LXL04_026235 | RubberDandelionOmics

Gene overview

LXL04_026235

Reference: OH-1004 Chr: Chr05 Coordinates: 123549727-123554180 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1422 bp · LXL04_026235|LXL04_026235|OH1004|cDNA

ATGGAATTTGGAAGAAGGGAAGACGCGTTCGttcttcttcgtcttcattTCGGCAGCTTCAAGAACAACACCCAGTTTCTCTCTTTTCCCGTTTGTTCCTTCTTTCTCCACCGCGACAGCCTAGAAGCTCCACCATTTTTCACCGTTCGTCTCCATCTCTCCACCCCGGTGTTCAACCTGGAGGCCAGCGAACGTCTTCGGGAGCAGCGAGTAACCTCCGGGAGGTCGGAAGTCCGCCGGGTTGCAGCGAACACTACAAG...

CDS

Download CDS FASTA

1422 bp · LXL04_026235|LXL04_026235|OH1004|CDS

ATGGAATTTGGAAGAAGGGAAGACGCGTTCGTTCTTCTTCGTCTTCATTTCGGCAGCTTCAAGAACAACACCCAGTTTCTCTCTTTTCCCGTTTGTTCCTTCTTTCTCCACCGCGACAGCCTAGAAGCTCCACCATTTTTCACCGTTCGTCTCCATCTCTCCACCCCGGTGTTCAACCTGGAGGCCAGCGAACGTCTTCGGGAGCAGCGAGTAACCTCCGGGAGGTCGGAAGTCCGCCGGGTTGCAGCGAACACTACAAG...

Protein

Download Protein FASTA

473 aa · LXL04_026235|LXL04_026235|OH1004|PROTEIN

MEFGRREDAFVLLRLHFGSFKNNTQFLSFPVCSFFLHRDSLEAPPFFTVRLHLSTPVFNLEASERLREQRVTSGRSEVRRVAANTTRNIAFRDERFRDNNNHPISASQTSSSLDAYSPATTYDVKVMHCQSATSIAYSPSEICFTSRFQHCSTTWTPAKLLLPFDASGHLYSLISADDTVIKFDDRNGFQKFEKIKNSSRQSRQPEELIGKMRECKRLIKEFDREVKDLKHTVKELNSYVALKKHNIENKRVDLFGGPVE...

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_026235`
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_026235

Location Chr05:123549727-123554180 (-)

Description Similar to NPSN11: Novel plant SNARE 11

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g35190`	t-SNARE involved in diverse vesicle trafficking and membrane fusion processes, including cell plate formation.	No verified direct reference in this release
`At1g48240`	Vesicle trafficking protein that functions in the secretory pathway.	No verified direct reference in this release
`At3g17440`	Vesicle trafficking protein that functions in the secretory pathway.	No verified direct reference in this release
`At1g75850`	Plays a role in vesicular protein sorting.	Arabidopsis VPS35, a retromer component, is required for vacuolar protein sorting and involved in plant growth and leaf senescence.2008 · DOI: 10.1093/pcp/pcn006
`At2g17790`	Plays a role in vesicular protein sorting.	Loss-of-function mutations of retromer large subunit genes suppress the phenotype of an Arabidopsis zig mutant that lacks Qb-SNARE VTI11.2010 · DOI: 10.1105/tpc.109.069294

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026235 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000911 cytokinesis by cell plate formation Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0006906 vesicle fusion Biological Process

GO:0015031 protein transport Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005770 late endosome Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

GO:0005794 Golgi apparatus Cellular Component

KEGG gene cross-reference

ath:AT1G48240

ath:AT1G75850

ath:AT2G17790

ath:AT2G35190

ath:AT3G17440

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.

Cytoplasm0.376

Rank 1 · LXL04_026235 · OH-1004

Nucleus0.323

Rank 2 · LXL04_026235 · OH-1004

Mitochondrion0.190

Rank 3 · LXL04_026235 · OH-1004

Cell membrane0.154

Rank 4 · LXL04_026235 · OH-1004

Endoplasmic reticulum0.115

Rank 5 · LXL04_026235 · 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.

PF03635.24Vps35330-394 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026235	`PF03635.24`	Vps35	330	394	4.8e-10	39.3

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
`Q944A9`	Arabidopsis thaliana	Novel plant SNARE 11	56.410%	Swiss-Prot	weak database homology
`Q9LNH6`	Arabidopsis thaliana	Novel plant SNARE 12	49.704%	Swiss-Prot	weak database homology
`Q9LRP1`	Arabidopsis thaliana	Novel plant SNARE 13	51.266%	Swiss-Prot	weak database homology
`F4I0P8`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35B	83.333%	Swiss-Prot	weak database homology
`Q7X659`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35A	73.333%	Swiss-Prot	weak database homology

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