TkA03G541940 | RubberDandelionOmics

Gene overview

TkA03G541940

Reference: TK1151 Chr: Chr03 Coordinates: 136483072-136486518 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2167 bp · TkA03G541940|TK1151|cDNA

AAGTAAGAAGATAATGGGAAAAAAAAACATAGAAAAATATTTCTTTCAAGTAAAAACAATTCAGACACACTTCAAAATATCTTGGAATTGAGAACTTCAGCCGGTGGCAGCTAAACAAGTAACGGATACAACAAGGCAAGAATTGAGCGTTACATTCACCTCTCTCTCTCTCTCTCTATCTCTCTCTCTCTCTCTCTCAAATTCATCATCACAGATTCACAGGTTCCTCAAGTAGCAATTGGGCTATACCGACCCCATTT...

CDS

Download CDS FASTA

1482 bp · TkA03G541940|TK1151|CDS

ATGGGGTTGATTTCTGGAATCCTGATGGGGACTGTATTTGGGATTGCGATTATGGCTGGTTGGCGGCAGATGATGAGATATCGAAGCAGTAAACGAATTGCCAAGGCAGTTGACATAAAACTCCTTGGATGTCTCAACAGAGATGACTTAAAGAAAATCTGTGGTGATAACTTTCCAGAATGGATATCTTTCCCTGTTTATGAACAGGTGAAATGGCTGAACAAACAATTGAGCAAACTCTGGCCATATGTTGAAGAAGC...

Protein

Download Protein FASTA

493 aa · TkA03G541940|TK1151|PROTEIN

MGLISGILMGTVFGIAIMAGWRQMMRYRSSKRIAKAVDIKLLGCLNRDDLKKICGDNFPEWISFPVYEQVKWLNKQLSKLWPYVEEAARIIIKESVEPLLEDYRPPGITSLKFDKLSLGTVAPKIEGIRVQSLKKGQITMDIDLRWGGDPNIVLGVQAALVANLPIQLKDLQVFTVVRVIFQLCEEIPCISAVVVALLSEPKPRIDYTLKAIGGSLTAMPGLSDMIDDTVNTIVTDMLQWPHRIVVPIGVAVDTSDLELK...

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	`TkA03G541940`
TK1151 ID	TkA03G541940
OH-1004 ID	LXL04_022703
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	79.100
Protein coverage (%)	TK1151 81.136 / OH-1004 92.184 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 TkA03G541940

Location Chr03:136483072-136486518 (+)

Description Similar to CLB: Calcium-dependent lipid-binding protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g61050`	May be involved in membrane trafficking (By similarity).	No verified direct reference in this release
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022703 · 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:0006351 DNA-templated transcription Biological Process

GO:0006869 lipid transport Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009958 positive gravitropism Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0012505 endomembrane system Cellular Component

GO:0031965 nuclear membrane Cellular Component

GO:0033011 perinuclear theca Cellular Component

KEGG gene cross-reference

ath:AT1G05500

ath:AT3G61050

ath:AT5G11100

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.

Cell membrane0.595

Rank 1 · TkA03G541940 · TK1151

Cytoplasm0.251

Rank 2 · TkA03G541940 · TK1151

Endoplasmic reticulum0.178

Rank 3 · TkA03G541940 · TK1151

Golgi apparatus0.110

Rank 4 · TkA03G541940 · TK1151

Nucleus0.087

Rank 5 · TkA03G541940 · 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.

PF17047SMP_LBD68-248 aa

PF25669SMP_MUG190-like68-132 aa

PF25669SMP_MUG190-like152-245 aa

PF11458Mistic224-240 aa

PF00168C2263-358 aa

PF11458Mistic280-319 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G541940	`PF17047`	SMP_LBD	68	248	1e-15	58.4
TkA03G541940	`PF25669`	SMP_MUG190-like	68	132	1.1e-12	48.7
TkA03G541940	`PF25669`	SMP_MUG190-like	152	245	1.1e-12	48.7
TkA03G541940	`PF11458`	Mistic	224	240	0.091	13.6
TkA03G541940	`PF00168`	C2	263	358	3.4e-21	76.1
TkA03G541940	`PF11458`	Mistic	280	319	0.091	13.6

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
`Q9LEX1`	Arabidopsis thaliana	sp\|Q9LEX1\|CLB_ARATH Calcium-dependent lipid-binding protein	69.200%	Swiss-Prot	High
`Q8L706`	Arabidopsis thaliana	sp\|Q8L706\|SYT5_ARATH Synaptotagmin-5	40.500%	Swiss-Prot	Medium
`A0JJX5`	Arabidopsis thaliana	sp\|A0JJX5\|SYT4_ARATH Synaptotagmin-4	39.700%	Swiss-Prot	Medium
`B6ETT4`	Arabidopsis thaliana	sp\|B6ETT4\|SYT2_ARATH Synaptotagmin-2	31.300%	Swiss-Prot	Medium
`Q9SKR2`	Arabidopsis thaliana	sp\|Q9SKR2\|SYT1_ARATH Synaptotagmin-1	31.000%	Swiss-Prot	Medium

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