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Aliases for SPNS3 Gene

Aliases for SPNS3 Gene

  • Sphingolipid Transporter 3 (Putative) 2 3 5
  • Spinster Homolog 3 (Drosophila) 2

External Ids for SPNS3 Gene

Previous GeneCards Identifiers for SPNS3 Gene

  • GC17P004284

Summaries for SPNS3 Gene

GeneCards Summary for SPNS3 Gene

SPNS3 (Sphingolipid Transporter 3 (Putative)) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include transmembrane transporter activity and sphingolipid transporter activity. An important paralog of this gene is SPNS1.

UniProtKB/Swiss-Prot for SPNS3 Gene

  • Sphingolipid transporter.

Additional gene information for SPNS3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SPNS3 Gene

Genomics for SPNS3 Gene

GeneHancer (GH) Regulatory Elements for SPNS3 Gene

Promoters and enhancers for SPNS3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I004433 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 557.7 +0.2 185 1.5 GLIS2 POLR2A CEBPB MAX CEBPG RUNX3 GABPA SPNS3 SPNS2 ENSG00000229782 PIR52974
GH17I004498 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.3 +66.2 66237 3.3 KLF17 SIN3A ZEB1 ZNF335 GLIS2 SCRT2 EGR2 ZNF398 ZEB2 GLIS1 SPNS2 ENSG00000229782 LOC100130950 RPAIN ZNF594 ENSG00000263272 ZNF232 PELP1 ENSG00000263164 SPNS3
GH17I004420 Enhancer 1 Ensembl ENCODE 6 -12.9 -12850 0.4 ARID4B ZNF2 IRF4 RAD21 ZNF143 RUNX3 CREM THAP11 ZNF654 RXRA ENSG00000229782 SPNS2 SPNS3 GC17P004368
GH17I004475 Enhancer 1.2 Ensembl ENCODE dbSUPER 4.6 +46.1 46052 9.1 ELF3 MLX ZFP64 ARID4B BATF THRB ZNF48 GLIS2 SCRT2 ETV6 GGT6 TAX1BP3 SPNS3 PFN1 ENSG00000262823 PIR52974
GH17I004436 Enhancer 0.7 Ensembl ENCODE 7.1 +3.2 3185 1.5 PKNOX1 NFE2 ZNF24 RUNX3 SPI1 SPNS3 PIR52974
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SPNS3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPNS3 gene promoter:

Genomic Locations for SPNS3 Gene

Genomic Locations for SPNS3 Gene
54,521 bases
Plus strand

Genomic View for SPNS3 Gene

Genes around SPNS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPNS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPNS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPNS3 Gene

Proteins for SPNS3 Gene

  • Protein details for SPNS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein spinster homolog 3
    Protein Accession:
    Secondary Accessions:
    • Q8IZ31

    Protein attributes for SPNS3 Gene

    512 amino acids
    Molecular mass:
    54769 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SPNS3 Gene


neXtProt entry for SPNS3 Gene

Post-translational modifications for SPNS3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SPNS3 Gene

Domains & Families for SPNS3 Gene

Gene Families for SPNS3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SPNS3 Gene


Suggested Antigen Peptide Sequences for SPNS3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
genes like me logo Genes that share domains with SPNS3: view

Function for SPNS3 Gene

Molecular function for SPNS3 Gene

UniProtKB/Swiss-Prot Function:
Sphingolipid transporter.

Phenotypes From GWAS Catalog for SPNS3 Gene

Gene Ontology (GO) - Molecular Function for SPNS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046624 sphingolipid transporter activity IBA --
genes like me logo Genes that share ontologies with SPNS3: view
genes like me logo Genes that share phenotypes with SPNS3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SPNS3

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SPNS3 Gene

Localization for SPNS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPNS3 Gene

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 SPNS3 gene
Compartment Confidence
plasma membrane 3
lysosome 3

Gene Ontology (GO) - Cellular Components for SPNS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0031982 vesicle IBA --
genes like me logo Genes that share ontologies with SPNS3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SPNS3 Gene

Pathways & Interactions for SPNS3 Gene

SuperPathways for SPNS3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPNS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003376 sphingosine-1-phosphate signaling pathway IBA --
GO:0006810 transport IEA --
GO:0006869 lipid transport IEA --
GO:0040011 locomotion IBA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SPNS3: view

No data available for Pathways by source and SIGNOR curated interactions for SPNS3 Gene

Drugs & Compounds for SPNS3 Gene

No Compound Related Data Available

Transcripts for SPNS3 Gene

Unigene Clusters for SPNS3 Gene

Spinster homolog 3 (Drosophila):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPNS3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: -
SP2: - -

Relevant External Links for SPNS3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SPNS3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPNS3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SPNS3 Gene

This gene is overexpressed in Whole Blood (x10.0) and Spleen (x4.3).

