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    SPNS1 SPNS lysolipid transporter 1, lysophospholipid [ Homo sapiens (human) ]

    Gene ID: 83985, updated on 17-Jun-2024

    Summary

    Official Symbol
    SPNS1provided by HGNC
    Official Full Name
    SPNS lysolipid transporter 1, lysophospholipidprovided by HGNC
    Primary source
    HGNC:HGNC:30621
    See related
    Ensembl:ENSG00000169682 MIM:612583; AllianceGenome:HGNC:30621
    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
    LAT; nrs; SPIN1; SPINL; HSpin1; PP2030; SLC62A1; SLC63A1
    Summary
    Predicted to enable transmembrane transporter activity. Predicted to be involved in lipid transport and transmembrane transport. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in lung (RPKM 11.3), placenta (RPKM 11.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPNS1 in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (28974778..28984765)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29255893..29265880)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (28986099..28995864)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NFATC2IP antisense RNA 1 Neighboring gene nuclear factor of activated T cells 2 interacting protein Neighboring gene ReSE screen-validated silencer GRCh37_chr16:28973628-28973836 Neighboring gene microRNA 4517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7324 Neighboring gene MPRA-validated peak2553 silencer Neighboring gene linker for activation of T cells Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29036345-29036846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7325 Neighboring gene nuclear pore complex interacting protein family, member B10, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ38358

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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 lysophospholipid transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in phospholipid efflux IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of lysosomal lumen pH IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in lysosomal membrane HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrial inner membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    protein spinster homolog 1
    Names
    SPNS sphingolipid transporter 1 (putative)
    solute carrier family 63 member 1
    sphingolipid transporter 1 (putative)
    spinster homolog 1
    spinster-like protein 1

    NCBI Reference Sequences (RefSeq)

    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_001142448.2NP_001135920.1  protein spinster homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_001135920.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode isoform 1.
      Source sequence(s)
      BC008325, BC065235, BG771918, CD368853
      Consensus CDS
      CCDS10646.1
      UniProtKB/Swiss-Prot
      B5MDM9, Q6P182, Q71RB5, Q7L541, Q86VU7, Q8N953, Q8TCS5, Q9BRN5, Q9H2V7
      Related
      ENSP00000454360.1, ENST00000565975.5
      Conserved Domains (1) summary
      cd17328
      Location:62479
      MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters
    2. NM_001142449.2NP_001135921.1  protein spinster homolog 1 isoform 4

      See identical proteins and their annotated locations for NP_001135921.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL390215, BG771918, CD368853
      Consensus CDS
      CCDS45453.1
      UniProtKB/Swiss-Prot
      Q9H2V7
      Related
      ENSP00000306050.10, ENST00000352260.11
      Conserved Domains (2) summary
      cd06174
      Location:62376
      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:79337
      MFS_1; Major Facilitator Superfamily
    3. NM_001142450.2NP_001135922.1  protein spinster homolog 1 isoform 2

      See identical proteins and their annotated locations for NP_001135922.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AL524908, BC008325, BG771918, CD368853
      Consensus CDS
      CCDS45454.1
      Related
      ENSP00000318228.8, ENST00000323081.12
      Conserved Domains (1) summary
      cd17328
      Location:1406
      MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters
    4. NM_001142451.2NP_001135923.1  protein spinster homolog 1 isoform 3

      See identical proteins and their annotated locations for NP_001135923.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      BC047741, BG771918
      Consensus CDS
      CCDS45452.1
      UniProtKB/Swiss-Prot
      Q9H2V7
      Related
      ENSP00000335494.8, ENST00000334536.12
      Conserved Domains (2) summary
      cd06174
      Location:62398
      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:65359
      MFS_1; Major Facilitator Superfamily
    5. NM_032038.3NP_114427.1  protein spinster homolog 1 isoform 1

      See identical proteins and their annotated locations for NP_114427.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 2 both encode isoform 1.
      Source sequence(s)
      BC008325, BG771918, CD368853
      Consensus CDS
      CCDS10646.1
      UniProtKB/Swiss-Prot
      B5MDM9, Q6P182, Q71RB5, Q7L541, Q86VU7, Q8N953, Q8TCS5, Q9BRN5, Q9H2V7
      Related
      ENSP00000309945.11, ENST00000311008.16
      Conserved Domains (1) summary
      cd17328
      Location:62479
      MFS_spinster_like; Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      28974778..28984765
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434739.1XP_047290695.1  protein spinster homolog 1 isoform X1

      UniProtKB/TrEMBL
      H3BR82
      Related
      ENSP00000456119.1, ENST00000566059.5
    2. XM_047434741.1XP_047290697.1  protein spinster homolog 1 isoform X4

    3. XM_006721096.5XP_006721159.1  protein spinster homolog 1 isoform X3

      Conserved Domains (2) summary
      cd06174
      Location:107472
      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:110404
      MFS_1; Major Facilitator Superfamily
    4. XM_047434740.1XP_047290696.1  protein spinster homolog 1 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      29255893..29265880
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314109.1XP_054170084.1  protein spinster homolog 1 isoform X1

      UniProtKB/TrEMBL
      H3BR82
    2. XM_054314112.1XP_054170087.1  protein spinster homolog 1 isoform X4

    3. XM_054314111.1XP_054170086.1  protein spinster homolog 1 isoform X3

    4. XM_054314110.1XP_054170085.1  protein spinster homolog 1 isoform X2