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SLC46A3 Gene

protein-coding   GIFtS: 46
GCID: GC13M029274

Solute Carrier Family 46, Member 3

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(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 46, Member 31 2
FKSG162
Solute Carrier Family 46 Member 32

External Ids:    HGNC: 275011   Entrez Gene: 2835372   Ensembl: ENSG000001395087   UniProtKB: Q7Z3Q13   

Export aliases for SLC46A3 gene to outside databases

Previous GC identifers: GC13M028173 GC13M010095


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SLC46A3 Gene:
SLC46A3 (solute carrier family 46, member 3) is a protein-coding gene. An important paralog of this gene is SLC46A1.


(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_000013.10  NT_024524.15  NC_018924.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC46A3 gene promoter:
         FOXF2   CUTL1   Meis-1b   PPAR-gamma1   POU2F1   POU2F1a   Cart-1   PPAR-gamma2   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC46A3 promoter sequence
   Search Chromatin IP Primers for SLC46A3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC46A3


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

Entrez Gene cytogenetic band: 13q12.3   Ensembl cytogenetic band:  13q12.3   HGNC cytogenetic band: 13q12.3

SLC46A3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC46A3 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M029274:  view genomic region     (about GC identifiers)

Start:
29,274,201 bp from pter      End:
29,293,150 bp from pter
Size:
18,950 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: S46A3_HUMAN, Q7Z3Q1 (See protein sequence)
Recommended Name: Solute carrier family 46 member 3 precursor  
Size: 461 amino acids; 51519 Da
Sequence caution: Sequence=BAC85896.1; Type=Frameshift; Positions=353;
Secondary accessions: Q3ZCV8 Q6NUK5 Q6P9B3 Q6ZVG5 Q96QA1
Alternative splicing: 3 isoforms:  Q7Z3Q1-1   Q7Z3Q1-2   Q7Z3Q1-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SLC46A3: NX_Q7Z3Q1

Explore proteomics data for SLC46A3 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn38, Asn46, Asn53

  • See SLC46A3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001129391.1  NP_861450.1  

    ENSEMBL proteins: 
     ENSP00000266943   ENSP00000370192  

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    Cloud-Clone Corp. Proteins for SLC46A3

     
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    antibodies-online peptides for SLC46A3

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    antibodies-online antibodies for SLC46A3 (5 products) 

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    antibodies-online kits for SLC46A3 (10 products) 


    (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

    IUPHAR Guide to PHARMACOLOGY protein family classification: SLC46A3
    SLC46 family of folate transporters

    2 InterPro protein domains:
     IPR011701 MFS
     IPR016196 MFS_dom_general_subst_transpt

    Graphical View of Domain Structure for InterPro Entry Q7Z3Q1

    ProtoNet protein and cluster: Q7Z3Q1

    UniProtKB/Swiss-Prot: S46A3_HUMAN, Q7Z3Q1
    Similarity: Belongs to the major facilitator superfamily. SLC46A family


    Find genes that share domains with SLC46A3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    Find genes that share ontologies with SLC46A3           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for SLC46A3:
     Decreased POU5F1-GFP protein e  Decreased number of cells in m 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SLC46A3

    miRNA
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    miRTarBase miRNAs that target SLC46A3:
    hsa-mir-192-5p (MIRT026114), hsa-mir-335-5p (MIRT016755), hsa-mir-124-3p (MIRT022155), hsa-mir-215-5p (MIRT024422)

    Block miRNA regulation of human, mouse, rat SLC46A3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SLC46A3 (see all 45):
    hsa-miR-520e hsa-miR-302d hsa-let-7d hsa-miR-4328 hsa-miR-106a hsa-miR-1273d hsa-let-7g hsa-miR-372
    SwitchGear 3'UTR luciferase reporter plasmidSLC46A3 3' UTR sequence
    Inhib. RNA
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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
    S46A3_HUMAN, Q7Z3Q1: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytoskeleton1
    cytosol1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0016021integral component of membrane IEA--
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with SLC46A3           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 SLC46A3
    Interactions:

        Search GeneGlobe Interaction Network for SLC46A3

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--
    GO:0055085transmembrane transport IEA--

    Find genes that share ontologies with SLC46A3           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 SLC46A3 (S46A3)



    (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 SLC46A3 gene (2 alternative transcripts): 
    NM_001135919.1  NM_181785.3  

    Unigene Cluster for SLC46A3:

    Solute carrier family 46, member 3
    Hs.117167  [show with all ESTs]
    Unigene Representative Sequence: BX649127
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000475385 ENST00000266943(uc001usg.3 uc001usi.3 uc001usj.3 uc001ush.3)
    ENST00000380814
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SLC46A3 (see all 45):
    hsa-miR-520e hsa-miR-302d hsa-let-7d hsa-miR-4328 hsa-miR-106a hsa-miR-1273d hsa-let-7g hsa-miR-372
    SwitchGear 3'UTR luciferase reporter plasmidSLC46A3 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat SLC46A3
      QuantiFast Probe-based Assays in human, mouse, rat SLC46A3

    Additional mRNA sequence: 

    AF315594.1 AK026720.1 AK093932.1 AK098426.1 AK124604.1 BC036662.1 BC060850.1 BC068556.1 
    BX537565.1 BX649127.1 

    8 DOTS entries:

    DT.441103  DT.100035860  DT.100784637  DT.100784636  DT.40247809  DT.120793778  DT.100784638  DT.40196354 

    Selected AceView cDNA sequences (see all 89):

