LXL04_022045 | RubberDandelionOmics

Gene overview

LXL04_022045

Reference: OH-1004 Chr: Chr04 Coordinates: 143931449-143935444 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1653 bp · LXL04_022045|LXL04_022045|OH1004|cDNA

ATGGGGTTTATCGGCGTTTTTTTGGGAATCGTTGGGGTCGGAATCGGGATTGTTGTTGGTCTTTGCCTTGGGTTTTACTTCTTCATCTATTCCGACCCCAAAAACGAACCATTCGAGGATCCTATCGTCAAGCCAATTTCCGAACTTGATACAACTAGTCTACAAGATTTATTACCCGAGATACCTCTATGGTTAAAGAATCCTGATTACGATCGTGTCGACTGGCTTAACGCATTTGTTTTAAATATGTGGCCTTATCT...

CDS

Download CDS FASTA

1653 bp · LXL04_022045|LXL04_022045|OH1004|CDS

ATGGGGTTTATCGGCGTTTTTTTGGGAATCGTTGGGGTCGGAATCGGGATTGTTGTTGGTCTTTGCCTTGGGTTTTACTTCTTCATCTATTCCGACCCCAAAAACGAACCATTCGAGGATCCTATCGTCAAGCCAATTTCCGAACTTGATACAACTAGTCTACAAGATTTATTACCCGAGATACCTCTATGGTTAAAGAATCCTGATTACGATCGTGTCGACTGGCTTAACGCATTTGTTTTAAATATGTGGCCTTATCT...

Protein

Download Protein FASTA

550 aa · LXL04_022045|LXL04_022045|OH1004|PROTEIN

MGFIGVFLGIVGVGIGIVVGLCLGFYFFIYSDPKNEPFEDPIVKPISELDTTSLQDLLPEIPLWLKNPDYDRVDWLNAFVLNMWPYLDKAICAAIRQSTEPIVADYVGQGHRPIESITFETLSLGTLPPIFQGIKVYETNENQLVMEPAIKWAGNPNIVIAVKISYFRIKIQLVDLQVFVLPRVTLKPLVSAFPCFANVVVSLLEKPHVDFGLKVLGGDIMAIPGLDRLVQEIIKKEVAKLYLWPQTLQIPILDSSLCVV...

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	`LXL04_022045`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_022045

Location Chr04:143931449-143935444 (-)

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_022045 · GCA_047496595.1_OSU_TarKok_2.0.

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.

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 membrane0.660

Rank 1 · LXL04_022045 · OH-1004

Cytoplasm0.224

Rank 2 · LXL04_022045 · OH-1004

Endoplasmic reticulum0.150

Rank 3 · LXL04_022045 · OH-1004

Nucleus0.087

Rank 4 · LXL04_022045 · OH-1004

Golgi apparatus0.087

Rank 5 · LXL04_022045 · OH-1004

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.

PF17047.12SMP_LBD69-252 aa

PF25669.2SMP_MUG190-like183-250 aa

PF00168.37C2265-364 aa

PF00168.37C2432-532 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022045	`PF17047.12`	SMP_LBD	69	252	7.9e-18	65.3
LXL04_022045	`PF25669.2`	SMP_MUG190-like	183	250	7.8e-09	36.1
LXL04_022045	`PF00168.37`	C2	265	364	7.9e-45	152.1
LXL04_022045	`PF00168.37`	C2	432	532	7.9e-45	152.1

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
`Q7XA06`	Arabidopsis thaliana	Synaptotagmin-3	58.652%	Swiss-Prot	strong database homology
`B6ETT4`	Arabidopsis thaliana	Synaptotagmin-2	51.455%	Swiss-Prot	strong database homology
`Q9SKR2`	Arabidopsis thaliana	Synaptotagmin-1	51.268%	Swiss-Prot	strong database homology
`Q8L706`	Arabidopsis thaliana	Synaptotagmin-5	31.469%	Swiss-Prot	moderate database homology
`A0JJX5`	Arabidopsis thaliana	Synaptotagmin-4	32.236%	Swiss-Prot	moderate database homology

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