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    SPHK1 sphingosine kinase 1 [ Homo sapiens (human) ]

    Gene ID: 8877, updated on 28-Oct-2024

    Summary

    Official Symbol
    SPHK1provided by HGNC
    Official Full Name
    sphingosine kinase 1provided by HGNC
    Primary source
    HGNC:HGNC:11240
    See related
    Ensembl:ENSG00000176170 MIM:603730; AllianceGenome:HGNC:11240
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPHK
    Summary
    The protein encoded by this gene catalyzes the phosphorylation of sphingosine to form sphingosine-1-phosphate (S1P), a lipid mediator with both intra- and extracellular functions. Intracellularly, S1P regulates proliferation and survival, and extracellularly, it is a ligand for cell surface G protein-coupled receptors. This protein, and its product S1P, play a key role in TNF-alpha signaling and the NF-kappa-B activation pathway important in inflammatory, antiapoptotic, and immune processes. Phosphorylation of this protein alters its catalytic activity and promotes its translocation to the plasma membrane. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2017]
    Expression
    Ubiquitous expression in gall bladder (RPKM 4.9), esophagus (RPKM 4.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SPHK1 in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (76383204..76387855)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (77279777..77284428)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (74379285..74383936)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene phosphoribosyl pyrophosphate synthetase associated protein 1 Neighboring gene RNA, U6 small nuclear 24, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74346967-74347514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9012 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74349963-74350827 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 43 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74364234-74364734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74364735-74365235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9015 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:74386817-74386991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74394983-74395483 Neighboring gene ubiquitin conjugating enzyme E2 O Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74418617-74419118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74419119-74419618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74429943-74430443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74432809-74433310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74437133-74437650 Neighboring gene ribosomal protein L7 pseudogene 49 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9016 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:74449240-74449408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12808 Neighboring gene aralkylamine N-acetyltransferase

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of sphingosine kinase 1 (SPHK1) in human B cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables D-erythro-sphingosine kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables D-erythro-sphingosine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables D-erythro-sphingosine kinase activity TAS
    Traceable Author Statement
    more info
     
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables acetyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables calmodulin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lipid binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables lipid kinase activity TAS
    Traceable Author Statement
    more info
     
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein phosphatase 2A binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sphingosine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sphingosine-1-phosphate receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in calcium-mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell population proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to growth factor stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cellular response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to vascular endothelial growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of apoptotic process TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of ceramide biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of NF-kappaB transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of angiogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell growth IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of fibroblast proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of interleukin-17 production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of mitotic cell cycle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of mitotic nuclear division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of non-canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of p38MAPK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of peptidyl-threonine phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of smooth muscle contraction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein acetylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of endocytosis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of endosomal vesicle fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of interleukin-1 beta production IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of microglial cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of neuroinflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of phagocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of tumor necrosis factor-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to tumor necrosis factor IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in sphingoid catabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in sphingolipid biosynthetic process TAS
    Traceable Author Statement
    more info
     
    involved_in sphingosine biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sphingosine biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in sphingosine biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sphingosine metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in sphingosine-1-phosphate receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in clathrin-coated pit IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endocytic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in presynapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in presynapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in presynapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    sphingosine kinase 1
    Names
    SK 1
    SPK 1
    acetyltransferase SPHK1
    NP_001136073.1
    NP_001136074.1
    NP_001342068.1
    NP_068807.2
    NP_892010.2

    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_001142601.2NP_001136073.1  sphingosine kinase 1 isoform 3

      See identical proteins and their annotated locations for NP_001136073.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate in-frame segment in the 5' coding region and uses a downstream start codon, compared to variant 2. Isoform 3 has a shorter N-terminus, compared to isoform 2. Variants 3, 4 and 5 encode the same isoform (3).
      Source sequence(s)
      AK022402, BC030553, DC384776
      Consensus CDS
      CCDS45785.1
      UniProtKB/Swiss-Prot
      Q8N632, Q96GK1, Q9HD92, Q9NY70, Q9NYA1, Q9NYL3
      UniProtKB/TrEMBL
      B3KVB3, Q53ZR5, Q96HV8
      Related
      ENSP00000465726.2, ENST00000592299.6
      Conserved Domains (1) summary
      PLN02958
      Location:11345
      PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
    2. NM_001142602.2NP_001136074.1  sphingosine kinase 1 isoform 3

      See identical proteins and their annotated locations for NP_001136074.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate in-frame segment in the 5' coding region and uses a downstream start codon, compared to variant 2. Isoform 3 has a shorter N-terminus, compared to isoform 2. Variants 3, 4 and 5 encode the same isoform (3).
      Source sequence(s)
      BC030553, BP304783, DC384776
      Consensus CDS
      CCDS45785.1
      UniProtKB/Swiss-Prot
      Q8N632, Q96GK1, Q9HD92, Q9NY70, Q9NYA1, Q9NYL3
      UniProtKB/TrEMBL
      B3KVB3, Q53ZR5, Q96HV8
      Related
      ENSP00000376285.2, ENST00000392496.3
      Conserved Domains (1) summary
      PLN02958
      Location:11345
      PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
    3. NM_001355139.2NP_001342068.1  sphingosine kinase 1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      BC030553, DA482243, DC384776
      Consensus CDS
      CCDS45785.1
      UniProtKB/Swiss-Prot
      Q8N632, Q96GK1, Q9HD92, Q9NY70, Q9NYA1, Q9NYL3
      UniProtKB/TrEMBL
      B3KVB3, Q53ZR5, Q96HV8
      Conserved Domains (1) summary
      PLN02958
      Location:11345
      PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
    4. NM_021972.4NP_068807.2  sphingosine kinase 1 isoform 1

      See identical proteins and their annotated locations for NP_068807.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) has multiple differences in the coding region, compared to variant 2. The resulting protein (isoform 1) has a shorter N-terminus and contains an additional in-frame portion of the 5' coding region, compared to isoform 2.
      Source sequence(s)
      AK022402, BC009419, BC030553, DC384776
      Consensus CDS
      CCDS59297.1
      UniProtKB/TrEMBL
      B3KVB3, Q96HV8
      Related
      ENSP00000468547.1, ENST00000590959.5
      Conserved Domains (1) summary
      cl27661
      Location:25359
      LCB5; Diacylglycerol kinase family enzyme [Lipid transport and metabolism, General function prediction only]
    5. NM_182965.3NP_892010.2  sphingosine kinase 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AK022402, BC030553, DC384776
      Consensus CDS
      CCDS11744.1
      UniProtKB/TrEMBL
      B3KVB3, Q96HV8
      Related
      ENSP00000313681.3, ENST00000323374.8
      Conserved Domains (2) summary
      PLN02958
      Location:97431
      PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
      pfam00781
      Location:102207
      DAGK_cat; Diacylglycerol kinase catalytic domain

    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
      76383204..76387855
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      77279777..77284428
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)