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SPHK1 sphingosine kinase 1 [ Homo sapiens (human) ]

Gene ID: 8877, updated on 27-Nov-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
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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
  • 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 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)