LXL04_007160 | RubberDandelionOmics

Gene overview

LXL04_007160

Reference: OH-1004 Chr: Chr02 Coordinates: 37747765-37751734 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2970 bp · LXL04_007160|LXL04_007160|OH1004|cDNA

ATGGTGCACACTGCATACGATACTCGCGAATTGCTCATTGATTGTCCGAAGAAGATCAATGCGGTCGAATACTACGGCGCAAAGCTACTCCTCGCTTGCTCCGACGGATCCCTACAAATCTACGGTTCGGAATCCGCTAACCGATCTTCTTCCTATCAAAATCTGGAACTCAAAAAGGAACTCTACGTGCTTGAAAGAAACGTCAGTGGATTCTCCAAAAAACAGGTGTGGTCAATGGAGGTATTGGCGTCGAGAGAGCT...

CDS

Download CDS FASTA

2970 bp · LXL04_007160|LXL04_007160|OH1004|CDS

ATGGTGCACACTGCATACGATACTCGCGAATTGCTCATTGATTGTCCGAAGAAGATCAATGCGGTCGAATACTACGGCGCAAAGCTACTCCTCGCTTGCTCCGACGGATCCCTACAAATCTACGGTTCGGAATCCGCTAACCGATCTTCTTCCTATCAAAATCTGGAACTCAAAAAGGAACTCTACGTGCTTGAAAGAAACGTCAGTGGATTCTCCAAAAAACAGGTGTGGTCAATGGAGGTATTGGCGTCGAGAGAGCT...

Protein

Download Protein FASTA

989 aa · LXL04_007160|LXL04_007160|OH1004|PROTEIN

MVHTAYDTRELLIDCPKKINAVEYYGAKLLLACSDGSLQIYGSESANRSSSYQNLELKKELYVLERNVSGFSKKQVWSMEVLASRELLLSLSESIAIHRLPNLEPVTVISKAKGAGAYSWDDRRGFLCFARQKRVCIFRHDGVRGFVEVKEFAVPDTVRSMSWCGENICVGVRREYTILNATNGTLYEIFPWGRIAPPVVVPFPSGELLLGKDNIGVLVDQNGKLMQEGRICWSEPPIRVVIQKPYAIALLPKHIEIRSL...

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_007160`
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_007160

Location Chr02:37747765-37751734 (-)

Description Similar to VPS39: Vacuolar sorting protein 39

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g36630`	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_007160 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0006914 autophagy Biological Process

GO:0007033 vacuole organization Biological Process

GO:0008333 endosome to lysosome transport Biological Process

GO:0015031 protein transport Biological Process

GO:0016192 vesicle-mediated transport Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0034058 endosomal vesicle fusion Biological Process

GO:0035542 regulation of SNARE complex assembly Biological Process

GO:0061909 autophagosome-lysosome fusion Biological Process

GO:0097352 autophagosome maturation Biological Process

GO:0097576 vacuole fusion Biological Process

KEGG gene cross-reference

ath:AT4G36630

hsa:23339

mmu:269338

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.

Cytoplasm0.512

Rank 1 · LXL04_007160 · OH-1004

Nucleus0.233

Rank 2 · LXL04_007160 · OH-1004

Golgi apparatus0.230

Rank 3 · LXL04_007160 · OH-1004

Lysosome / Vacuole0.186

Rank 4 · LXL04_007160 · OH-1004

Cell membrane0.126

Rank 5 · LXL04_007160 · 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.

PF00780.29CNH61-278 aa

PF10366.16Vps39_1494-603 aa

PF10367.16zf-Vps39_C936-973 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007160	`PF00780.29`	CNH	61	278	3.6e-25	90.0
LXL04_007160	`PF10366.16`	Vps39_1	494	603	2e-23	83.4
LXL04_007160	`PF10367.16`	zf-Vps39_C	936	973	2e-16	60.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8L5Y0`	Arabidopsis thaliana	Vacuolar sorting protein 39	61.515%	Swiss-Prot	strong database homology

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