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SPNS1 Gene(Protein Coding)

Sphingolipid Transporter 1 (Putative)

GCID:
GC16P028974
GIFtS:
42
Genes Participants
UDN Logo

Aliases for SPNS1 Gene

Aliases for SPNS1 Gene

  • Sphingolipid Transporter 1 (Putative) 2 3 5
  • Spinster-Like Protein 1 3 4
  • HSpin1 3 4
  • SPIN1 3 4
  • SPNS Sphingolipid Transporter 1 (Putative) 3
  • Spinster Homolog 1 (Drosophila) 2
  • Protein Spinster Homolog 1 3
  • Spinster Homolog 1 3
  • PP2030 3
  • SPINL 3
  • LAT 3
  • Nrs 3

External Ids for SPNS1 Gene

Previous GeneCards Identifiers for SPNS1 Gene

  • GC16P028897
  • GC16P028986
  • GC16P026853

Summaries for SPNS1 Gene

GeneCards Summary for SPNS1 Gene

SPNS1 (Sphingolipid Transporter 1 (Putative)) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include transporter activity and sphingolipid transporter activity. An important paralog of this gene is SPNS2.

UniProtKB/Swiss-Prot for SPNS1 Gene

  • Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death.

Additional gene information for SPNS1 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 SPNS1 Gene

Genomics for SPNS1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SPNS1 Gene

Promoters and enhancers for SPNS1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH16I028973 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 572.3 +0.5 501 2.4 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF416 ZNF143 SPNS1 ENSG00000261067 ENSG00000261766 ATXN2L NPIPB12 NFATC2IP ENSG00000260853 CDIPT SULT1A2 ENSG00000247735
GH16I029803 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 58.9 +834.2 834222 10.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 PRRT2 ENSG00000259952 ENSG00000280607 GC16P029807 GC16P029809 GC16P029941 PIR38319 MAZ PIR52049 PIR43581
GH16I029862 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 41.8 +888.9 888901 2.1 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC CDIPT-AS1 CDIPT ENSG00000278713 SRCAP SPNS1 INO80E ENSG00000260853 NFATC2IP PRR14 ENSG00000260367
GH16I029273 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 53.2 +299.7 299679 0.6 HDGF PKNOX1 FOXA2 ARNT YBX1 ZBTB7B TCF12 ZNF280A E2F8 ZNF207 ENSG00000277999 ENSG00000260853 NPIPB12 ATXN2L INO80E SPNS1 NFATC2IP NPIPB13 ENSG00000260367 SMG1P2
GH16I029942 Enhancer 1.6 FANTOM5 Ensembl ENCODE 47.8 +969.8 969761 3.7 FEZF1 ZNF213 SP3 MEF2D ZNF610 GLIS1 RCOR2 NBN KDM1A WT1 INO80E SRCAP ENSG00000260853 ZNF785 NPIPB12 SPNS1 ENSG00000260367 PRR14 SMG1P5 NFATC2IP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SPNS1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SPNS1 gene promoter:

Genomic Locations for SPNS1 Gene

Genomic Locations for SPNS1 Gene
chr16:28,974,221-28,984,762
(GRCh38/hg38)
Size:
10,542 bases
Orientation:
Plus strand
chr16:28,985,542-28,995,869
(GRCh37/hg19)

Genomic View for SPNS1 Gene

Genes around SPNS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPNS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPNS1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SPNS1 Gene

Proteins for SPNS1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SPNS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H2V7-SPNS1_HUMAN
    Recommended name:
    Protein spinster homolog 1
    Protein Accession:
    Q9H2V7
    Secondary Accessions:
    • B5MDM9
    • Q6P182
    • Q71RB5
    • Q7L541
    • Q86VU7
    • Q8N953
    • Q8TCS5
    • Q9BRN5

