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Aliases for SLC52A1 Gene

Aliases for SLC52A1 Gene

  • Solute Carrier Family 52 Member 1 2 3 5
  • Solute Carrier Family 52 (Riboflavin Transporter), Member 1 2 3
  • Porcine Endogenous Retrovirus A Receptor 2 3 4
  • G Protein-Coupled Receptor 172B 2 3
  • Riboflavin Transporter 1 2 4
  • PERV-A Receptor 2 3 4
  • GPR172B 3 4
  • HRFT1 3 4
  • PAR2 3 4
  • RFT1 3 4
  • Solute Carrier Family 52, Riboflavin Transporter, Member 1 3
  • G-Protein Coupled Receptor GPCR42 3
  • Protein GPR172B 4
  • GPCR42 3
  • RBFVD 3
  • RFVT1 3

External Ids for SLC52A1 Gene

Previous HGNC Symbols for SLC52A1 Gene

  • GPR172B

Previous GeneCards Identifiers for SLC52A1 Gene

  • GC17M004936

Summaries for SLC52A1 Gene

Entrez Gene Summary for SLC52A1 Gene

  • Biological redox reactions require electron donors and acceptor. Vitamin B2 is the source for the flavin in flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) which are common redox reagents. This gene encodes a member of the riboflavin (vitamin B2) transporter family. Haploinsufficiency of this protein can cause maternal riboflavin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2013]

GeneCards Summary for SLC52A1 Gene

SLC52A1 (Solute Carrier Family 52 Member 1) is a Protein Coding gene. Diseases associated with SLC52A1 include Riboflavin Deficiency and Madras Motor Neuron Disease. Among its related pathways are Metabolism of water-soluble vitamins and cofactors and Metabolism. GO annotations related to this gene include virus receptor activity and riboflavin transporter activity. An important paralog of this gene is SLC52A2.

UniProtKB/Swiss-Prot for SLC52A1 Gene

  • Riboflavin transporter. Riboflavin transport is Na(+)-independent but moderately pH-sensitive. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin. Weakly inhibited by flavin adenine dinucleotide (FAD). In case of infection by retroviruses, acts as a cell receptor to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A).

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC52A1 Gene

Genomics for SLC52A1 Gene

Regulatory Elements for SLC52A1 Gene

Enhancers for SLC52A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G005044 1.1 ENCODE 7.4 +6.8 6756 2.3 HDGF PKNOX1 FOXA2 ARNT CREB3L1 ARID4B SIN3A DMAP1 FEZF1 ZNF2 SPAG7 CAMTA2 ENO3 NUP88 ENSG00000234203 INCA1 KIF1C PFN1 ZFP3 ZNF232
GH17G005035 0.4 Ensembl 13.6 +16.5 16509 0.6 MLLT1 SLC52A1 CAMTA2 LOC105371502
GH17G005047 1.2 FANTOM5 ENCODE 0.7 +4.4 4447 0.8 HDAC1 PKNOX1 SREBF2 ARID4B ZNF335 ZNF366 SCRT2 ZNF207 PCBP1 CREM CAMTA2 ENO3 SPAG7 ZFP3 PFN1 KIF1C INCA1 USP6 SLC52A1 LOC105371502
GH17G005048 0.8 Ensembl ENCODE 0.7 +2.2 2165 2.4 KLF1 GLIS1 ZMYM3 KLF17 ZNF600 ENO3 SPAG7 CHRNE CAMTA2 ZFP3 PFN1 INCA1 KIF1C LOC101928000 ZNF232
GH17G005041 1.3 Ensembl ENCODE 0.4 +9.5 9540 1.4 PKNOX1 AGO1 ARID4B SIN3A YY1 TCF12 GLIS2 KLF7 FOS DEK SPAG7 ENO3 ENSG00000234203 KIF1C INCA1 CAMTA2 ZFP3 PFN1 SLC52A1 LOC105371502
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC52A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SLC52A1 Gene

Chromosome:
17
Start:
5,032,600 bp from pter
End:
5,052,009 bp from pter
Size:
19,410 bases
Orientation:
Minus strand

Genomic View for SLC52A1 Gene

Genes around SLC52A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC52A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC52A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC52A1 Gene

