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    SLC52A3 solute carrier family 52 member 3 [ Homo sapiens (human) ]

    Gene ID: 113278, updated on 1-Mar-2024

    Summary

    Official Symbol
    SLC52A3provided by HGNC
    Official Full Name
    solute carrier family 52 member 3provided by HGNC
    Primary source
    HGNC:HGNC:16187
    See related
    Ensembl:ENSG00000101276 MIM:613350; AllianceGenome:HGNC:16187
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RFT2; BVVLS; RFVT3; hRFT2; BVVLS1; C20orf54; bA371L19.1
    Summary
    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]
    Expression
    Biased expression in testis (RPKM 24.2), small intestine (RPKM 7.2) and 7 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SLC52A3 in Genome Data Viewer
    Location:
    20p13
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (760080..780033, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (804408..824432, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (740724..756628, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:642152-642765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:642766-643378 Neighboring gene sulfiredoxin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:653674-654187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12583 Neighboring gene Sharpr-MPRA regulatory region 5118 Neighboring gene scratch family transcriptional repressor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:669184-669764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:669765-670343 Neighboring gene MPRA-validated peak4111 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:700539-701043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:714587-715087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:749319-749818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:756400-757102 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:771562-772313 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:798226-798402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:803889-804420 Neighboring gene CRISPRi-validated cis-regulatory element chr20.80 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12585 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:822609-823591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:825145-825958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17447 Neighboring gene family with sequence similarity 110 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:836793-837779 Neighboring gene ribosomal protein S10 pseudogene 5 Neighboring gene uncharacterized LOC124904854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:853162-853662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:853663-854163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17448 Neighboring gene angiopoietin 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC10698

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables riboflavin transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables riboflavin transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables riboflavin transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    Process Evidence Code Pubs
    involved_in cellular response to heat IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in flavin adenine dinucleotide biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in riboflavin metabolic process TAS
    Traceable Author Statement
    more info
     
    involved_in riboflavin transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in riboflavin transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in apical plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    solute carrier family 52, riboflavin transporter, member 3
    Names
    SLC52A3a
    SLC52A3b
    riboflavin transporter 2
    solute carrier family 52 (riboflavin transporter), member 3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_027687.2 RefSeqGene

      Range
      12486..20906
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1394

    mRNA and Protein(s)

    1. NM_001370085.1NP_001357014.1  solute carrier family 52, riboflavin transporter, member 3

      Status: REVIEWED

      Source sequence(s)
      AL118502
      Consensus CDS
      CCDS13007.1
      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
      Related
      ENSP00000217254.7, ENST00000217254.11
      Conserved Domains (1) summary
      pfam06237
      Location:298395
      DUF1011; Protein of unknown function (DUF1011)
    2. NM_001370086.1NP_001357015.1  solute carrier family 52, riboflavin transporter, member 3

      Status: REVIEWED

      Source sequence(s)
      AL118502
      Consensus CDS
      CCDS13007.1
      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
      Related
      ENSP00000494009.1, ENST00000488495.3
      Conserved Domains (1) summary
      pfam06237
      Location:298395
      DUF1011; Protein of unknown function (DUF1011)
    3. NM_033409.4NP_212134.3  solute carrier family 52, riboflavin transporter, member 3

      See identical proteins and their annotated locations for NP_212134.3

      Status: REVIEWED

      Source sequence(s)
      AI244952, AK074650, BC009750, DA302552, DA358731
      Consensus CDS
      CCDS13007.1
      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
      Related
      ENSP00000494193.1, ENST00000645534.1
      Conserved Domains (1) summary
      pfam06237
      Location:298395
      DUF1011; Protein of unknown function (DUF1011)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      760080..780033 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439868.1XP_047295824.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    2. XM_024451821.1XP_024307589.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
      Conserved Domains (1) summary
      pfam06237
      Location:298395
      DUF1011; Protein of unknown function (DUF1011)
    3. XM_047439867.1XP_047295823.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      804408..824432 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322921.1XP_054178896.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    2. XM_054322919.1XP_054178894.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40
    3. XM_054322920.1XP_054178895.1  solute carrier family 52, riboflavin transporter, member 3 isoform X1

      UniProtKB/Swiss-Prot
      A0A2I6BQ49, A8K6P1, K0A6P4, Q5W1A0, Q5W1A1, Q8NCL7, Q96GD5, Q9NQ40