LXL04_005460 | RubberDandelionOmics

Gene overview

LXL04_005460

Reference: OH-1004 Chr: Chr01 Coordinates: 164587163-164588742 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

867 bp · LXL04_005460|LXL04_005460|OH1004|cDNA

ATGAGCTTTCAAGATCTTGAATCCGGTCGTCAGTTCAATTCAAAGCGAGGTGGATACACTAATGGCGTCAGGAAACAGGATCCGACTCAAGCTATTGCTTCCGGAATTTTCCAGATCAATACCGCCGTCTCTACGTTTCAGAGGCTAGTCAATACCCTTGGTACACCTAAAGATACCCCCGAACTTCGAGAAAAACTGCACAAAACAAGATTACATATTGGGCAATTGGTGAAGGACACTTCAGAAAAACTGAAGCAAGC...

CDS

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867 bp · LXL04_005460|LXL04_005460|OH1004|CDS

ATGAGCTTTCAAGATCTTGAATCCGGTCGTCAGTTCAATTCAAAGCGAGGTGGATACACTAATGGCGTCAGGAAACAGGATCCGACTCAAGCTATTGCTTCCGGAATTTTCCAGATCAATACCGCCGTCTCTACGTTTCAGAGGCTAGTCAATACCCTTGGTACACCTAAAGATACCCCCGAACTTCGAGAAAAACTGCACAAAACAAGATTACATATTGGGCAATTGGTGAAGGACACTTCAGAAAAACTGAAGCAAGC...

Protein

Download Protein FASTA

288 aa · LXL04_005460|LXL04_005460|OH1004|PROTEIN

MSFQDLESGRQFNSKRGGYTNGVRKQDPTQAIASGIFQINTAVSTFQRLVNTLGTPKDTPELREKLHKTRLHIGQLVKDTSEKLKQASETDHRAQVTASKKITDAKLAKDFQAVLKEFQKAQRLAAERETAYTPFVPQAVLPSSYAASEMDISSDKNPEQRALLVESRRQEVLLLDNEIAFNEAIIEEREQGIIEIQNQIGEVNEIFKDLAVLVHEQGAMIDDIGSNIENSHAATSQARVHLSKASKTQRANSSMVNYLL...

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_005460`
TK1151 ID	TkA03G453060
OH-1004 ID	LXL04_005460
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)	96.500
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_005460

Location Chr01:164587163-164588742 (+)

Description Similar to SYP22: Syntaxin-22

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g46860`	May provide the t-SNARE function in the vacuolar assembly.	The occurrence of 'bulbs', a complex configuration of the vacuolar membrane, is affected by mutations of vacuolar SNARE and phospholipase in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2011.04665.x SGR1, SGR2, SGR3: novel genetic loci involved in shoot gravitropism in Arabidopsis thaliana.1996 · DOI: 10.1104/pp.110.3.945
`At4g17730`	May function in the docking or fusion of transport vesicles with the prevacuolar membrane.	No verified direct reference in this release
`At5g16830`	May function in the docking or fusion of transport vesicles with the prevacuolar membrane.	No verified direct reference in this release
`At1g32270`	Vesicle trafficking protein that functions in the secretory pathway.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_005460 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006623 protein targeting to vacuole Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006891 intra-Golgi vesicle-mediated transport Biological Process

GO:0006896 Golgi to vacuole transport Biological Process

GO:0006906 vesicle fusion Biological Process

GO:0009597 detection of virus Biological Process

GO:0009660 amyloplast organization Biological Process

GO:0009959 negative gravitropism Biological Process

GO:0010118 stomatal movement Biological Process

GO:0045324 late endosome to vacuole transport Biological Process

GO:0048278 vesicle docking Biological Process

GO:0061025 membrane fusion Biological Process

KEGG gene cross-reference

ath:AT1G32270

ath:AT4G17730

ath:AT5G16830

ath:AT5G46860

pon:100174669

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.

Cytoplasm0.333

Rank 1 · LXL04_005460 · OH-1004

Golgi apparatus0.275

Rank 2 · LXL04_005460 · OH-1004

Lysosome / Vacuole0.271

Rank 3 · LXL04_005460 · OH-1004

Cell membrane0.224

Rank 4 · LXL04_005460 · OH-1004

Endoplasmic reticulum0.167

Rank 5 · LXL04_005460 · 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.

PF14523.13Syntaxin_229-164 aa

PF29732.1Syntaxin_R9BP38-119 aa

PF05739.27SNARE185-259 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005460	`PF14523.13`	Syntaxin_2	29	164	1.2e-38	132.8
LXL04_005460	`PF29732.1`	Syntaxin_R9BP	38	119	5.3e-06	27.0
LXL04_005460	`PF05739.27`	SNARE	185	259	1.9e-22	79.6

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`P93654`	Arabidopsis thaliana	Syntaxin-22	74.615%	Swiss-Prot	strong database homology
`O04378`	Arabidopsis thaliana	Syntaxin-23	75.410%	Swiss-Prot	strong database homology
`Q39233`	Arabidopsis thaliana	Syntaxin-21	60.741%	Swiss-Prot	strong database homology
`Q9C615`	Arabidopsis thaliana	Putative syntaxin-24	52.814%	Swiss-Prot	strong database homology

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