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SLC46A2 Gene

protein-coding   GIFtS: 46
GCID: GC09M115641

Solute Carrier Family 46, Member 2

(Previous name: thymic stromal co-transporter)
(Previous symbol: TSCOT)
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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 21 2
TSCOT1 2 3 5
Thymic Stromal Co-Transporter1 2
Ly1102
Thymic Stromal Cotransporter Homolog2
Solute Carrier Family 46 Member 23

External Ids:    HGNC: 160551   Entrez Gene: 578642   Ensembl: ENSG000001194577   OMIM: 6089565   UniProtKB: Q9BY103   

Export aliases for SLC46A2 gene to outside databases

Previous GC identifers: GC09M114683 GC09M085239


(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 SLC46A2 Gene:
SLC46A2 (solute carrier family 46, member 2) is a protein-coding gene. GO annotations related to this gene include symporter activity. An important paralog of this gene is SLC46A3.

UniProtKB/Swiss-Prot: TSCOT_HUMAN, Q9BY10
Function: May act as a transporter (By similarity)




(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_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC46A2 gene promoter:
         USF1   Roaz   GATA-2   CREB   FAC1   Ik-2   POU2F1   deltaCREB   USF-1   POU2F1a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC46A2 promoter sequence
   Search Chromatin IP Primers for SLC46A2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC46A2


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

Entrez Gene cytogenetic band: 9q32   Ensembl cytogenetic band:  9q32   HGNC cytogenetic band: 9q32

SLC46A2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC46A2 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M115641:  view genomic region     (about GC identifiers)

Start:
115,641,200 bp from pter      End:
115,653,193 bp from pter
Size:
11,994 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: TSCOT_HUMAN, Q9BY10 (See protein sequence)
Recommended Name: Thymic stromal cotransporter homolog  
Size: 475 amino acids; 51067 Da
Secondary accessions: B1ALK1 Q86VT0 Q96NE2

Explore the universe of human proteins at neXtProt for SLC46A2: NX_Q9BY10

Explore proteomics data for SLC46A2 at MOPED

Post-translational modifications: 

  • Glycosylated (By similarity)1
  • Glycosylation2 at Asn55
  • Modification sites at PhosphoSitePlus

  • See SLC46A2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_149040.3  
    ENSEMBL proteins: 
     ENSP00000363345   ENSP00000474847  

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    antibodies-online proteins for SLC46A2 (3 products) 

     
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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

    IUPHAR Guide to PHARMACOLOGY protein family classification: Thymic stromal co-transporter
    SLC46 family of folate transporters

    3 InterPro protein domains:
     IPR001958 Tet-R_TetA/multi-R_MdtG
     IPR011701 MFS
     IPR016196 MFS_dom_general_subst_transpt

    Graphical View of Domain Structure for InterPro Entry Q9BY10

    ProtoNet protein and cluster: Q9BY10

    UniProtKB/Swiss-Prot: TSCOT_HUMAN, Q9BY10
    Similarity: Belongs to the major facilitator superfamily. SLC46A family


    Find genes that share domains with SLC46A2           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TSCOT_HUMAN, Q9BY10
    Function: May act as a transporter (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015293symporter activity NAS10978518
         
    Find genes that share ontologies with SLC46A2           About GenesLikeMe


    Phenotypes:
         3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Slc46a2):
     cellular  hematopoietic system  immune system 

    Find genes that share phenotypes with SLC46A2           About GenesLikeMe

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SLC46A2

    miRNA
    Products:
        
    miRTarBase miRNAs that target SLC46A2:
    hsa-mir-335-5p (MIRT017709)

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    Selected qRT-PCR Assays for microRNAs that regulate SLC46A2 (see all 16):
    hsa-miR-498 hsa-miR-520e hsa-miR-302d hsa-miR-520f hsa-miR-302e hsa-miR-520a-3p hsa-miR-372 hsa-miR-520d-3p
    SwitchGear 3'UTR luciferase reporter plasmidSLC46A2 3' UTR sequence
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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
    TSCOT_HUMAN, Q9BY10: Cell membrane; Multi-pass membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0009986cell surface IEA--
    GO:0016021integral component of membrane NAS10978518

    Find genes that share ontologies with SLC46A2           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 SLC46A2
    Interactions:

        Search GeneGlobe Interaction Network for SLC46A2

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport ----
    GO:0043029T cell homeostasis IEA--
    GO:0045580regulation of T cell differentiation IEA--
    GO:0048538thymus development IEA--
    GO:0055085transmembrane transport ----

    Find genes that share ontologies with SLC46A2           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 SLC46A2 (TSCOT)



    (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 SLC46A2 gene: 
    NM_033051.3  

    Unigene Cluster for SLC46A2:

    Solute carrier family 46, member 2
    Hs.512668  [show with all ESTs]
    Unigene Representative Sequence: NM_033051
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000374228(uc004bgk.3) ENST00000491462
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SLC46A2 (see all 16):
    hsa-miR-498 hsa-miR-520e hsa-miR-302d hsa-miR-520f hsa-miR-302e hsa-miR-520a-3p hsa-miR-372 hsa-miR-520d-3p
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      QuantiFast Probe-based Assays in human, mouse, rat SLC46A2

    Additional mRNA sequence: 

    AF242557.1 AK055571.1 AK314414.1 BC048285.1 

    4 DOTS entries:

    DT.86836556  DT.100741591  DT.99960599  DT.70103533 

    14 AceView cDNA sequences:

    AF242557 BF437230 NM_033051 AK055571 AW593113 BC048285 BI906680 BX115452 
    BI821567 BP367784 AW451553 AI312783 AI867430 AW138604 

