LXL04_022399 | RubberDandelionOmics

Gene overview

LXL04_022399

Reference: OH-1004 Chr: Chr04 Coordinates: 149535777-149539641 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2523 bp · LXL04_022399|LXL04_022399|OH1004|cDNA

ATGGCAGGCGTTTCCATCGCCGCAGAATGGCAACTTCTCGGCGACAAGTACTACCGAAAGCCAGAGCTCTATCAATTACGATGGAAAAACATCGATCTTGCTCGAAACAAGGTCGCCTGCGCCCCATTCGGCGGTCCAATTGCCGTCATTCGCGACGAGTCCAAGATCGTCCAGCTCTACGCCGAATCCGCCCTTCGTAAACTCCGAATTTTCAACTCCGCCGGCCGACAAATCTCCGAAACCGTTTGGAGAAACCCCGG...

CDS

Download CDS FASTA

2523 bp · LXL04_022399|LXL04_022399|OH1004|CDS

ATGGCAGGCGTTTCCATCGCCGCAGAATGGCAACTTCTCGGCGACAAGTACTACCGAAAGCCAGAGCTCTATCAATTACGATGGAAAAACATCGATCTTGCTCGAAACAAGGTCGCCTGCGCCCCATTCGGCGGTCCAATTGCCGTCATTCGCGACGAGTCCAAGATCGTCCAGCTCTACGCCGAATCCGCCCTTCGTAAACTCCGAATTTTCAACTCCGCCGGCCGACAAATCTCCGAAACCGTTTGGAGAAACCCCGG...

Protein

Download Protein FASTA

840 aa · LXL04_022399|LXL04_022399|OH1004|PROTEIN

MAGVSIAAEWQLLGDKYYRKPELYQLRWKNIDLARNKVACAPFGGPIAVIRDESKIVQLYAESALRKLRIFNSAGRQISETVWRNPGGRMIGLSWTDEQVLVCVTQDGTVYRYDIHSKIIEPNVSMGTECFEHSVVECVFWGNGVVCINEAFQLFCIPDLKNPKPCKLADTGLEEFPLCMAVIEPQYTLSGNVEVLLGVGDHVLLVEEDGVQTVGDGLGTLQKMVISHNGKLMASFTHDGQLLVMPTDFSSIIFEYSCES...

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_022399`
TK1151 ID	TkA05G464810
OH-1004 ID	LXL04_022399
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.500
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_022399

Location Chr04:149535777-149539641 (+)

Description Similar to VCL1: Protein VACUOLELESS1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g38020`	Required for vacuole biogenesis and vacuole enlargment in dividing and expanding cells.	VACUOLELESS1 is an essential gene required for vacuole formation and morphogenesis in Arabidopsis.2001 · DOI: 10.1016/s1534-5807(01)00024-7 Geminating pollen has tubular vacuoles, displays highly dynamic vacuole biogenesis, and requires VACUOLESS1 for proper function.2004 · DOI: 10.1104/pp.103.037382

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_022399 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0007033 vacuole organization Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0009860 pollen tube growth Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0016197 endosomal transport Biological Process

GO:0034058 endosomal vesicle fusion Biological Process

GO:0035542 regulation of SNARE complex assembly Biological Process

GO:0042144 vacuole fusion, non-autophagic Biological Process

GO:0045992 negative regulation of embryonic development Biological Process

GO:0046718 symbiont entry into host cell Biological Process

GO:0051469 vesicle fusion with vacuole Biological Process

KEGG gene cross-reference

ath:AT2G38020

bta:505361

ddi:DDB_G0270754

hsa:64601

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.

Cytoplasm0.555

Rank 1 · LXL04_022399 · OH-1004

Nucleus0.250

Rank 2 · LXL04_022399 · OH-1004

Lysosome / Vacuole0.212

Rank 3 · LXL04_022399 · OH-1004

Golgi apparatus0.209

Rank 4 · LXL04_022399 · OH-1004

Cell membrane0.124

Rank 5 · LXL04_022399 · 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.

PF04841.20Vps16_N8-407 aa

PF04840.19Vps16_C506-829 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022399	`PF04841.20`	Vps16_N	8	407	1.1e-81	275.4
LXL04_022399	`PF04840.19`	Vps16_C	506	829	5.6e-68	230.1

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
`Q93VQ0`	Arabidopsis thaliana	Protein VACUOLELESS1	72.654%	Swiss-Prot	strong database homology

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