Protein differential expression in normal tissues from HIPED for SPNS3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SPNS3 Gene

Protein tissue co-expression partners for SPNS3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SPNS3 Gene:


SOURCE GeneReport for Unigene cluster for SPNS3 Gene:

genes like me logo Genes that share expression patterns with SPNS3: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPNS3 Gene

Orthologs for SPNS3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPNS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SPNS3 34 33
  • 97.53 (n)
(Bos Taurus)
Mammalia SPNS3 33 34
  • 85.03 (n)
(Canis familiaris)
Mammalia SPNS3 34 33
  • 83.09 (n)
(Mus musculus)
Mammalia Spns3 33 16 34
  • 81.49 (n)
(Rattus norvegicus)
Mammalia Spns3 33
  • 81.2 (n)
(Ornithorhynchus anatinus)
Mammalia SPNS3 34
  • 58 (a)
(Gallus gallus)
Aves SPNS3 33 34
  • 59.03 (n)
(Anolis carolinensis)
Reptilia SPNS3 34
  • 56 (a)
(Danio rerio)
Actinopterygii spns3 33 34
  • 57.16 (n)
fruit fly
(Drosophila melanogaster)
Insecta spin 34
  • 31 (a)
(Caenorhabditis elegans)
Secernentea spin-1 34
  • 33 (a)
spin-2 34
  • 33 (a)
spin-4 34
  • 32 (a)
spin-3 34
  • 31 (a)
(Oryza sativa)
Liliopsida Os04g0525900 33
  • 40.61 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5353 34
  • 29 (a)
Species where no ortholog for SPNS3 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SPNS3 Gene

Gene Tree for SPNS3 (if available)
Gene Tree for SPNS3 (if available)

Paralogs for SPNS3 Gene

Paralogs for SPNS3 Gene

(3) SIMAP similar genes for SPNS3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SPNS3: view

Variants for SPNS3 Gene

Sequence variations from dbSNP and Humsavar for SPNS3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs368604785 A colorectal cancer sample 4,487,874(+) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1000005581 -- 4,476,840(+) C/G intron_variant
rs1000116387 -- 4,455,605(+) C/T intron_variant
rs1000144381 -- 4,484,673(+) C/T intron_variant
rs1000153229 -- 4,450,856(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SPNS3 Gene

Variant ID Type Subtype PubMed ID
dgv3087n100 CNV loss 25217958
dgv5430n54 CNV gain 21841781
dgv883e212 CNV loss 25503493
esv1095840 CNV deletion 17803354
esv2148441 CNV deletion 18987734
esv2659289 CNV deletion 23128226
esv2715553 CNV deletion 23290073
esv2715554 CNV deletion 23290073
esv2762544 CNV gain 21179565
esv3444474 CNV insertion 20981092
esv3582496 CNV loss 25503493
esv3639773 CNV gain 21293372
esv3639779 CNV gain 21293372
esv3639781 CNV gain 21293372
esv3639782 CNV gain 21293372
esv3639783 CNV gain 21293372
esv3892954 CNV gain 25118596
esv3892955 CNV gain 25118596
nsv1058176 CNV gain 25217958
nsv1065759 CNV gain 25217958
nsv1123088 CNV deletion 24896259
nsv1138492 CNV deletion 24896259
nsv457650 CNV gain 19166990
nsv513461 CNV insertion 21212237
nsv574267 CNV loss 21841781
nsv574268 CNV gain 21841781
nsv574269 CNV gain 21841781
nsv833345 CNV loss 17160897

Variation tolerance for SPNS3 Gene

Residual Variation Intolerance Score: 89.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.87; 74.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPNS3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPNS3 Gene

Disorders for SPNS3 Gene

Additional Disease Information for SPNS3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SPNS3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SPNS3 Gene

Publications for SPNS3 Gene

  1. Identification of six putative human transporters with structural similarity to the drug transporter SLC22 family. (PMID: 17714910) Jacobsson JA … Fredriksson R (Genomics 2007) 2 3 4 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58
  5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PMID: 23251661) Comuzzie AG … Butte NF (PloS one 2012) 3 58

Products for SPNS3 Gene

Sources for SPNS3 Gene

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