    AI770039 CR611527 BM713250 BU070379 CA943831 CD107826 BX489263 BC036662 
    BX649127 AK026720 BG741755 AW473770 CD237026 CB987082 AK098426 AA365841 
    NM_181785 BX101888 CA440782 BE827009 BX537565 AF315594 AI251022 BG565830 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SLC46A3    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7
    SP1:                          -           -                 -         
    SP2:                          -           -                           
    SP3:                                      -                           
    SP4:                                                                  
    SP5:                                                                  


    ECgene alternative splicing isoforms for SLC46A3

    (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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    SLC46A3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCTTTTCACA
    SLC46A3 Expression
    About this image

    SLC46A3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC46A3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.117167
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    In Situ
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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 SLC46A3 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc46a31 , 5 solute carrier family 46, member 31, 5 76.52(n)1
    75(a)1
      5 (87.58 cM)5
    717061  NM_027872.31  NP_082148.11 
     1478784375 
    chicken
    (Gallus gallus)
    Aves SLC46A31 solute carrier family 46, member 3 61.44(n)
    51.63(a)
      418924  NM_001030828.1  NP_001025999.1 
    lizard
    (Anolis carolinensis)
    Reptilia SLC46A36
    solute carrier family 46, member 3
    43(a)
    1 ↔ 1
    3(185553298-185564488)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia slc46a31 solute carrier family 46, member 3 54.75(n)
    44.59(a)
      100492828  XM_002934031.2  XP_002934077.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:dkey-5g14.11 si:dkey-5g14.1 52.7(n)
    42.76(a)
      556497  XM_679321.5  XP_684413.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG158901 CG15890 39.94(n)
    28.57(a)
      32401  NM_132740.1  NP_572968.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y4C6B.56
    Y43F8A.56
    Protein Y43F8A.5 (Y43F8A.5) mRNA, complete cds
    22(a)
    16(a)
    many ↔ many
    many ↔ many
    IV(5319253-5325040) WBGene00021159
    V(19384887-19390120) WBGene00012811


    ENSEMBL Gene Tree for SLC46A3 (if available)
    TreeFam Gene Tree for SLC46A3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC46A3 gene
    SLC46A12  SLC46A22  
    1 SIMAP similar gene for SLC46A3 using alignment to 1 protein entry:     S46A3_HUMAN:
    SLC46A1

    Find genes that share paralogs with SLC46A3           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 SLC46A3 (see all 368)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1440160811,2
    --29273802(+) AGCCCA/CGAAGA 2 -- int10--------
    rs360467971,2
    C--29273899(+) ATTGA-/TTTTCT 2 -- int10--------
    rs1440587121,2
    C--29274041(+) TAAAGA/GACCTA 2 -- int10--------
    rs1822717961,2
    --29274213(+) GTCATG/TTAGTT 2 -- int10--------
    rs157241,2
    C,F,A,H--29274345(+) GCACAC/TAAAGA 2 -- ut31 ese330Minor allele frequency- T:0.48MN EA NA NS CSA WA 3294
    rs1868828131,2
    --29274550(+) TGAGCA/GTAAGG 2 -- ut310--------
    rs17711611,2
    C,F,O,H--29274632(+) CCGTGC/TTGACG 2 -- ut31 ese318Minor allele frequency- T:0.02MN NS EA NA WA CSA 1000
    rs47696361,2
    C,F,A,H--29274633(+) CGTGTT/CGACGG 2 -- ut31 ese317Minor allele frequency- C:0.49NS EA NA WA 2340
    rs17920761,2
    C,F,H--29274651(-) TAGTCC/GTTAAA 2 -- ut315Minor allele frequency- G:0.00MN NS EA 558
    rs17711621,2
    C,F,O,A,H--29274654(+) AAGGAG/CTACAA 2 -- ut3115Minor allele frequency- C:0.44NA NS EA WA CSA 924

    HapMap Linkage Disequilibrium report for SLC46A3 (29274201 - 29293150 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for SLC46A3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv974CNV Insertion18451855
    nsv832571CNV Loss17160897

    Site Specific Mutation Identification with PCR Assays
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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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    Find genes that share disorders with SLC46A3           About GenesLikeMe

    Genetic Association Database (GAD): SLC46A3

    Export disorders for SLC46A3 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 SLC46A3 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with SLC46A3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. (PubMed id 20708005)1, 4 Chalasani N....Rotter J.I. (Gastroenterology 2010)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    4. Large-scale proteomics and phosphoproteomics of urinary exosomes. (PubMed id 19056867)1 Gonzales P.A....Knepper M.A. (J. Am. Soc. Nephrol. 2009)
    5. Identification of candidate genes for human pituitary development by EST analysis. (PubMed id 19284880)1 Ma Y....Hao X. (BMC Genomics 2009)
    6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    7. 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)
    8. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)2 Dunham A.... Ross M.T. (Nature 2004)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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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: 283537 HGNC: 27501 AceView: LOC283537 Ensembl:ENSG00000139508 euGenes: HUgn283537
    ECgene: SLC46A3 H-InvDB: SLC46A3

    (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 SLC46A3 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 SLC46A3 gene:
    Search GeneIP for patents involving SLC46A3

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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