    Protein attributes for SPNS1 Gene

    Size:
    528 amino acids
    Molecular mass:
    56630 Da
    Quaternary structure:
    • Interacts with BCL2 and BCL2L1.
    SequenceCaution:
    • Sequence=AAQ15259.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAQ15259.1; Type=Frameshift; Positions=97; Evidence={ECO:0000305};

    Alternative splice isoforms for SPNS1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPNS1 Gene

Protein Expression for SPNS1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SPNS1 Gene

No Post-translational modifications

Other Protein References for SPNS1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPNS1 Gene

Domains & Families for SPNS1 Gene

Gene Families for SPNS1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SPNS1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SPNS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H2V7

UniProtKB/Swiss-Prot:

SPNS1_HUMAN :
  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
Family:
  • Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.
genes like me logo Genes that share domains with SPNS1: view

Function for SPNS1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for SPNS1 Gene

UniProtKB/Swiss-Prot Function:
Sphingolipid transporter (By similarity). May be involved in necrotic or autophagic cell death.

Phenotypes From GWAS Catalog for SPNS1 Gene

Gene Ontology (GO) - Molecular Function for SPNS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12815463
GO:0046624 sphingolipid transporter activity IBA --
genes like me logo Genes that share ontologies with SPNS1: view
genes like me logo Genes that share phenotypes with SPNS1: view

Animal Models for SPNS1 Gene

MGI Knock Outs for SPNS1:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SPNS1 Gene

Localization for SPNS1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPNS1 Gene

Mitochondrion inner membrane; Multi-pass membrane protein. Note=Colocalizes with SDHB.

Subcellular locations from

COMPARTMENTS
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 SPNS1 gene
Compartment Confidence
lysosome 5
plasma membrane 3
mitochondrion 3
nucleus 2
cytosol 2
golgi apparatus 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
  • Cytosol (1)
  • Golgi apparatus (1)
  • Nucleoli fibrillar center (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPNS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005743 mitochondrial inner membrane IEA --
GO:0005765 lysosomal membrane IDA,HDA 17897319
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SPNS1: view

Pathways & Interactions for SPNS1 Gene

SuperPathways for SPNS1 Gene

PathCards logo More details on SuperPathways for SPNS1
No Data Available

Gene Ontology (GO) - Biological Process for SPNS1 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 SPNS1: view

No data available for Pathways by source and SIGNOR curated interactions for SPNS1 Gene

Drugs & Compounds for SPNS1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SPNS1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SPNS1 Gene

(9) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(322) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SPNS1 Gene

Spinster homolog 1 (Drosophila):
Representative Sequences:

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPNS1 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c
SP1: -
SP2:
SP3: -
SP4: - - - - - -
SP5: -
SP6: - - - - -
SP7: -
SP8: - - - - - - - -
SP9: -

Relevant External Links for SPNS1 Gene

GeneLoc Exon Structure for
SPNS1
ECgene alternative splicing isoforms for
SPNS1

Expression for SPNS1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SPNS1 Gene

mRNA expression in normal human tissues for SPNS1 Gene
mRNA expression by GTEx for SPNS1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPNS1 Gene

This gene is overexpressed in Adrenal (13.0), Peripheral blood mononuclear cells (10.9), Monocytes (7.3), and Lung (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SPNS1 Gene



Protein tissue co-expression partners for SPNS1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SPNS1 Gene:

SPNS1

SOURCE GeneReport for Unigene cluster for SPNS1 Gene:

Hs.617449

Evidence on tissue expression from TISSUES for SPNS1 Gene

  • Nervous system(4.7)
  • Skin(4.6)
  • Blood(4.4)
  • Pancreas(4.4)
  • Eye(2.7)
  • Lung(2.3)
genes like me logo Genes that share expression patterns with SPNS1: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPNS1 Gene

