TkA03G128010 | RubberDandelionOmics

Gene overview

TkA03G128010

Reference: TK1151 Chr: Chr03 Coordinates: 32850177-32855168 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1711 bp · TkA03G128010|TK1151|cDNA

GGAAGGGTGAATGTGAGTACAGACTCAGGGGCTAGAGAGATAGCAGCAGCTTTGCTTTTGACCGGTCAAGTTGTTGCTGTTTTGGAATTATTGAAGAGTTTTAATTATTGTGATATGAAGATATGTGAGGAGATTTTGAAGAAGGGAAATCATGATGTTTGTTTGTTAGGGCTTTATAAATACAACTCAATGCATCGTGAAGCTCTTAAACTTCTTCATGAGTTAGTGGAGGATTCTAAATTGGAACACCCTAAAATCAC...

CDS

Download CDS FASTA

2970 bp · TkA03G128010|TK1151|CDS

ATGGTGCACACTGCATACGATACTCGCGAATTGCTCATTGATTGTCCGAAGAAGATCAATGCGGTCGAATACTACGGCGCAAAGCTACTCCTCGCTTGCTCCGACGGATCCCTACAAATCTACGGTTCGGAATCCGCTAACCGATCTTCTTCCTATCAAAATCTGGAACTCAAGAAGGAACTCTACGTGCTTGAAAGAAACGTCAGTGGATTCTCCAAAAAACAGGTGTGGTCAATGGAGGTATTGGCGTCGAGAGAGCT...

Protein

Download Protein FASTA

989 aa · TkA03G128010|TK1151|PROTEIN

MVHTAYDTRELLIDCPKKINAVEYYGAKLLLACSDGSLQIYGSESANRSSSYQNLELKKELYVLERNVSGFSKKQVWSMEVLASRELLLSLSESIAIHRLPNLEPVTVISKAKGAGAYSWDDRRGFLCFARQKRVCIFRHDGVRGFVEVKEFAVPDTVRSMSWCGENICVGVRREYTILNATNGTLYEIFPWGRIAPPVVVPFPSGELLLGKDNIGVLVDQNGKLMQEGRICWSEPPIRVVIQKPYAIALLPKHIEIRSL...

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	`TkA03G128010`
TK1151 ID	TkA03G128010
OH-1004 ID	LXL04_007160
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	99.700
Protein coverage (%)	TK1151 99.798 / OH-1004 99.798 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 TkA03G128010

Location Chr03:32850177-32855168 (-)

Description Similar to VPS39: Vacuolar sorting protein 39

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g36630`	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_007160 · 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:0006886 intracellular protein transport Biological Process

GO:0006914 autophagy Biological Process

GO:0007033 vacuole organization Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0034058 endosomal vesicle fusion Biological Process

GO:0035542 regulation of SNARE complex assembly Biological Process

GO:0061909 autophagosome-lysosome fusion Biological Process

GO:0097352 autophagosome maturation Biological Process

GO:0097576 vacuole fusion Biological Process

KEGG gene cross-reference

ath:AT4G36630

hsa:23339

mmu:269338

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.

Cytoplasm0.511

Rank 1 · TkA03G128010 · TK1151

Nucleus0.236

Rank 2 · TkA03G128010 · TK1151

Golgi apparatus0.228

Rank 3 · TkA03G128010 · TK1151

Lysosome / Vacuole0.186

Rank 4 · TkA03G128010 · TK1151

Cell membrane0.125

Rank 5 · TkA03G128010 · 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.

PF00780CNH61-278 aa

PF10367zf-Vps39_C194-207 aa

PF00637Clathrin344-360 aa

PF10366Vps39_1494-603 aa

PF00637Clathrin494-558 aa

PF00637Clathrin623-741 aa

PF24925DUF7746771-811 aa

PF00780CNH850-916 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G128010	`PF00780`	CNH	61	278	3.6e-25	90.0
TkA03G128010	`PF10367`	zf-Vps39_C	194	207	2e-16	60.0
TkA03G128010	`PF00637`	Clathrin	344	360	0.008	16.6
TkA03G128010	`PF10366`	Vps39_1	494	603	1.6e-23	83.7
TkA03G128010	`PF00637`	Clathrin	494	558	0.008	16.6
TkA03G128010	`PF00637`	Clathrin	623	741	0.008	16.6
TkA03G128010	`PF24925`	DUF7746	771	811	0.15	12.9
TkA03G128010	`PF00780`	CNH	850	916	3.6e-25	90.0
TkA03G128010	`PF10366`	Vps39_1	897	933	1.6e-23	83.7
TkA03G128010	`PF13771`	zf-HC5HC2H	913	976	0.17	12.8
TkA03G128010	`PF10367`	zf-Vps39_C	936	973	2e-16	60.0
TkA03G128010	`PF09943`	DUF2175	944	982	0.2	12.6

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
`Q8L5Y0`	Arabidopsis thaliana	sp\|Q8L5Y0\|VPS39_ARATH Vacuolar sorting protein 39	61.800%	Swiss-Prot	High

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