TkA01G085460 | RubberDandelionOmics

Gene overview

TkA01G085460

Reference: TK1151 Chr: Chr01 Coordinates: 21795418-21798802 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1967 bp · TkA01G085460|TK1151|cDNA

AAATCATCTCCGTTTCGATTTCTTAATCCATCGTGTTTATCTTCCTTTTACACCAATGATTCAATCATTCAGACATTCTCTATATACGATTCATAAACCGAGATCTAGTCCTTCTCTATAACTCAAATGAAATAGTGTTAAAGATGAACTTTATTGGTAGCTTATTTGGAACTATCGGGTTTGTATTTGGAATCCCCGTCGGTCTTTTTCTGGGGTTTCTTATTTTTATTAAGACGGAGTCTACAGATGTGAAGATTCCG...

CDS

Download CDS FASTA

1644 bp · TkA01G085460|TK1151|CDS

ATGAACTTTATTGGTAGCTTATTTGGAACTATCGGGTTTGTATTTGGAATCCCCGTCGGTCTTTTTCTGGGGTTTCTTATTTTTATTAAGACGGAGTCTACAGATGTGAAGATTCCGTTTATTAGACCGATTCAAGAGCTTGATAAAAGCTCATTGGTTGATATTCTACCCGAAATTCCATTATGGGTGAAGCATCCAGACTATGAACGAATTGATTGGTTTAATGATGTAGTTCGTGATATGTGGCCTTATATTGATAA...

Protein

Download Protein FASTA

547 aa · TkA01G085460|TK1151|PROTEIN

MNFIGSLFGTIGFVFGIPVGLFLGFLIFIKTESTDVKIPFIRPIQELDKSSLVDILPEIPLWVKHPDYERIDWFNDVVRDMWPYIDKAICGMIRSLSEPIFSEYIGMYHLKSIDFETLTLGTLPPIVQGIKVHELNENHLVFDLMVKWAGNPNIILVLKLLSLPIKVQLIDIQITAAFRITLKPFVPTFPCFSNAQFSLMEKPEVDFGLKVMGGDLMAIPGIHHYVQRIINEQVSSVYLWPQTLEIPVLDASTGAAKKPM...

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	`TkA01G085460`
TK1151 ID	TkA01G085460
OH-1004 ID	LXL04_005012
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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 TkA01G085460

Location Chr01:21795418-21798802 (+)

Description Similar to SYT3: Synaptotagmin-3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g04220`	May be involved in membrane trafficking.	No verified direct reference in this release
`At1g20080`	May play an important role in regulating an unconventional protein trafficking from the cytosol to the extracellular matrix.	Golgi apparatus-localized synaptotagmin 2 is required for unconventional secretion in Arabidopsis.2011 · DOI: 10.1371/journal.pone.0026477
`At2g20990`	Plays an important role in maintaining plasma membrane integrity during freezing and osmotic stresses.	Arabidopsis synaptotagmin 1 is required for the maintenance of plasma membrane integrity and cell viability.2008 · DOI: 10.1105/tpc.108.063859 Calcium-dependent freezing tolerance in Arabidopsis involves membrane resealing via synaptotagmin SYT1.2008 · DOI: 10.1105/tpc.108.062679 Arabidopsis synaptotagmin SYTA regulates endocytosis and virus movement protein cell-to-cell transport.2010 · DOI: 10.1073/pnas.0909080107 Arabidopsis synaptotagmin SYT1, a type I signal-anchor protein, requires tandem C2 domains for delivery to the plasma membrane.2010 · DOI: 10.1074/jbc.m109.084046
`At1g05500`	May be involved in membrane trafficking.	No verified direct reference in this release
`At5g11100`	May be involved in membrane trafficking.	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_005012 · 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:0006612 protein targeting to membrane Biological Process

GO:0006869 lipid transport Biological Process

GO:0006897 endocytosis Biological Process

GO:0007029 endoplasmic reticulum organization Biological Process

GO:0009306 protein secretion Biological Process

GO:0009409 response to cold Biological Process

GO:0009612 response to mechanical stimulus Biological Process

GO:0009615 response to virus Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0046740 transport of virus in host, cell to cell Biological Process

GO:0061817 endoplasmic reticulum-plasma membrane tethering Biological Process

GO:0000139 Golgi membrane Cellular Component

KEGG gene cross-reference

ath:AT1G05500

ath:AT1G20080

ath:AT2G20990

ath:AT5G04220

ath:AT5G11100

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.

Cell membrane0.516

Rank 1 · TkA01G085460 · TK1151

Cytoplasm0.244

Rank 2 · TkA01G085460 · TK1151

Endoplasmic reticulum0.214

Rank 3 · TkA01G085460 · TK1151

Golgi apparatus0.129

Rank 4 · TkA01G085460 · TK1151

Lysosome / Vacuole0.111

Rank 5 · TkA01G085460 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF17047SMP_LBD67-248 aa

PF25669SMP_MUG190-like70-132 aa

PF25669SMP_MUG190-like161-248 aa

PF25608NAL1_N207-247 aa

PF00168C2261-364 aa

PF10358NT-C2285-320 aa

PF28777Pro_N_rel408-434 aa

PF00168C2425-530 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G085460	`PF17047`	SMP_LBD	67	248	5.3e-16	59.3
TkA01G085460	`PF25669`	SMP_MUG190-like	70	132	2.1e-11	44.5
TkA01G085460	`PF25669`	SMP_MUG190-like	161	248	2.1e-11	44.5
TkA01G085460	`PF25608`	NAL1_N	207	247	0.013	16.0
TkA01G085460	`PF00168`	C2	261	364	1.3e-45	154.6
TkA01G085460	`PF10358`	NT-C2	285	320	0.16	12.3
TkA01G085460	`PF28777`	Pro_N_rel	408	434	0.071	14.0
TkA01G085460	`PF00168`	C2	425	530	1.3e-45	154.6
TkA01G085460	`PF25608`	NAL1_N	429	464	0.013	16.0
TkA01G085460	`PF17047`	SMP_LBD	457	527	5.3e-16	59.3
TkA01G085460	`PF10358`	NT-C2	481	542	0.16	12.3
TkA01G085460	`PF25669`	SMP_MUG190-like	516	543	2.1e-11	44.5

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
`Q7XA06`	Arabidopsis thaliana	sp\|Q7XA06\|SYT3_ARATH Synaptotagmin-3	56.100%	Swiss-Prot	High
`B6ETT4`	Arabidopsis thaliana	sp\|B6ETT4\|SYT2_ARATH Synaptotagmin-2	51.800%	Swiss-Prot	High
`Q9SKR2`	Arabidopsis thaliana	sp\|Q9SKR2\|SYT1_ARATH Synaptotagmin-1	46.700%	Swiss-Prot	Medium
`Q8L706`	Arabidopsis thaliana	sp\|Q8L706\|SYT5_ARATH Synaptotagmin-5	31.700%	Swiss-Prot	Medium
`A0JJX5`	Arabidopsis thaliana	sp\|A0JJX5\|SYT4_ARATH Synaptotagmin-4	30.900%	Swiss-Prot	Medium

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