LXL04_015068 | RubberDandelionOmics

Gene overview

LXL04_015068

Reference: OH-1004 Chr: Chr03 Coordinates: 62940042-62940857 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

489 bp · LXL04_015068|LXL04_015068|OH1004|cDNA

ATGTTTTCTGGTTTAAGATCTTCCATATGTTGTTTGTTGGCATATTCAGATATGAGAGCCTTCGATGAGTTAAGAAAGCTGGAAATGTTCTTCAAGGAGGAAGACAGACATGGCTGTTCAGTAGTAGACCTGTATGAACTTGTCCAACATGCTGGAAACATTTTACCTAGACTGTATCTTCTATGTACAGTAGGGTCTGTTTACATAAAATCAAAAGAAGCTCCTGCTAATAGAGATGAGGATACTGTCATGGATGCTGT...

CDS

Download CDS FASTA

477 bp · LXL04_015068|LXL04_015068|OH1004|CDS

ATGTTTTCTGGTTTAAGATCTTCCATATGTTGTTTGTTGGCATATTCAGATATGAGAGCCTTCGATGAGTTAAGAAAGCTGGAAATGTTCTTCAAGGAGGAAGACAGACATGGCTGTTCAGTAGTAGACCTGTATGAACTTGTCCAACATGCTGGAAACATTTTACCTAGACTGTATCTTCTATGTACAGTAGGGTCTGTTTACATAAAATCAAAAGAAGCTCCTGCTAATAGAGATGAGGATACTGTCATGGATGCTGT...

Protein

Download Protein FASTA

158 aa · LXL04_015068|LXL04_015068|OH1004|PROTEIN

MFSGLRSSICCLLAYSDMRAFDELRKLEMFFKEEDRHGCSVVDLYELVQHAGNILPRLYLLCTVGSVYIKSKEAPANRDEDTVMDAVEFVLQNFSEMNKLWVWIKVQGPARVRDKMEKERNELRDLFIFDCRLLLQKIYIAKRKLERAISSLPKKHID

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_015068`
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_015068

Location Chr03:62940042-62940857 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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_015068 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006886 intracellular protein transport Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0045053 protein retention in Golgi apparatus Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005768 endosome Cellular Component

GO:0005770 late endosome Cellular Component

GO:0005771 multivesicular body Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005829 cytosol Cellular Component

GO:0010008 endosome membrane Cellular Component

GO:0016020 membrane Cellular Component

KEGG gene cross-reference

ath:AT1G75850

ath:AT2G17790

ath:AT3G51310

ddi:DDB_G0293218

mgr:MGG_05089

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.

Cytoplasm0.485

Rank 1 · LXL04_015068 · OH-1004

Nucleus0.406

Rank 2 · LXL04_015068 · OH-1004

Cell membrane0.122

Rank 3 · LXL04_015068 · OH-1004

Mitochondrion0.087

Rank 4 · LXL04_015068 · OH-1004

Golgi apparatus0.067

Rank 5 · LXL04_015068 · 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_015068	`PF03635.24`	Vps35	18	77	5.9e-40	138.2
LXL04_015068	`PF03635.24`	Vps35	79	126	5.9e-40	138.2

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	53.333%	Swiss-Prot	strong database homology
`Q7X659`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35A	53.247%	Swiss-Prot	moderate database homology
`A8R7K9`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 35C	47.222%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card