TkA01G443290 | RubberDandelionOmics

Gene overview

TkA01G443290

Reference: TK1151 Chr: Chr01 Coordinates: 110887700-110902148 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3408 bp · TkA01G443290|TK1151|cDNA

CTACGTCCTTCTCCACAAAGACGTCTACGTCTTCAGCCTTCTCTGTCGCTCCCTCCACAAACTAAGCGTCGAAGCCCCTGTTTCCTTCCCCCATCTCCGGCGACGTCGCCGTCCTCCCCCATCTCAGCCTCGAAGGCCACCATCTTCAATTTCTATTCAAGTCACACGAAATCTGAAGAAAAACCCATATCCATCCCCATCCGAGACGCTTCCTATCCTTCATTAGCCGTGCTAATGCTCTCCGTTGGCCTTGTCATCCA...

CDS

Download CDS FASTA

2613 bp · TkA01G443290|TK1151|CDS

ATGGAGGTATTGGCGTCGAGAGAGCTTCTGCTGTCGCTATCTGAGTCGATTGCGATCCATAGGTTACCCAATTTGGAACCGGTAACGGTGATTTCCAAGGCAAAAGGAGCCGGCGCATATTCATGGGATGATCGCAGAGGATTCTTATGCTTCGCTAGGCAAAAGCGAGTTTGCATTTTCAAACACGATGGAGTGAGGGGATTCGTGGAGGTGAAAGAATTTGCGGTTCCAGATACAGTCAGATCAATGTCTTGGTGTGG...

Protein

Download Protein FASTA

870 aa · TkA01G443290|TK1151|PROTEIN

MEVLASRELLLSLSESIAIHRLPNLEPVTVISKAKGAGAYSWDDRRGFLCFARQKRVCIFKHDGVRGFVEVKEFAVPDTVRSMSWCGENICVGVRREYTILNATNGTLYEIFPWGRIAPPVVVPFPSGELLLGKDNIGVLVDQNGKLMQEGRICWSEPPIRVVIQKPYAIALLPKHIEIRSLRVPFPLIQTIVIRNVRHIQKGNNGIIVSLERSLFGLFPVPLGAQIVQLTASGNFEEALALCKLLPPEDSSLRASKEQL...

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	`TkA01G443290`
TK1151 ID	TkA01G443290
OH-1004 ID	LXL04_007160
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	93.700
Protein coverage (%)	TK1151 99.770 / OH-1004 91.911 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA01G443290

Location Chr01:110887700-110902148 (+)

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.

Open Annotation Module

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.

Cytoplasm0.510

Rank 1 · TkA01G443290 · TK1151

Nucleus0.259

Rank 2 · TkA01G443290 · TK1151

Golgi apparatus0.186

Rank 3 · TkA01G443290 · TK1151

Lysosome / Vacuole0.179

Rank 4 · TkA01G443290 · TK1151

Cell membrane0.132

Rank 5 · TkA01G443290 · 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.

PF00780CNH1-200 aa

PF10367zf-Vps39_C116-129 aa

PF00637Clathrin266-283 aa

PF10366Vps39_1421-484 aa

PF00637Clathrin422-452 aa

PF00637Clathrin504-622 aa

PF10366Vps39_1652-662 aa

PF24925DUF7746652-692 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G443290	`PF00780`	CNH	1	200	7.3e-23	82.4
TkA01G443290	`PF10367`	zf-Vps39_C	116	129	1.6e-16	60.3
TkA01G443290	`PF00637`	Clathrin	266	283	1.4	9.4
TkA01G443290	`PF10366`	Vps39_1	421	484	3e-10	41.0
TkA01G443290	`PF00637`	Clathrin	422	452	1.4	9.4
TkA01G443290	`PF00637`	Clathrin	504	622	1.4	9.4
TkA01G443290	`PF10366`	Vps39_1	652	662	3e-10	41.0
TkA01G443290	`PF24925`	DUF7746	652	692	0.14	13.1
TkA01G443290	`PF00780`	CNH	731	799	7.3e-23	82.4
TkA01G443290	`PF10366`	Vps39_1	778	814	3e-10	41.0
TkA01G443290	`PF13771`	zf-HC5HC2H	794	857	0.16	12.9
TkA01G443290	`PF10367`	zf-Vps39_C	817	854	1.6e-16	60.3
TkA01G443290	`PF09943`	DUF2175	825	863	0.18	12.8

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	59.000%	Swiss-Prot	High

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