LXL04_010596 | RubberDandelionOmics

Gene overview

LXL04_010596

Reference: OH-1004 Chr: Chr02 Coordinates: 149460897-149464820 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3000 bp · LXL04_010596|LXL04_010596|OH1004|cDNA

ATGGCTAAACCCCTGTTGAAATCACGCACGATCCTCGAACCTTTTGCACAATTCAACGCATCTTCATCATCAATTCGATCTCTAGCTCTCTTTTCCGCCTCACCTTCCGAAACCCTAATATACGTCGGCACTGTCTCCGGTAAACTCCTCTTACTCTCTCTTCATCATCCCAATTCCAATTCCAGTAGTAGCCACAACCAAGAGAATAACAGTAACAATGAGAATAGTGATAACGACGATAAAATCAAATTCGTGCGGCA...

CDS

Download CDS FASTA

3000 bp · LXL04_010596|LXL04_010596|OH1004|CDS

ATGGCTAAACCCCTGTTGAAATCACGCACGATCCTCGAACCTTTTGCACAATTCAACGCATCTTCATCATCAATTCGATCTCTAGCTCTCTTTTCCGCCTCACCTTCCGAAACCCTAATATACGTCGGCACTGTCTCCGGTAAACTCCTCTTACTCTCTCTTCATCATCCCAATTCCAATTCCAGTAGTAGCCACAACCAAGAGAATAACAGTAACAATGAGAATAGTGATAACGACGATAAAATCAAATTCGTGCGGCA...

Protein

Download Protein FASTA

999 aa · LXL04_010596|LXL04_010596|OH1004|PROTEIN

MAKPLLKSRTILEPFAQFNASSSSIRSLALFSASPSETLIYVGTVSGKLLLLSLHHPNSNSSSSHNQENNSNNENSDNDDKIKFVRHMSISDRAVESIHVFGEIEKVLVLSDGFIHFIDLELAKPVKKIGALTDVSAVARRLRCNGNEGFTKLTVGGGGDTSSSSSFLQRLGGGGGGGRLNGGNADDLPIDDNCVFAAAVGKKLILVGLVARSNDSYDYDSVAGSLVTMKEIQCVDIVKEVVWINDSIIVGSSSGYYLCS...

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_010596`
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_010596

Location Chr02:149460897-149464820 (-)

Description Similar to VPS3: Vacuolar sorting protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g22860`	Essential protein required during embryogenesis.	Distinct sets of tethering complexes, SNARE complexes, and Rab GTPases mediate membrane fusion at the vacuole in Arabidopsis.2018 · DOI: 10.1073/pnas.1717839115

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_010596 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0007165 signal transduction Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0034058 endosomal vesicle fusion Biological Process

GO:0035542 regulation of SNARE complex assembly Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005769 early endosome Cellular Component

GO:0010008 endosome membrane Cellular Component

KEGG gene cross-reference

ath:AT1G22860

bta:514660

dre:565026

hsa:9392

mmu:73122

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.

Nucleus0.416

Rank 1 · LXL04_010596 · OH-1004

Cytoplasm0.376

Rank 2 · LXL04_010596 · OH-1004

Lysosome / Vacuole0.126

Rank 3 · LXL04_010596 · OH-1004

Golgi apparatus0.117

Rank 4 · LXL04_010596 · OH-1004

Cell membrane0.114

Rank 5 · LXL04_010596 · 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.

PF10366.16Vps39_1555-632 aa

PF00637.27Clathrin709-852 aa

PF10367.16zf-Vps39_C934-974 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010596	`PF10366.16`	Vps39_1	555	632	6.3e-07	30.4
LXL04_010596	`PF00637.27`	Clathrin	709	852	6.7e-09	36.4
LXL04_010596	`PF10367.16`	zf-Vps39_C	934	974	7.7e-17	61.3

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
`F4I312`	Arabidopsis thaliana	Vacuolar sorting protein 3	56.207%	Swiss-Prot	strong database homology

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