Proteins for SLC52A1 Gene

  • Protein details for SLC52A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NWF4-S52A1_HUMAN
    Recommended name:
    Solute carrier family 52, riboflavin transporter, member 1
    Protein Accession:
    Q9NWF4
    Secondary Accessions:
    • B5MEV1
    • B5MEV2
    • Q6P9E0
    • Q86UT0

    Protein attributes for SLC52A1 Gene

    Size:
    448 amino acids
    Molecular mass:
    46317 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SLC52A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC52A1 Gene

Post-translational modifications for SLC52A1 Gene

  • Glycosylation at Asn178
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC52A1 Gene

No data available for DME Specific Peptides for SLC52A1 Gene

Domains & Families for SLC52A1 Gene

Gene Families for SLC52A1 Gene

Protein Domains for SLC52A1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC52A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NWF4

UniProtKB/Swiss-Prot:

S52A1_HUMAN :
  • Belongs to the riboflavin transporter family.
Family:
  • Belongs to the riboflavin transporter family.
genes like me logo Genes that share domains with SLC52A1: view

Function for SLC52A1 Gene

Molecular function for SLC52A1 Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1.38 uM for riboflavin {ECO:0000269 PubMed:20463145};
UniProtKB/Swiss-Prot Function:
Riboflavin transporter. Riboflavin transport is Na(+)-independent but moderately pH-sensitive. Activity is strongly inhibited by riboflavin analogs, such as lumiflavin. Weakly inhibited by flavin adenine dinucleotide (FAD). In case of infection by retroviruses, acts as a cell receptor to retroviral envelopes similar to the porcine endogenous retrovirus (PERV-A).

Gene Ontology (GO) - Molecular Function for SLC52A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IEA --
GO:0032217 riboflavin transporter activity TAS --
genes like me logo Genes that share ontologies with SLC52A1: view
genes like me logo Genes that share phenotypes with SLC52A1: view

Human Phenotype Ontology for SLC52A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for SLC52A1 Gene

miRTarBase miRNAs that target SLC52A1

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SLC52A1 Gene

Localization for SLC52A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC52A1 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC52A1 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for SLC52A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 20463145
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SLC52A1: view

Pathways & Interactions for SLC52A1 Gene

genes like me logo Genes that share pathways with SLC52A1: view

Interacting Proteins for SLC52A1 Gene

Selected Interacting proteins: Q9NWF4-S52A1_HUMAN for SLC52A1 Gene via IID

Symbol External ID(s) Details
PLA2G4A

Gene Ontology (GO) - Biological Process for SLC52A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006771 riboflavin metabolic process TAS --
GO:0006810 transport IEA --
GO:0032218 riboflavin transport IDA 20463145
GO:0046718 viral entry into host cell IEA --
genes like me logo Genes that share ontologies with SLC52A1: view

No data available for SIGNOR curated interactions for SLC52A1 Gene

Drugs & Compounds for SLC52A1 Gene

(1) Drugs for SLC52A1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Riboflavin Approved, Vet_approved Nutra 174
genes like me logo Genes that share compounds with SLC52A1: view

Transcripts for SLC52A1 Gene

Unigene Clusters for SLC52A1 Gene

Solute carrier family 52, riboflavin transporter, member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC52A1 Gene

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

Relevant External Links for SLC52A1 Gene

GeneLoc Exon Structure for
SLC52A1
ECgene alternative splicing isoforms for
SLC52A1

Expression for SLC52A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC52A1 Gene

mRNA differential expression in normal tissues according to GTEx for SLC52A1 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x16.3), Skin - Sun Exposed (Lower leg) (x9.2), and Skin - Not Sun Exposed (Suprapubic) (x5.1).

Protein differential expression in normal tissues from HIPED for SLC52A1 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC52A1 Gene



Protein tissue co-expression partners for SLC52A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLC52A1 Gene:

SLC52A1

SOURCE GeneReport for Unigene cluster for SLC52A1 Gene:

Hs.632247

mRNA Expression by UniProt/SwissProt for SLC52A1 Gene:

Q9NWF4-S52A1_HUMAN
Tissue specificity: Widely expressed. Highly expressed in the testis, placenta and small intestine. Expressed at lower level in other tissues.

