LXL04_018452 | RubberDandelionOmics

Gene overview

LXL04_018452

Reference: OH-1004 Chr: Chr04 Coordinates: 13161015-13163048 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

621 bp · LXL04_018452|LXL04_018452|OH1004|cDNA

atGTTCACTGTTGAGAAGCATTGGGGAAGTAATTTACCTGGTTGGGGTTTATTTGAACTAATAAAAGGGCTCATTAAAGATTTGGATGGTGATGACAATTATGAGATGGGTGAGGACGACTTTAAGGAAGCGCAGAATTCTATTGCACGTTTAATCCAAATGTTGTATAATGATGATCCACGAGAGATGTTAAAGATTATACATATGGTGAAGAAGCATATTATGATTGGAGGACCCAAGCGGCTTCCCTTCACAATCCC...

CDS

Download CDS FASTA

621 bp · LXL04_018452|LXL04_018452|OH1004|CDS

ATGTTCACTGTTGAGAAGCATTGGGGAAGTAATTTACCTGGTTGGGGTTTATTTGAACTAATAAAAGGGCTCATTAAAGATTTGGATGGTGATGACAATTATGAGATGGGTGAGGACGACTTTAAGGAAGCGCAGAATTCTATTGCACGTTTAATCCAAATGTTGTATAATGATGATCCACGAGAGATGTTAAAGATTATACATATGGTGAAGAAGCATATTATGATTGGAGGACCCAAGCGGCTTCCCTTCACAATCCC...

Protein

Download Protein FASTA

206 aa · LXL04_018452|LXL04_018452|OH1004|PROTEIN

MFTVEKHWGSNLPGWGLFELIKGLIKDLDGDDNYEMGEDDFKEAQNSIARLIQMLYNDDPREMLKIIHMVKKHIMIGGPKRLPFTIPSLIYNALKTIEVLSMVPAPDLALRLYLECAEAANDCDLEPLGYVVNETFRILIFLRVNEEVTFFFFNVVQLGMSLSTQEKLMVPGVTGDSKDKEAKVVDNLILRCLYSTWVCHFQDISI

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_018452`
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_018452

Location Chr04:13161015-13163048 (+)

Description Similar to VPS35B: Vacuolar protein sorting-associated protein 35B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At3g51310`	Plays a role in vesicular protein sorting.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018452 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006624 vacuolar protein processing Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0007040 lysosome organization Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0010821 regulation of mitochondrion organization Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0031648 protein destabilization Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0032463 negative regulation of protein homooligomerization Biological Process

GO:0036010 protein localization to endosome Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

KEGG gene cross-reference

ath:AT1G75850

ath:AT2G17790

ath:AT3G51310

ddi:DDB_G0293218

mmu:65114

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.

Nucleus0.411

Rank 1 · LXL04_018452 · OH-1004

Cytoplasm0.404

Rank 2 · LXL04_018452 · OH-1004

Mitochondrion0.117

Rank 3 · LXL04_018452 · OH-1004

Cell membrane0.091

Rank 4 · LXL04_018452 · OH-1004

Endoplasmic reticulum0.087

Rank 5 · LXL04_018452 · 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.

PF03635.24Vps3517-100 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_018452	`PF03635.24`	Vps35	17	100	7e-15	55.3

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
`F4I0P8`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35B	45.699%	Swiss-Prot	moderate database homology
`Q7X659`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35A	43.617%	Swiss-Prot	moderate database homology
`A8R7K9`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35C	44.149%	Swiss-Prot	moderate database homology

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