGACGAATTGAATTCCTTCAAAATTCATCCTAAAAACATTCAATTTCATTCTATCCTTGCAAGCTTCCATTATTAGATCACAATCAACACAGCCACTTTTGCTTTTCTCCACTGCATTCTCATTCTGCTGTATCATCTTGCTGCTCACATCCAACACATCTCTGACCTTTACCCTCATCGTTATCTGCTATATCGTCATTCTGTCTCGACCAAACACTTCGATTCGAGCATTTTCCCTCAATTTCAGTCTCCA...

CDS

Download CDS FASTA

2124 bp · TkA07G397540|TK1151|CDS

ATGGCGGAATCAGCAACAAACGAACTGCTTAAACCTGAAGGTGAAACAATAGATGTTAGTAAATCTGTTTTTAATCTAGGAGCTGTTGTTGGTGATCTAACCATTGATGAAGATGCAAGCAGCAATGATATATCATTGGAAGGACTACAACAGGAGCTTGAAGAGTGCAAAGCCGATGAGGTTGTTGCAAACATATTATCAAAAGGGGTGAAATTGAGAGAGTATACTAAAGGAGTTGAAAACAACTTACGCCAAGTTGA...

Protein

Download Protein FASTA

707 aa · TkA07G397540|TK1151|PROTEIN

MAESATNELLKPEGETIDVSKSVFNLGAVVGDLTIDEDASSNDISLEGLQQELEECKADEVVANILSKGVKLREYTKGVENNLRQVELDSIQEYITESDNLVSLHDQIRDCDVILSQMETLLGGFQVEIGSISSDIKILQEKSLDMGLKLKNRKVAESKLAKFVEDIIIPPRMIEIIVDGEVNDEYLRTLEILSKKLKFVEVDSMVKTSNALKDVQPELEKLRQKAIAKVFEFMIQKLYALRKPKTNIQILQQSILLKYK...

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	`TkA07G397540`
TK1151 ID	TkA07G397540
OH-1004 ID	LXL04_030324
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA07G397540

Location Chr07:99882167-99887097 (+)

Description Similar to VPS52: Vacuolar protein sorting-associated protein 52 A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g71270`	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
`At1g71300`	May be involved in retrograde transport of early and late endosomes to the late Golgi.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030324 · 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:0006605 protein targeting Biological Process

GO:0006896 Golgi to vacuole transport Biological Process

GO:0007041 lysosomal transport Biological Process

GO:0009860 pollen tube growth Biological Process

GO:0015031 protein transport Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0090119 vesicle-mediated cholesterol transport Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0000938 GARP complex Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT1G71270

ath:AT1G71300

cfa:474871

hsa:6293

mmu:224705

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.

Cytoplasm0.537

Rank 1 · TkA07G397540 · TK1151

Golgi apparatus0.495

Rank 2 · TkA07G397540 · TK1151

Cell membrane0.147

Rank 3 · TkA07G397540 · TK1151

Endoplasmic reticulum0.109

Rank 4 · TkA07G397540 · TK1151

Lysosome / Vacuole0.107

Rank 5 · TkA07G397540 · 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.

PF09763Sec3_CC75-191 aa

PF04129Vps52_CC94-266 aa

PF20655Vps52_C225-273 aa

PF20655Vps52_C283-586 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G397540	`PF09763`	Sec3_CC	75	191	1.8e-08	35.0
TkA07G397540	`PF04129`	Vps52_CC	94	266	5.1e-63	212.6
TkA07G397540	`PF20655`	Vps52_C	225	273	8.5e-126	420.2
TkA07G397540	`PF20655`	Vps52_C	283	586	8.5e-126	420.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q94KD3`	Arabidopsis thaliana	sp\|Q94KD3\|VP52A_ARATH Vacuolar protein sorting-associated protein 52 A	78.600%	Swiss-Prot	High
`Q9FVV6`	Arabidopsis thaliana	sp\|Q9FVV6\|VP52B_ARATH Vacuolar protein sorting-associated protein 52 B	73.500%	Swiss-Prot	High

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