Evidence on tissue expression from TISSUES for SLC52A1 Gene

  • Intestine(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC52A1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • urinary
Organs:
Head and neck:
  • brain
  • ear
  • face
  • head
  • larynx
  • lip
  • mouth
  • neck
  • pharynx
  • tongue
Thorax:
  • heart
Abdomen:
  • adrenal gland
  • kidney
General:
  • blood
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • sweat gland
genes like me logo Genes that share expression patterns with SLC52A1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for SLC52A1 Gene

Orthologs for SLC52A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC52A1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPR172B 34
  • 99.48 (n)
SLC52A1 35
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia GPR172B 35
  • 84 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Slc52a2 35
  • 80 (a)
OneToMany
dog
(Canis familiaris)
Mammalia -- 35
  • 69 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 61 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 49 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 54 (a)
OneToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.6678 34
zebrafish
(Danio rerio)
Actinopterygii zgc:91890 35
  • 39 (a)
ManyToMany
wufc11c06 34
fruit fly
(Drosophila melanogaster)
Insecta CG11576 35
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rft-1 35
  • 32 (a)
ManyToMany
rft-2 35
  • 28 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1348 35
  • 31 (a)
OneToMany
Species where no ortholog for SLC52A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SLC52A1 Gene

ENSEMBL:
Gene Tree for SLC52A1 (if available)
TreeFam:
Gene Tree for SLC52A1 (if available)

Paralogs for SLC52A1 Gene

Paralogs for SLC52A1 Gene

(3) SIMAP similar genes for SLC52A1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SLC52A1: view

Variants for SLC52A1 Gene

Sequence variations from dbSNP and Humsavar for SLC52A1 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000302751 -- 5,032,880(+) CCTGG(C/G)CCACA intron-variant, upstream-variant-2KB, utr-variant-3-prime
rs1000690866 -- 5,032,559(+) GAAAG(A/G)CACTA intron-variant, downstream-variant-500B, upstream-variant-2KB
rs1001330085 -- 5,034,227(+) TACAC(A/T)CAGCA intron-variant, reference, missense
rs1002265136 -- 5,035,429(+) TGCGA(C/G)ACTCA intron-variant, utr-variant-5-prime
rs1003266819 -- 5,037,020(+) AATCA(A/G)TATCT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SLC52A1 Gene

Variant ID Type Subtype PubMed ID
dgv5431n54 CNV loss 21841781
nsv574273 CNV gain 21841781
nsv833350 CNV loss 17160897

Variation tolerance for SLC52A1 Gene

Residual Variation Intolerance Score: 82.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.83; 91.73% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC52A1 Gene

Human Gene Mutation Database (HGMD)
SLC52A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC52A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC52A1 Gene

Disorders for SLC52A1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SLC52A1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
riboflavin deficiency
  • rbfvd
madras motor neuron disease
  • mmnd
brown-vialetto-van laere syndrome
  • bvvls
glutaric acidemia iic
  • glutaric acidemia iia
ariboflavinosis
  • riboflavin deficiency
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

S52A1_HUMAN
  • Riboflavin deficiency (RBFVD) [MIM:615026]: A disorder caused by a primary defect in riboflavin metabolism, or by dietary riboflavin deficiency. Riboflavin deficiency during pregnancy results in hypoglycemia, metabolic acidosis, dicarboxylic aciduria and elevated plasma acylcarnitine levels in the newborn. Treatment with oral riboflavin results in complete resolution of the clinical and biochemical findings. {ECO:0000269 PubMed:21089064}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SLC52A1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC52A1
genes like me logo Genes that share disorders with SLC52A1: view

No data available for Genatlas for SLC52A1 Gene

Publications for SLC52A1 Gene

  1. Identification of receptors for pig endogenous retrovirus. (PMID: 12740431) Ericsson T.A. … Patience C. (Proc. Natl. Acad. Sci. U.S.A. 2003) 2 3 4 22 64
  2. Identification and functional characterization of a novel human and rat riboflavin transporter, RFT1. (PMID: 18632736) Yonezawa A. … Inui K. (Am. J. Physiol. 2008) 2 3 4 64
  3. Maternal riboflavin deficiency, resulting in transient neonatal-onset glutaric aciduria Type 2, is caused by a microdeletion in the riboflavin transporter gene GPR172B. (PMID: 21089064) Ho G. … Christodoulou J. (Hum. Mutat. 2011) 3 4 64
  4. 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 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for SLC52A1 Gene

Sources for SLC52A1 Gene

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