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SLC52A1 Gene

protein-coding   GIFtS: 43
GCID: GC17M004936

Solute Carrier Family 52 (Riboflavin Transporter), Member...

(Previous name: G protein-coupled receptor 172B)
(Previous symbol: GPR172B)
  See SLC52A1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Solute Carrier Family 52 (Riboflavin Transporter), Member 11 2     PERV-A Receptor 22 3
GPR172B1 2 3 5     GPCR422 5
PAR22 3 5     RBFVD2 5
G Protein-Coupled Receptor 172B1 2     RFVT12
Riboflavin Transporter 11 3     G-Protein Coupled Receptor GPCR422
Porcine Endogenous Retrovirus A Receptor 22 3     Solute Carrier Family 52, Riboflavin Transporter, Member 12
RFT12 3     Protein GPR172B3
hRFT12 3     FLJ100605

External Ids:    HGNC: 302251   Entrez Gene: 550652   Ensembl: ENSG000001325177   OMIM: 6078835   UniProtKB: Q9NWF43   

Export aliases for SLC52A1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 (riboflavin transporter), member 1) is a protein-coding gene. Diseases associated with SLC52A1 include riboflavin deficiency, and pituitary hormone deficiency, combined, 6. 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: S52A1_HUMAN, Q9NWF4
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)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000017.10  NT_010718.17  NC_018928.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SLC52A1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC52A1 promoter sequence
   Search Chromatin IP Primers for SLC52A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC52A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17p13.2   Ensembl cytogenetic band:  17p13.2   HGNC cytogenetic band: 17p13.3

SLC52A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC52A1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M004936:  view genomic region     (about GC identifiers)

Start:
4,935,895 bp from pter      End:
4,955,304 bp from pter
Size:
19,410 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: S52A1_HUMAN, Q9NWF4 (See protein sequence)
Recommended Name: Solute carrier family 52, riboflavin transporter, member 1  
Size: 448 amino acids; 46317 Da
Secondary accessions: B5MEV1 B5MEV2 Q6P9E0 Q86UT0
Alternative splicing: 2 isoforms:  Q9NWF4-1   Q9NWF4-2   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for SLC52A1: NX_Q9NWF4

Explore proteomics data for SLC52A1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn178
  • Modification sites at PhosphoSitePlus

  • See SLC52A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001098047.1  NP_060456.3  

    ENSEMBL proteins: 
     ENSP00000254853   ENSP00000443026   ENSP00000399979  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SLC: Solute carriers

    1 InterPro protein domain:
     IPR009357 Endogenous_retrovirus_rcpt

    Graphical View of Domain Structure for InterPro Entry Q9NWF4

    ProtoNet protein and cluster: Q9NWF4

    UniProtKB/Swiss-Prot: S52A1_HUMAN, Q9NWF4
    Similarity: Belongs to the riboflavin transporter family


    Find genes that share domains with SLC52A1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: S52A1_HUMAN, Q9NWF4
    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)
    Biophysicochemical properties: Kinetic parameters: KM=1.38 uM for riboflavin;

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001618virus receptor activity IEA--
    GO:0032217riboflavin transporter activity IDA--
         
    Find genes that share ontologies with SLC52A1           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for SLC52A1:
     Decreased POU5F1-GFP protein e  Decreased Salmonella enterica  

    Animal Models:
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    miRNA
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    miRTarBase miRNAs that target SLC52A1:
    hsa-mir-335-5p (MIRT017822)

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    S52A1_HUMAN, Q9NWF4: Cell membrane; Multi-pass membrane protein

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral component of plasma membrane IDA--

    Find genes that share ontologies with SLC52A1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLC52A1
    Interactions:

        Search GeneGlobe Interaction Network for SLC52A1

    1 Interacting protein for SLC52A1 (Q9NWF43) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PLA2G4AP477123I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032218riboflavin transport IDA--

    Find genes that share ontologies with SLC52A1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SLC52A1 (S52A1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SLC52A1 gene (2 alternative transcripts): 
    NM_001104577.1  NM_017986.3  

    Unigene Cluster for SLC52A1:

    Solute carrier family 52, riboflavin transporter, member 1
    Hs.632247  [show with all ESTs]
    Unigene Representative Sequence: AK123566
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000254853 ENST00000573674(uc010ckw.3) ENST00000512825(uc010ckx.3)
    ENST00000575919 ENST00000424747(uc002gap.4 uc002gao.4)
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    Additional mRNA sequence: 

    AB362533.1 AK000922.1 AK123566.1 AY070775.1 BC060810.1 BC092473.1 

    4 DOTS entries:

    DT.100777299  DT.100777298  DT.101976417  DT.100706422 

    Selected AceView cDNA sequences (see all 36):

    W88426 AA584364 AY070775 CB994183 CR617996 AK000922 CB994020 AU136797 
    BX105196 BX359558 BX398125 AK123566 CB959884 CF780882 BQ007381 CB995258 
    AL542947 BX359993 CB997888 BX397457 AU117441 BU752646 NM_017986 BC060810 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SLC52A1    About this scheme

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


    ECgene alternative splicing isoforms for SLC52A1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SLC52A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGAGGCCAGG
    SLC52A1 Expression
    About this image

