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Aliases for SLC46A2 Gene

Aliases for SLC46A2 Gene

  • Solute Carrier Family 46 Member 2 2 3 4 5
  • Thymic Stromal Co-Transporter 2 3
  • TSCOT 3 4
  • Thymic Stromal Cotransporter Homolog 3
  • Solute Carrier Family 46, Member 2 2
  • Ly110 3

External Ids for SLC46A2 Gene

Previous HGNC Symbols for SLC46A2 Gene


Previous GeneCards Identifiers for SLC46A2 Gene

  • GC09M114683
  • GC09M115641
  • GC09M085239

Summaries for SLC46A2 Gene

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 for SLC46A2 Gene

  • May act as a transporter.

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC46A2 Gene

Genomics for SLC46A2 Gene

Regulatory Elements for SLC46A2 Gene

Enhancers for SLC46A2 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
GH09G112860 1.6 FANTOM5 Ensembl ENCODE dbSUPER 23 +28.3 28327 4.4 ZFP64 ZNF140 ZMYM3 MAX ZNF101 ZNF697 EGR1 EED ZNF433 ZBTB11 SLC46A2 SNX30 ZFP37 ENSG00000226609 SLC31A2 PRPF4 RNF183 ENSG00000271631 FKBP15 PIR49803
GH09G112866 1.4 Ensembl ENCODE dbSUPER 22.8 +22.5 22520 4.5 HDGF PKNOX1 FOXA2 CREB3L1 ARNT ARID4B FOS ZNF263 SP3 NCOA1 SLC46A2 ENSG00000226609 SNX30 SLC31A2 INIP PIR49803
GH09G112844 1.4 Ensembl ENCODE dbSUPER 12.1 +45.9 45878 0.7 CBX3 ARNT ARID4B ZBTB40 ZSCAN9 RAD21 CHAMP1 RFX5 YY1 ETS1 ENSG00000226609 SNX30 SLC46A2 PIR49803
GH09G112858 1.2 Ensembl ENCODE dbSUPER 12.3 +32.1 32141 1.6 CTCF HLF CEBPB YBX1 CEBPG CBX5 IKZF1 NBN TCF7 ZNF652 ENSG00000226609 SLC46A2 SNX30 PIR49803
GH09G112763 1.4 Ensembl ENCODE dbSUPER 9.4 +126.1 126145 1.8 HDAC1 TBP PKNOX1 MLX ARID4B DMAP1 RARA ZNF121 EGR1 FOS INIP SLC46A2 ENSG00000226609 SNX30 PIR49803
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC46A2 on UCSC Golden Path with GeneCards custom track

Promoters for SLC46A2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000240036 242 201 CTCF HDAC6 SUZ12 MYC EZH2

Genomic Location for SLC46A2 Gene

112,878,920 bp from pter
112,890,942 bp from pter
12,023 bases
Minus strand

Genomic View for SLC46A2 Gene

Genes around SLC46A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC46A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC46A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC46A2 Gene

Proteins for SLC46A2 Gene

  • Protein details for SLC46A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Thymic stromal cotransporter homolog
    Protein Accession:
    Secondary Accessions:
    • B1ALK1
    • Q86VT0
    • Q96NE2

    Protein attributes for SLC46A2 Gene

    475 amino acids
    Molecular mass:
    51067 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SLC46A2 Gene

Post-translational modifications for SLC46A2 Gene

Other Protein References for SLC46A2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SLC46A2 Gene

Domains & Families for SLC46A2 Gene

Gene Families for SLC46A2 Gene

Protein Domains for SLC46A2 Gene

Suggested Antigen Peptide Sequences for SLC46A2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the major facilitator superfamily. SLC46A family.
  • Belongs to the major facilitator superfamily. SLC46A family.
genes like me logo Genes that share domains with SLC46A2: view

Function for SLC46A2 Gene

Molecular function for SLC46A2 Gene

UniProtKB/Swiss-Prot Function:
May act as a transporter.

Gene Ontology (GO) - Molecular Function for SLC46A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015293 symporter activity NAS 10978518
genes like me logo Genes that share ontologies with SLC46A2: view
genes like me logo Genes that share phenotypes with SLC46A2: view

Animal Models for SLC46A2 Gene

MGI Knock Outs for SLC46A2:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC46A2

CRISPR Products

miRNA for SLC46A2 Gene

miRTarBase miRNAs that target SLC46A2

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC46A2 Gene

Localization for SLC46A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC46A2 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

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 SLC46A2 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for SLC46A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0009986 cell surface IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS,IEA 10978518
genes like me logo Genes that share ontologies with SLC46A2: view

Pathways & Interactions for SLC46A2 Gene

SuperPathways for SLC46A2 Gene

No Data Available

Interacting Proteins for SLC46A2 Gene

Gene Ontology (GO) - Biological Process for SLC46A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0043029 T cell homeostasis IEA --
GO:0045580 regulation of T cell differentiation IEA --
GO:0048538 thymus development IEA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SLC46A2: view

No data available for Pathways by source and SIGNOR curated interactions for SLC46A2 Gene

Drugs & Compounds for SLC46A2 Gene

No Compound Related Data Available

Transcripts for SLC46A2 Gene

mRNA/cDNA for SLC46A2 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(14) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLC46A2 Gene

Solute carrier family 46, member 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC46A2 Gene

No ASD Table

Relevant External Links for SLC46A2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC46A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC46A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC46A2 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x16.7), Skin - Not Sun Exposed (Suprapubic) (x12.3), Whole Blood (x6.2), Lung (x4.4), and Bladder (x4.3).

