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    SPNS3 SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative) [ Homo sapiens (human) ]

    Gene ID: 201305, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SPNS3provided by HGNC
    Official Full Name
    SPNS lysolipid transporter 3, sphingosine-1-phosphate (putative)provided by HGNC
    Primary source
    HGNC:HGNC:28433
    See related
    Ensembl:ENSG00000182557 MIM:611701; AllianceGenome:HGNC:28433
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SLC62A3; SLC63A3
    Summary
    Predicted to enable transmembrane transporter activity. Predicted to be involved in lipid transport and transmembrane transport. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in bone marrow (RPKM 8.7), spleen (RPKM 1.4) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPNS3 in Genome Data Viewer
    Location:
    17p13.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4433940..4488204)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4323199..4378061)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4337235..4391499)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ubiquitin conjugating enzyme E2 G1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4220485-4221252 Neighboring gene major facilitator superfamily domain containing 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4236451-4237364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4240300-4241080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8034 Neighboring gene Sharpr-MPRA regulatory region 13848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11539 Neighboring gene RNA, 7SL, cytoplasmic 774, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:4286079-4286578 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8037 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4298989-4299759 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4299760-4300529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4315987-4316488 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4337297-4337951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4342684-4343184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4351479-4351979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4353153-4353653 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4379777-4380645 Neighboring gene uncharacterized LOC124903899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4384268-4385023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11541 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:4392946-4394145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8039 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4402340-4402975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4402976-4403610 Neighboring gene SPNS2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4405882-4406398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4406399-4406914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4407104-4407604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4407605-4408105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4408166-4408835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4408836-4409504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4415494-4416140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4417497-4418154 Neighboring gene SPNS lysolipid transporter 2, sphingosine-1-phosphate Neighboring gene MYB binding protein 1a

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia. Hong Y, et al. Bioengineered, 2021 Dec. PMID 34608834, Free PMC Article
    2. Upregulation of FHL1, SPNS3, and MPZL2 predicts poor prognosis in pediatric acute myeloid leukemia patients with FLT3-ITD mutation. Eshibona N, et al. Leuk Lymphoma, 2022 Aug. PMID 35249471
    3. Identification of six putative human transporters with structural similarity to the drug transporter SLC22 family. Jacobsson JA, et al. Genomics, 2007 Nov. PMID 17714910
    4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Upregulation of FHL1, SPNS3, and MPZL2 predicts poor prognosis in pediatric acute myeloid leukemia patients with FLT3-ITD mutation.
      Title: Upregulation of FHL1, SPNS3, and MPZL2 predicts poor prognosis in pediatric acute myeloid leukemia patients with FLT3-ITD mutation.
    2. Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia.
      Title: Bioinformatics-based identification of SPNS3 (Spinster homolog 3) as a prognostic biomarker of apoptosis resistance in acute myeloid leukemia.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC29671

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein spinster homolog 3
    Names
    SPNS sphingolipid transporter 3 (putative)
    solute carrier family 63 member 3
    sphingolipid transporter 3 (putative)
    spinster homolog 3

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001320449.2 → NP_001307378.1  protein spinster homolog 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC116910, AK172832, BC023646
      UniProtKB/Swiss-Prot
      Q6ZMD2
      Conserved Domains (2) summary
      cd06174
      Location:10 → 339
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:9 → 287
      MFS_1; Major Facilitator Superfamily

    2. NM_182538.5 → NP_872344.3  protein spinster homolog 3 isoform 1

      See identical proteins and their annotated locations for NP_872344.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC116910, AC127521, AK172832
      Consensus CDS
      CCDS11045.1
      UniProtKB/Swiss-Prot
      Q6ZMD2, Q8IZ31
      Related
      ENSP00000347721.2, ENST00000355530.7
      Conserved Domains (2) summary
      cd06174
      Location:49 → 466
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:51 → 414
      MFS_1; Major Facilitator Superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      4433940..4488204
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435588.1 → XP_047291544.1  protein spinster homolog 3 isoform X4

    2. XM_011523724.1 → XP_011522026.1  protein spinster homolog 3 isoform X2

      Conserved Domains (2) summary
      cd06174
      Location:49 → 393
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:51 → 389
      MFS_1; Major Facilitator Superfamily

    3. XM_011523723.1 → XP_011522025.1  protein spinster homolog 3 isoform X1

      Conserved Domains (2) summary
      cd06174
      Location:49 → 374
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:51 → 374
      MFS_1; Major Facilitator Superfamily

    4. XM_011523725.1 → XP_011522027.1  protein spinster homolog 3 isoform X3

      Conserved Domains (2) summary
      cd06174
      Location:49 → 415
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:51 → 363
      MFS_1; Major Facilitator Superfamily

    5. XM_047435589.1 → XP_047291545.1  protein spinster homolog 3 isoform X5

    6. XM_011523728.3 → XP_011522030.1  protein spinster homolog 3 isoform X6

      Conserved Domains (1) summary
      pfam07690
      Location:4 → 218
      MFS_1; Major Facilitator Superfamily

    7. XM_017024345.3 → XP_016879834.1  protein spinster homolog 3 isoform X7

      Conserved Domains (1) summary
      cd17328
      Location:16 → 223
      MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters

    RNA

    1. XR_934008.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      4323199..4378061
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315417.1 → XP_054171392.1  protein spinster homolog 3 isoform X4

    2. XM_054315415.1 → XP_054171390.1  protein spinster homolog 3 isoform X2

    3. XM_054315414.1 → XP_054171389.1  protein spinster homolog 3 isoform X1

    4. XM_054315416.1 → XP_054171391.1  protein spinster homolog 3 isoform X3

    5. XM_054315418.1 → XP_054171393.1  protein spinster homolog 3 isoform X5

    6. XM_054315419.1 → XP_054171394.1  protein spinster homolog 3 isoform X6

    7. XM_054315420.1 → XP_054171395.1  protein spinster homolog 3 isoform X7

    RNA

    1. XR_008484797.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZMD2.2 GenPept UniProtKB/Swiss-Prot:Q6ZMD2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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