    SLC52A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC52A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.632247

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

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SLC52A1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    54(a)
    1 → many
    GL344487.1(21-24731)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.66782 Xenopus laevis transcribed sequence with weak similarity more 80.27(n)    BJ059115.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc11c062 wufc11c06 71.95(n)   323832  BC055241.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG115766
    --
    30(a)
    1 → many
    3R(27632588-27635907)
    worm
    (Caenorhabditis elegans)
    Secernentea rft-16
    rft-26
    Protein Y47D7A.16 (Y47D7A.16) mRNA, complete cds
    Protein Y47D7A.14, isoform a (Y47D7A.14) mRNA, com...
    32(a)
    28(a)
    many ↔ many
    many ↔ many
    V(4438968-4443172) WBGene00044637
    V(4443073-4450555) WBGene00021626
            Species with no ortholog for SLC52A1

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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC52A1 gene
    SLC52A22  SLC52A32  
    3 SIMAP similar genes for SLC52A1 using alignment to 2 protein entries:     S52A1_HUMAN (see all proteins):
    GPCR    SLC52A2    SLC52A3

    Find genes that share paralogs with SLC52A1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SLC52A1 (see all 172)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1813435071,2
    --4922907(+) GGTTTC/GCTTTA 2 -- ds50010--------
    rs1859382111,2
    --4922984(+) CGCGGC/TGGCTC 2 -- ds50010--------
    rs1412711651,2
    C--4922996(+) CGCCTA/GTAATC 2 -- ds50010--------
    rs1469298511,2
    --4923017(+) GGGAGG/TCCAAG 2 -- ds50010--------
    rs1131573911,2
    C,F--4923057(+) GACCAT/GCCTGA 2 -- ds50011Minor allele frequency- G:0.00WA 2
    rs2016211541,2
    --4923076(+) TGAAA-/CCCCCC 2 -- ds50010--------
    rs1116757491,2
    F--4923082(+) CCCCCC/TGTCTC 2 -- ds50011Minor allele frequency- T:0.50CSA 2
    rs1123860201,2
    C,F--4923106(+) AAATTT/AGCCGG 2 -- ds50011Minor allele frequency- A:0.50CSA 2
    rs345564301,2
    C,F--4923111(+) AGCCGG/ATCGTG 2 -- ds50013Minor allele frequency- A:0.33NA 6
    rs3468201,2
    C,F,O,A,H--4923336(-) GCTTAC/TCTCTT 2 -- ds500127Minor allele frequency- T:0.07MN NS EA NA WA CSA 2511

    HapMap Linkage Disequilibrium report for SLC52A1 (4935895 - 4955304 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SLC52A1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SLC52A1
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607883   
    OMIM disorders: 615026  
    UniProtKB/Swiss-Prot: S52A1_HUMAN, Q9NWF4
  • 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. Note=The disease is
    caused by mutations affecting the gene represented in this entry

  • 2 diseases for SLC52A1:    
    About MalaCards
    riboflavin deficiency    pituitary hormone deficiency, combined, 6


    Find genes that share disorders with SLC52A1           About GenesLikeMe


    Export disorders for SLC52A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SLC52A1 gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with SLC52A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of receptors for pig endogenous retrovirus. (PubMed id 12740431)1, 2, 3, 9 Ericsson T.A.... Patience C. (Proc. Natl. Acad. Sci. U.S.A. 2003)
    2. Identification and functional characterization of a novel human and rat riboflavin transporter, RFT1. (PubMed id 18632736)1, 2, 3 Yonezawa A.... Inui K. (Am. J. Physiol. 2008)
    3. Maternal riboflavin deficiency, resulting in transient neonatal-onset glutaric aciduria Type 2, is caused by a microdeletion in the riboflavin transporter gene GPR172B. (PubMed id 21089064)1, 2 Ho G.... Christodoulou J. (Hum. Mutat. 2011)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. Differentiation-dependent regulation of intestinal vitamin B(2) uptake: studies utilizing human-derived intestinal epithelial Caco-2 cells and native rat intestine. (PubMed id 23413253)1 Subramanian V.S....Said H.M. (Am. J. Physiol. Gastrointest. Liver Physiol. 2013)
    7. Novel riboflavin transporter family RFVT/SLC52: identification, nomenclature, functional characterization and genetic diseases of RFVT/SLC52. (PubMed id 23506902)1 Yonezawa A. and Inui K. (Mol. Aspects Med. 2013)
    8. Binding of transcription factor activating protein 2 I^ on the 5'-proximal promoter region of human porcine endogenous retrovirus subgroup A receptor 2/GPR172B. (PubMed id 22702469)1 Nakaya Y....Miyazawa T. (Xenotransplantation 2012)
    9. Identification and comparative functional characterization of a new human riboflavin transporter hRFT3 expressed in the brain. (PubMed id 20463145)2 Yao Y.... Inui K. (J. Nutr. 2010)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55065 HGNC: 30225 AceView: GPR172B Ensembl:ENSG00000132517 euGenes: HUgn55065
    ECgene: SLC52A1 H-InvDB: SLC52A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SLC52A1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SLC52A1 gene:
    Search GeneIP for patents involving SLC52A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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