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Aliases for SLC52A3 Gene

Aliases for SLC52A3 Gene

  • Solute Carrier Family 52 (Riboflavin Transporter), Member 3 2 3
  • C20orf54 3 4 6
  • RFT2 3 4 6
  • Riboflavin Transporter 2 3 4
  • BVVLS1 3 6
  • RFVT3 3 4
  • HRFT2 3 4
  • Solute Carrier Family 52, Riboflavin Transporter, Member 3 3
  • Chromosome 20 Open Reading Frame 54 2
  • Solute Carrier Family 52 Member 3 3
  • Hypothetical Protein LOC113278 2
  • BA371L19.1 3
  • BVVLS 3

External Ids for SLC52A3 Gene

Previous HGNC Symbols for SLC52A3 Gene

  • C20orf54

Summaries for SLC52A3 Gene

Entrez Gene Summary for SLC52A3 Gene

  • This gene encodes a riboflavin transporter protein that is strongly expressed in the intestine and likely plays a role in intestinal absorption of riboflavin. The protein is predicted to have eleven transmembrane domains and a cell surface localization signal in the C-terminus. Mutations at this locus have been associated with Brown-Vialetto-Van Laere syndrome and Fazio-Londe disease. [provided by RefSeq, Mar 2012]

GeneCards Summary for SLC52A3 Gene

SLC52A3 (Solute Carrier Family 52 (Riboflavin Transporter), Member 3) is a Protein Coding gene. Diseases associated with SLC52A3 include brown-vialetto-van laere syndrome 1 and fazio-londe disease. Among its related pathways are Disease and Metabolism. GO annotations related to this gene include riboflavin transporter activity. An important paralog of this gene is SLC52A2.

UniProtKB/Swiss-Prot for SLC52A3 Gene

  • Transporter for riboflavin, which must be obtained as a nutrient via intestinal absorption. Riboflavin transport is Na(+)-independent at low pH but significantly reduced by Na(+) depletion under neutral pH conditions. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), by methylene blue, and to a lesser extent by amiloride.

Gene Wiki entry for SLC52A3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC52A3 Gene

Genomics for SLC52A3 Gene

Genomic Location for SLC52A3 Gene

Start:
760,080 bp from pter
End:
776,015 bp from pter
Size:
15,936 bases
Orientation:
Minus strand

Genomic View for SLC52A3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SLC52A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC52A3 Gene

No data available for Regulatory Elements for SLC52A3 Gene

Proteins for SLC52A3 Gene

  • Protein details for SLC52A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQ40-S52A3_HUMAN
    Recommended name:
    Solute carrier family 52, riboflavin transporter, member 3
    Protein Accession:
    Q9NQ40
    Secondary Accessions:
    • A8K6P1
    • Q5W1A0
    • Q5W1A1
    • Q8NCL7
    • Q96GD5

    Protein attributes for SLC52A3 Gene

    Size:
    469 amino acids
    Molecular mass:
    50805 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC52A3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC52A3 Gene

Proteomics data for SLC52A3 Gene at MOPED

Post-translational modifications for SLC52A3 Gene

  • Glycosylation at Asn94 and Asn168
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC52A3 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for SLC52A3 Gene

Domains for SLC52A3 Gene

Gene Families for SLC52A3 Gene

HGNC:
  • SLC :Solute carriers

Protein Domains for SLC52A3 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q9NQ40

UniProtKB/Swiss-Prot:

S52A3_HUMAN :
  • Q9NQ40
Family:
  • Belongs to the riboflavin transporter family.
genes like me logo Genes that share domains with SLC52A3: view

No data available for Suggested Antigen Peptide Sequences for SLC52A3 Gene

Function for SLC52A3 Gene

Molecular function for SLC52A3 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.98 uM for riboflavin {ECO:0000269 PubMed:20463145};
UniProtKB/Swiss-Prot Function:
Transporter for riboflavin, which must be obtained as a nutrient via intestinal absorption. Riboflavin transport is Na(+)-independent at low pH but significantly reduced by Na(+) depletion under neutral pH conditions. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), by methylene blue, and to a lesser extent by amiloride.

