U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 201305, updated on 5-Mar-2024

Summary

Go to the top of the page Help
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 integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in bone marrow (RPKM 8.7), spleen (RPKM 1.4) and 4 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SPNS3 in Genome Data Viewer
Location:
17p13.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4433940..4488204)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4323199..4378061)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC29671

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables transmembrane transporter activity IEA
Inferred from Electronic Annotation
more info
  
enables 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

Go to the top of the page Help
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)

Go to the top of the page Help

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_2023_10

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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous