LXL04_015486 | RubberDandelionOmics

Gene overview

LXL04_015486

Reference: OH-1004 Chr: Chr03 Coordinates: 73506261-73511109 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1857 bp · LXL04_015486|LXL04_015486|OH1004|cDNA

atggGCTTCTTTACCGGTCTCTTTTTTGGTGTCGCATTTGGTCTCGGTTTCATAGTCTGCGTTGCTCGCCACCAGATCATCCGATCTGCTCGTCGTGCTGATCTGGCTGCAACCATCGCGGCTTTTGCAAGGATGACAGTTGCGGATTCCAGAAAGCTTCTTCCAGGAGATTATTATCCTCCATGGGTGTTAAATTGGCTTAATCTGATAATGAACAAGATCTGGCCGTATGTTGATGAGGCAGCATCGGATCTAATAAG...

CDS

Download CDS FASTA

1857 bp · LXL04_015486|LXL04_015486|OH1004|CDS

ATGGGCTTCTTTACCGGTCTCTTTTTTGGTGTCGCATTTGGTCTCGGTTTCATAGTCTGCGTTGCTCGCCACCAGATCATCCGATCTGCTCGTCGTGCTGATCTGGCTGCAACCATCGCGGCTTTTGCAAGGATGACAGTTGCGGATTCCAGAAAGCTTCTTCCAGGAGATTATTATCCTCCATGGGTGTTAAATTGGCTTAATCTGATAATGAACAAGATCTGGCCGTATGTTGATGAGGCAGCATCGGATCTAATAAG...

Protein

Download Protein FASTA

618 aa · LXL04_015486|LXL04_015486|OH1004|PROTEIN

MGFFTGLFFGVAFGLGFIVCVARHQIIRSARRADLAATIAAFARMTVADSRKLLPGDYYPPWVLNWLNLIMNKIWPYVDEAASDLIRSSVEPILEQYKPMILSSLKFSKLTLGTVAPQFTGVSVEEGDPGEITMEMEIQWDGNPNVILDIVTRVGVALPIQVKNIAFTGVFRLIFKPLVDEFPCFGAVLFSLREKKQLDFTLKVIGGDLSALPGVSDAIEETIKDAVEDSVTWPVRIVIPILAGDYSDLELKPCGILEVK...

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_015486`
TK1151 ID	TkA02G326340
OH-1004 ID	LXL04_015486
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	88.600
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_015486

Location Chr03:73506261-73511109 (-)

Description Similar to SYT4: Synaptotagmin-4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g11100`	May be involved in membrane trafficking.	No verified direct reference in this release
`At1g05500`	May be involved in membrane trafficking.	No verified direct reference in this release
`At3g61050`	May be involved in membrane trafficking (By similarity).	No verified direct reference in this release
`At5g04220`	May be involved in membrane trafficking.	No verified direct reference in this release
`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_015486 · GCA_047496595.1_OSU_TarKok_2.0.

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.

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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 membrane0.470

Rank 1 · LXL04_015486 · OH-1004

Cytoplasm0.315

Rank 2 · LXL04_015486 · OH-1004

Endoplasmic reticulum0.216

Rank 3 · LXL04_015486 · OH-1004

Golgi apparatus0.158

Rank 4 · LXL04_015486 · OH-1004

Nucleus0.129

Rank 5 · LXL04_015486 · OH-1004

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.

PF17047.12SMP_LBD65-241 aa

PF00168.37C2255-359 aa

PF00168.37C2433-517 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015486	`PF17047.12`	SMP_LBD	65	241	3.5e-14	53.4
LXL04_015486	`PF00168.37`	C2	255	359	4.6e-52	175.3
LXL04_015486	`PF00168.37`	C2	433	517	4.6e-52	175.3

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
`A0JJX5`	Arabidopsis thaliana	Synaptotagmin-4	68.939%	Swiss-Prot	strong database homology
`Q8L706`	Arabidopsis thaliana	Synaptotagmin-5	66.344%	Swiss-Prot	strong database homology
`Q9LEX1`	Arabidopsis thaliana	Calcium-dependent lipid-binding protein	41.000%	Swiss-Prot	moderate database homology
`Q7XA06`	Arabidopsis thaliana	Synaptotagmin-3	32.742%	Swiss-Prot	moderate database homology
`Q9SKR2`	Arabidopsis thaliana	Synaptotagmin-1	31.862%	Swiss-Prot	moderate database homology

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