Orthologs for SPNS1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SPNS1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SPNS1 33 34
  • 99.81 (n)
dog
(Canis familiaris)
 Mammalia SPNS1 33 34
  • 91.25 (n)
cow
(Bos Taurus)
 Mammalia SPNS1 33 34
  • 91.04 (n)
mouse
(Mus musculus)
 Mammalia Spns1 33 16 34
  • 87.88 (n)
rat
(Rattus norvegicus)
 Mammalia Spns1 33
  • 87.75 (n)
oppossum
(Monodelphis domestica)
 Mammalia SPNS1 34
  • 86 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia SPNS1 34
  • 82 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SPNS1 34
  • 71 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia spns1 33
  • 69.92 (n)
Str.16886 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.16646 33
zebrafish
(Danio rerio)
 Actinopterygii spns1 33 34
  • 64.81 (n)
spinl 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006346 33
  • 56.05 (n)
fruit fly
(Drosophila melanogaster)
 Insecta spin 33 34
  • 54.4 (n)
worm
(Caenorhabditis elegans)
 Secernentea C13C4.5 33
  • 45.99 (n)
spin-2 34
  • 38 (a)
 ManyToMany
spin-1 34
  • 36 (a)
 ManyToMany
spin-3 34
  • 36 (a)
 ManyToMany
spin-4 34
  • 36 (a)
 ManyToMany
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G65687 33
  • 39.16 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.5353 34
  • 33 (a)
 OneToMany
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.12624 33
Species where no ortholog for SPNS1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • chicken (Gallus gallus)
  • 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 urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SPNS1 Gene

ENSEMBL:
Gene Tree for SPNS1 (if available)
TreeFam:
Gene Tree for SPNS1 (if available)

Paralogs for SPNS1 Gene

Paralogs for SPNS1 Gene

(2) SIMAP similar genes for SPNS1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with SPNS1: view

Variants for SPNS1 Gene

Sequence variations from dbSNP and Humsavar for SPNS1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000370819 -- 28,980,318(+) A/G intron_variant
rs1000392918 -- 28,974,166(+) C/T upstream_transcript_variant
rs1000443518 -- 28,974,002(+) T/C upstream_transcript_variant
rs1000480150 -- 28,974,580(+) A/C upstream_transcript_variant
rs1001129876 -- 28,985,089(+) G/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SPNS1 Gene

Variant ID Type Subtype PubMed ID
nsv952964 CNV deletion 24416366
nsv571808 CNV gain 21841781
nsv571805 CNV loss 21841781
nsv519100 CNV gain 19592680
nsv518648 CNV loss 19592680
nsv457480 CNV gain 19166990
nsv1059555 CNV gain 25217958
esv3892826 CNV gain+loss 25118596
esv3638351 CNV gain 21293372
esv3582129 CNV loss 25503493
esv3570454 CNV gain 25503493
esv2758640 CNV gain+loss 17122850
dgv4987n54 CNV gain 21841781
dgv2831n100 CNV gain 25217958
dgv2830n100 CNV gain 25217958

Variation tolerance for SPNS1 Gene

Residual Variation Intolerance Score: 25.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.33; 53.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPNS1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPNS1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPNS1 Gene

Disorders for SPNS1 Gene

Additional Disease Information for SPNS1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SPNS1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SPNS1 Gene

Publications for SPNS1 Gene

  1. HSpin1, a transmembrane protein interacting with Bcl-2/Bcl-xL, induces a caspase-independent autophagic cell death. (PMID: 12815463) Yanagisawa H … Yamamoto D (Cell death and differentiation 2003) 2 3 4 58
  2. Mutations in the novel membrane protein spinster interfere with programmed cell death and cause neural degeneration in Drosophila melanogaster. (PMID: 11340170) Nakano Y … Yamamoto D (Molecular and cellular biology 2001) 2 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. N-terminome analysis of the human mitochondrial proteome. (PMID: 25944712) Vaca Jacome AS … Carapito C (Proteomics 2015) 4 58
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58

Products for SPNS1 Gene

Sources for SPNS1 Gene

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