Gene Ontology (GO) - Molecular Function for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
GO:0032217 riboflavin transporter activity IDA 20463145
genes like me logo Genes that share ontologies with SLC52A3: view

Phenotypes for SLC52A3 Gene

MGI mutant phenotypes for SLC52A3:
inferred from 1 alleles
GenomeRNAi human phenotypes for SLC52A3:
genes like me logo Genes that share phenotypes with SLC52A3: view

Animal Model Products

CRISPR Products

miRNA for SLC52A3 Gene

miRTarBase miRNAs that target SLC52A3

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SLC52A3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for SLC52A3 Gene

Localization for SLC52A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC52A3 Gene

Apical cell membrane; Multi-pass membrane protein.

Gene Ontology (GO) - Cellular Components for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 20463145
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with SLC52A3: view

No data available for Subcellular locations from COMPARTMENTS for SLC52A3 Gene

Pathways for SLC52A3 Gene

SuperPathways for SLC52A3 Gene

genes like me logo Genes that share pathways with SLC52A3: view

Interacting Proteins for SLC52A3 Gene

Selected Interacting proteins: Q9NQ40-S52A3_HUMAN for SLC52A3 Gene via I2D

Symbol External ID(s) Details
HOMER2
TRIP13

Gene Ontology (GO) - Biological Process for SLC52A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006766 vitamin metabolic process TAS --
GO:0006767 water-soluble vitamin metabolic process TAS --
GO:0006771 riboflavin metabolic process TAS --
GO:0007605 sensory perception of sound IMP 20206331
GO:0032218 riboflavin transport IDA 20463145
genes like me logo Genes that share ontologies with SLC52A3: view

Transcripts for SLC52A3 Gene

Unigene Clusters for SLC52A3 Gene

Solute carrier family 52, riboflavin transporter, member 3:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SLC52A3

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC52A3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6
SP1: -
SP2: -
SP3:

Relevant External Links for SLC52A3 Gene

GeneLoc Exon Structure for
SLC52A3
ECgene alternative splicing isoforms for
SLC52A3

Expression for SLC52A3 Gene

mRNA expression in normal human tissues for SLC52A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC52A3 Gene

This gene is overexpressed in Testis (12.0).

Protein differential expression in normal tissues for SLC52A3 Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for SLC52A3 Gene

SOURCE GeneReport for Unigene cluster for SLC52A3 Gene Hs.283865

mRNA Expression by UniProt/SwissProt for SLC52A3 Gene

Q9NQ40-S52A3_HUMAN
Tissue specificity: Predominantly expressed in testis. Highly expressed in small intestine and prostate.
genes like me logo Genes that share expressions with SLC52A3: view

Expression partners for SLC52A3 Gene

In Situ Assay Products

Orthologs for SLC52A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC52A3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SLC52A3 35
  • 83.51 (n)
  • 79.44 (a)
SLC52A3 36
  • 79 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SLC52A3 35
  • 85.5 (n)
  • 81.66 (a)
SLC52A3 36
  • 81 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Slc52a3 35
  • 77.58 (n)
  • 75.76 (a)
Slc52a3 16
Slc52a3 36
  • 75 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SLC52A3 35
  • 98.79 (n)
  • 98.51 (a)
SLC52A3 36
  • 96 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Slc52a3 35
  • 77.63 (n)
  • 75.97 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 64 (a)
OneToMany
-- 36
  • 59 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia SLC52A3 36
  • 62 (a)
OneToOne
chicken
(Gallus gallus)
Aves C20H20ORF54 35
  • 67.27 (n)
  • 60.63 (a)
SLC52A3 36
  • 58 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC52A3 36
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486825 35
  • 60.8 (n)
  • 57.56 (a)
zebrafish
(Danio rerio)
Actinopterygii slc52a3 35
  • 60.36 (n)
  • 58.54 (a)
slc52a3 36
  • 56 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2663 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000181 35
  • 52.77 (n)
  • 39.28 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG11576 35
  • 53.22 (n)
  • 41.81 (a)
CG11576 36
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y47D7A.16 35
  • 41.19 (n)
  • 36.3 (a)
rft-1 36
  • 35 (a)
ManyToMany
rft-2 36
  • 30 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1348 36
  • 38 (a)
OneToMany
Species with no ortholog for SLC52A3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC52A3 Gene