Protein differential expression in normal tissues from HIPED for SLC46A2 Gene

This gene is overexpressed in Breast (47.4) and Heart (21.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC46A2 Gene

Protein tissue co-expression partners for SLC46A2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC46A2 Gene:


SOURCE GeneReport for Unigene cluster for SLC46A2 Gene:


mRNA Expression by UniProt/SwissProt for SLC46A2 Gene:

Tissue specificity: Strongly expressed in the adult thymus. Expressed in spleen, lymph nodes, thymus, PBL, bone marrow and fetal liver.

Evidence on tissue expression from TISSUES for SLC46A2 Gene

  • Lung(4.2)
  • Blood(4)
genes like me logo Genes that share expression patterns with SLC46A2: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC46A2 Gene

Orthologs for SLC46A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC46A2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC46A2 34 35
  • 99.51 (n)
(Bos Taurus)
Mammalia SLC46A2 34
  • 85.55 (n)
  • 81 (a)
(Canis familiaris)
Mammalia SLC46A2 34 35
  • 85.55 (n)
(Mus musculus)
Mammalia Slc46a2 34 16 35
  • 80.69 (n)
(Rattus norvegicus)
Mammalia Slc46a2 34
  • 80.1 (n)
(Monodelphis domestica)
Mammalia SLC46A2 35
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia SLC46A2 35
  • 73 (a)
(Gallus gallus)
Aves SLC46A2 34 35
  • 63.55 (n)
(Anolis carolinensis)
Reptilia SLC46A2 35
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487203 34
  • 54.91 (n)
(Danio rerio)
Actinopterygii LOC100002406 34
  • 55.13 (n)
SLC46A2 35
  • 45 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG30344 35
  • 17 (a)
CG42514 35
  • 17 (a)
CG30345 35
  • 16 (a)
CG8046 35
  • 16 (a)
CG15553 35
  • 15 (a)
CG8008 35
  • 15 (a)
CG15890 35
  • 14 (a)
CG31321 35
  • 13 (a)
(Caenorhabditis elegans)
Secernentea Y4C6B.5 35
  • 21 (a)
Y43F8A.5 35
  • 14 (a)
Species where no ortholog for SLC46A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)

Evolution for SLC46A2 Gene

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

Paralogs for SLC46A2 Gene

Paralogs for SLC46A2 Gene

genes like me logo Genes that share paralogs with SLC46A2: view

Variants for SLC46A2 Gene

Sequence variations from dbSNP and Humsavar for SLC46A2 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000474313 -- 112,883,068(+) CAGGT(C/T)AACGG intron-variant, nc-transcript-variant
rs1000529327 -- 112,892,528(+) ATTTC(A/G)GTTCT upstream-variant-2KB
rs1000703755 -- 112,888,781(+) GTATT(A/T)TAATG intron-variant
rs1000767641 -- 112,890,062(+) TCAGT(A/G)TCAGG nc-transcript-variant, reference, missense
rs1001135592 -- 112,888,526(+) TACAA(C/T)GACAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLC46A2 Gene

Variant ID Type Subtype PubMed ID
esv2422302 CNV deletion 17116639
esv2759710 CNV gain 17122850
nsv529036 CNV loss 19592680

Variation tolerance for SLC46A2 Gene

Residual Variation Intolerance Score: 84.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.93; 67.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC46A2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC46A2 Gene

Disorders for SLC46A2 Gene

Relevant External Links for SLC46A2

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for SLC46A2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SLC46A2 Gene

Publications for SLC46A2 Gene

  1. Characterization of the mouse gene, human promoter and human cDNA of TSCOT reveals strong interspecies homology. (PMID: 10978518) Chen C. … Flomerfelt F.A. (Biochim. Biophys. Acta 2000) 2 3 4 22 64
  2. A putative 12-transmembrane domain cotransporter associated with apical membranes of the epididymal duct. (PMID: 12826694) Obermann H. … Kirchhoff C. (J. Androl. 2003) 2 3 22 64
  3. Polymorphisms in 9q32 and TSCOT are linked to cervical cancer in affected sib-pairs with high mean age at diagnosis. (PMID: 18392855) Engelmark M.T. … Gyllensten U.B. (Hum. Genet. 2008) 3 22 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for SLC46A2 Gene

Sources for SLC46A2 Gene

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