LXL04_008514 | RubberDandelionOmics

Gene overview

LXL04_008514

Reference: OH-1004 Chr: Chr02 Coordinates: 101629636-101630453 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

489 bp · LXL04_008514|LXL04_008514|OH1004|cDNA

ATGTTTGCTGGTTTAAGATCTTCCATATGTTGTTTGTTGGCATATTCAGATATGAGAGCCTTCGATGAGTTAAGAAAGCTGGAAATGTTCTTCAAGGAGGAAGACAGACATGGCTGTTCAGTAGTAGACCTGTATGAACTTGTCCAACATGCTGGAAACATTTTACCTAGACTGTATCTTCTATGTACAGTAGGGTCTGTTTACATAAAATCAAAAGAAGCTCCTGCTAATAGAGATGAGGATACTGTCATGGATGCTGT...

CDS

Download CDS FASTA

489 bp · LXL04_008514|LXL04_008514|OH1004|CDS

ATGTTTGCTGGTTTAAGATCTTCCATATGTTGTTTGTTGGCATATTCAGATATGAGAGCCTTCGATGAGTTAAGAAAGCTGGAAATGTTCTTCAAGGAGGAAGACAGACATGGCTGTTCAGTAGTAGACCTGTATGAACTTGTCCAACATGCTGGAAACATTTTACCTAGACTGTATCTTCTATGTACAGTAGGGTCTGTTTACATAAAATCAAAAGAAGCTCCTGCTAATAGAGATGAGGATACTGTCATGGATGCTGT...

Protein

Download Protein FASTA

162 aa · LXL04_008514|LXL04_008514|OH1004|PROTEIN

MFAGLRSSICCLLAYSDMRAFDELRKLEMFFKEEDRHGCSVVDLYELVQHAGNILPRLYLLCTVGSVYIKSKEAPANRDEDTVMDAVEFVLQNFSEMNKLWVWMEVQGTARVRDKMEKERNELCDLFIFDCRLLLQKIYIAKRKLERAISSLPKKHIDYILE

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_008514`
TK1151 ID	TkA03G363710
OH-1004 ID	LXL04_008514
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	99.300
Protein coverage (%)	TK1151 100.000 / OH-1004 82.716 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

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_008514

Location Chr02:101629636-101630453 (-)

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_008514 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0031647 regulation of protein stability Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0036010 protein localization to endosome Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0045053 protein retention in Golgi apparatus Biological Process

GO:0045056 transcytosis Biological Process

GO:0045732 positive regulation of protein catabolic process Biological Process

GO:0090141 positive regulation of mitochondrial fission Biological Process

GO:0099074 mitochondrion to lysosome vesicle-mediated transport Biological Process

GO:0099639 neurotransmitter receptor transport, endosome to plasma membrane Biological Process

KEGG gene cross-reference

ath:AT1G75850

ath:AT2G17790

ath:AT3G51310

bta:521864

ddi:DDB_G0293218

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.

Cytoplasm0.481

Rank 1 · LXL04_008514 · OH-1004

Nucleus0.385

Rank 2 · LXL04_008514 · OH-1004

Mitochondrion0.111

Rank 3 · LXL04_008514 · OH-1004

Cell membrane0.109

Rank 4 · LXL04_008514 · OH-1004

Golgi apparatus0.069

Rank 5 · LXL04_008514 · 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.

PF03635.24Vps3518-77 aa

PF03635.24Vps3579-126 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008514	`PF03635.24`	Vps35	18	77	5e-40	138.4
LXL04_008514	`PF03635.24`	Vps35	79	126	5e-40	138.4

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	51.111%	Swiss-Prot	strong database homology
`Q7X659`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35A	52.597%	Swiss-Prot	moderate database homology
`A8R7K9`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35C	46.111%	Swiss-Prot	moderate database homology

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