ENSEMBL:
Gene Tree for SLC52A3 (if available)
TreeFam:
Gene Tree for SLC52A3 (if available)

Paralogs for SLC52A3 Gene

Paralogs for SLC52A3 Gene

Selected SIMAP similar genes for SLC52A3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SLC52A3: view

Variants for SLC52A3 Gene

Sequence variations from dbSNP and Humsavar for SLC52A3 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type MAF
rs497494 -- 774,528(+) tgaga(C/T)aaaga intron-variant
rs527448 -- 775,463(+) TTGTA(C/T)AGATG intron-variant
rs527655 -- 775,534(+) CTCAG(C/T)CTCCA intron-variant
rs527659 -- 775,539(+) TCTCC(A/G)GAAGT intron-variant
rs539934 -- 771,724(+) ACAGA(A/G)CCCTC intron-variant

Relevant External Links for SLC52A3 Gene

HapMap Linkage Disequilibrium report
SLC52A3
Human Gene Mutation Database (HGMD)
SLC52A3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SLC52A3 Gene

Disorders for SLC52A3 Gene

(2) OMIM Diseases for SLC52A3 Gene (613350)

UniProtKB/Swiss-Prot

S52A3_HUMAN
  • Brown-Vialetto-Van Laere syndrome 1 (BVVLS1) [MIM:211530]: A rare neurologic disorder characterized by sensorineural hearing loss and a variety of cranial nerve palsies, which develop over a relatively short period of time in a previously healthy individual. Sensorineural hearing loss may precede the neurological signs. The course is invariably progressive, but the rate of decline is variable within and between families. With disease evolution, long tract signs, lower motor neuron signs, cerebellar ataxia and lower cranial nerve (III-VI) palsies develop, giving rise to a complex picture resembling amyotrophic lateral sclerosis. Diaphragmatic weakness and respiratory compromise are some of the most distressing features, leading to recurrent chest infections and respiratory failure, which are often the cause of patients demise. {ECO:0000269 PubMed:20206331}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Fazio-Londe disease (FALOND) [MIM:211500]: A rare neurological disease characterized by progressive weakness of the muscles innervated by cranial nerves of the lower brain stem. It may present in childhood with severe neurological deterioration with hypotonia, respiratory insufficiency leading to premature death, or later in life with bulbar weakness which progresses to involve motor neurons throughout the neuroaxis. Clinical manifestations include dysarthria, dysphagia, facial weakness, tongue weakness, and fasciculations of the tongue and facial muscles. {ECO:0000269 PubMed:21110228}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with SLC52A3: view

No data available for University of Copenhagen DISEASES , Novoseek inferred disease relationships , Genatlas and External Links for SLC52A3 Gene

Publications for SLC52A3 Gene

  1. Identification and functional characterization of rat riboflavin transporter 2. (PMID: 19122205) Yamamoto S. … Yuasa H. (J. Biochem. 2009) 2 3 4
  2. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 2 3 4
  3. Functional involvement of RFVT3/SLC52A3 in intestinal riboflavin absorption. (PMID: 24264046) Yoshimatsu H. … Matsubara K. (Am. J. Physiol. Gastrointest. Liver Physiol. 2014) 3 4
  4. Brown-Vialetto-Van Laere syndrome, a ponto-bulbar palsy with deafness, is caused by mutations in c20orf54. (PMID: 20206331) Green P. … Josifova D.J. (Am. J. Hum. Genet. 2010) 3 4
  5. Identification and comparative functional characterization of a new human riboflavin transporter hRFT3 expressed in the brain. (PMID: 20463145) Yao Y. … Inui K. (J. Nutr. 2010) 3 4

Products for SLC52A3 Gene

Sources for SLC52A3 Gene

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