    GeneLoc Exon Structure


    (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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    SLC46A2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SLC46A2 Expression
    About this image


    SLC46A2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Blood (Hematopoietic System)
             Monocytes Peripheral Blood
     
     Thymus (Hematopoietic System)
     
     Epidermis (Integumentary System)
    SLC46A2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC46A2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.512668

    UniProtKB/Swiss-Prot: TSCOT_HUMAN, Q9BY10
    Tissue specificity: Strongly expressed in the adult thymus. Expressed in spleen, lymph nodes, thymus, PBL, bone
    marrow and fetal liver

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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 SLC46A2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc46a21 , 5 solute carrier family 46, member 21, 5 80.69(n)1
    78.01(a)1
      4 (32.81 cM)5
    309361  NM_021053.41  NP_066395.31 
     599051265 
    chicken
    (Gallus gallus)
    Aves SLC46A21 solute carrier family 46, member 2 63.55(n)
    60.75(a)
      431636  XM_429188.4  XP_429188.3 
    lizard
    (Anolis carolinensis)
    Reptilia SLC46A26
    solute carrier family 46, member 2
    56(a)
    1 ↔ 1
    2(57928634-57940156)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004872031 thymic stromal cotransporter homolog 54.91(n)
    50.81(a)
      100487203  XM_002936694.2  XP_002936740.2 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1000024061 thymic stromal cotransporter homolog 55.13(n)
    47.36(a)
      100002406  XM_001921427.4  XP_001921462.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG303446
    CG425146
    (see all 8)
    --
    17(a)
    17(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    2R(5032754-5036017)
    3L(16484938-16489336)
    worm
    (Caenorhabditis elegans)
    Secernentea Y4C6B.56
    Y43F8A.56
    Protein Y43F8A.5 (Y43F8A.5) mRNA, complete cds
    21(a)
    14(a)
    many ↔ many
    many ↔ many
    IV(5319253-5325040) WBGene00021159
    V(19384887-19390120) WBGene00012811


    ENSEMBL Gene Tree for SLC46A2 (if available)
    TreeFam Gene Tree for SLC46A2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC46A2 gene
    SLC46A32  SLC46A12  

    Find genes that share paralogs with SLC46A2           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 SLC46A2 (see all 397)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1386974341,2
    --115640792(+) AGTGAA/GGTTGG 1 -- int10--------
    rs1872943781,2
    --115640808(+) TTGAAC/TGTGAT 1 -- int10--------
    rs1440027541,2
    --115640913(+) GACATC/TCCTAT 1 -- int10--------
    rs1473103631,2
    --115640948(+) ATAGAC/TAGTAC 1 -- int10--------
    rs577173801,2
    C,F--115640973(+) GACACA/GGTCAC 1 -- int15Minor allele frequency- G:0.12WA NA EA 362
    rs107393791,2
    C,F,A,H--115640976(+) ACAGTG/CACGTG 1 -- int116Minor allele frequency- C:0.09EA NS NA WA CSA 803
    rs560242591,2
    C--115640979(+) GTCACG/ATGCTA 1 -- int14Minor allele frequency- A:0.13NA WA EA 360
    rs1922807331,2
    --115641022(+) CTGGAA/CCTTAT 1 -- int10--------
    rs1181744191,2
    C,F--115641039(+) TGTCAT/CAGAGT 1 -- int11Minor allele frequency- C:0.02NA 120
    rs49791761,2
    C,F,H--115641181(+) GGGAAA/GGAACG 1 -- int126Minor allele frequency- G:0.11NA NS EA WA 2466

    HapMap Linkage Disequilibrium report for SLC46A2 (115641200 - 115653193 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SLC46A2:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422302CNV Deletion17116639
    nsv529036CNV Loss19592680
    nsv893733CNV Gain21882294
    dgv2414e1CNV Complex17122850
    dgv2411e1CNV Complex17122850
    dgv2412e1CNV Complex17122850

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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: 608956    OMIM disorders: --


    Find genes that share disorders with SLC46A2           About GenesLikeMe

    Genetic Association Database (GAD): SLC46A2

    Export disorders for SLC46A2 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 SLC46A2 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with SLC46A2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of the mouse gene, human promoter and human cDNA of TSCOT reveals strong interspecies homology. (PubMed id 10978518)1, 2, 3, 9 Chen C....Flomerfelt F.A. (Biochim. Biophys. Acta 2000)
    2. A putative 12-transmembrane domain cotransporter associated with apical membranes of the epididymal duct. (PubMed id 12826694)1, 3, 9 Obermann H....Kirchhoff C. (J. Androl. 2003)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. Polymorphisms in 9q32 and TSCOT are linked to cervical cancer in affected sib-pairs with high mean age at diagnosis. (PubMed id 18392855)1, 9 Engelmark M.T....Gyllensten U.B. (Hum. Genet. 2008)
    6. A putative 12 transmembrane domain cotransporter expressed in thymic cortical epithelial cells. (PubMed id 10706709)1, 9 Kim M.G....Schwartz R.H. (J. Immunol. 2000)
    7. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
    8. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    9. 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)
    10. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)

    (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: 57864 HGNC: 16055 AceView: TSCOT Ensembl:ENSG00000119457 euGenes: HUgn57864
    ECgene: SLC46A2 H-InvDB: SLC46A2

    (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 SLC46A2 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 SLC46A2 gene:
    Search GeneIP for patents involving SLC46A2

    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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