LXL04_003792 | RubberDandelionOmics

Gene overview

LXL04_003792

Reference: OH-1004 Chr: Chr01 Coordinates: 102506020-102511824 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1210 bp · LXL04_003792|LXL04_003792|OH1004|cDNA

ATGGCGCTTCCCTCTCCATATTTACCCTCCCGGGCTTTCGttgccaccaccaccaccgtaCCAAGATTCATTGCTATTGAGGTTGTCTCGGAAACAAAATCGAAATCAAATTCGGAAACAAAATCCCCTCGATTCATCTGCAATTTCACATTATGGAATGTTCACTTTACAGAAGCATCTTTAGCTGGTGTGGCTCCACTGATGCAAAAAGTACACAGTGAGATATGCGTTGTGGATACTGAAATTCTAGCTGCTGTTCG...

CDS

Download CDS FASTA

1176 bp · LXL04_003792|LXL04_003792|OH1004|CDS

ATGGCGCTTCCCTCTCCATATTTACCCTCCCGGGCTTTCGTTGCCACCACCACCACCGTACCAAGATTCATTGCTATTGAGGTTGTCTCGGAAACAAAATCGAAATCAAATTCGGAAACAAAATCCCCTCGATTCATCTGCAATTTCACATTATGGAATGTTCACTTTACAGAAGCATCTTTAGCTGGTGTGGCTCCACTGATGCAAAAAGTACACAGTGAGATATGCGTTGTGGATACTGAAATTCTAGCTGCTGTTCG...

Protein

Download Protein FASTA

391 aa · LXL04_003792|LXL04_003792|OH1004|PROTEIN

MALPSPYLPSRAFVATTTTVPRFIAIEVVSETKSKSNSETKSPRFICNFTLWNVHFTEASLAGVAPLMQKVHSEICVVDTEILAAVRQQSNSGTKAKEDLAAATRAVEELMYKVREIKTKAEQSETMVQEICRDIKKLDFAKEHITTTITALHRLTMLGTGKETEDSSLLQHLTDACLVVDALELSVREELVKNFCDRELISYQQIFEGAELAKLDKTERRYAWVKRRLRTNEEIWKIFPSSWNVDYLPCIQFCKLTRSQ...

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_003792`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_003792

Location Chr01:102506020-102511824 (+)

Description Similar to VPS53: Vacuolar protein sorting-associated protein 53 A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g50500`	Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN).	Mutation in a homolog of yeast Vps53p accounts for the heat and osmotic hypersensitive phenotypes in Arabidopsis hit1-1 mutant.2006 · DOI: 10.1007/s00425-005-0216-6 The POK/AtVPS52 protein localizes to several distinct post-Golgi compartments in sporophytic and gametophytic cells.2008 · DOI: 10.1093/jxb/ern162 Involvement of the Arabidopsis HIT1/AtVPS53 tethering protein homologue in the acclimation of the plasma membrane to heat stress.2011 · DOI: 10.1093/jxb/err060 The Arabidopsis hit1-1 mutant has a plasma membrane profile distinct from that of wild-type plants at optimal growing temperature.2011 · DOI: 10.4161/psb.6.8.15842
`At1g50970`	Involved in retrograde transport from early and late endosomes to late Golgi, leading to the membrane fusion between late Golgi and endosomal vesicles.	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_003792 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006622 protein targeting to lysosome Biological Process

GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0007009 plasma membrane organization Biological Process

GO:0007041 lysosomal transport Biological Process

GO:0009408 response to heat Biological Process

GO:0010286 heat acclimation Biological Process

GO:0015031 protein transport Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0042147 retrograde transport, endosome to Golgi Biological Process

GO:0090119 vesicle-mediated cholesterol transport Biological Process

GO:0000139 Golgi membrane Cellular Component

KEGG gene cross-reference

ath:AT1G50500

ath:AT1G50970

gga:417622

hsa:55275

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.

Cytoplasm0.410

Rank 1 · LXL04_003792 · OH-1004

Nucleus0.289

Rank 2 · LXL04_003792 · OH-1004

Cell membrane0.168

Rank 3 · LXL04_003792 · OH-1004

Endoplasmic reticulum0.152

Rank 4 · LXL04_003792 · OH-1004

Golgi apparatus0.129

Rank 5 · LXL04_003792 · 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.

PF04100.19Vps53_N53-163 aa

PF04100.19Vps53_N159-302 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003792	`PF04100.19`	Vps53_N	53	163	2.4e-81	274.4
LXL04_003792	`PF04100.19`	Vps53_N	159	302	2.4e-81	274.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q0WQF4`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 53 A	53.094%	Swiss-Prot	moderate database homology
`F4I7Y2`	Arabidopsis thaliana	Vacuolar protein sorting-associated protein 53 B	39.414%	Swiss-Prot	moderate database homology

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