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SPHK2 sphingosine kinase 2 [ Homo sapiens (human) ]

Gene ID: 56848, updated on 27-Nov-2024

Summary

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Official Symbol
SPHK2provided by HGNC
Official Full Name
sphingosine kinase 2provided by HGNC
Primary source
HGNC:HGNC:18859
See related
Ensembl:ENSG00000063176 MIM:607092; AllianceGenome:HGNC:18859
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
SK 2; SK-2; SPK 2; SPK-2
Summary
This gene encodes one of two sphingosine kinase isozymes that catalyze the phosphorylation of sphingosine into sphingosine 1-phosphate. Sphingosine 1-phosphate mediates many cellular processes including migration, proliferation and apoptosis, and also plays a role in several types of cancer by promoting angiogenesis and tumorigenesis. The encoded protein may play a role in breast cancer proliferation and chemoresistance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in kidney (RPKM 6.4), duodenum (RPKM 5.5) and 25 other tissues See more
Orthologs
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Genomic context

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See SPHK2 in Genome Data Viewer
Location:
19q13.33
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48619506..48630405)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51613990..51624887)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (49122763..49133662)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 83 member E Neighboring gene sperm acrosome associated 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49117268-49117444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49117749-49118580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49118581-49119412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49119413-49120243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:49121076-49121906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14903 Neighboring gene ribosomal protein L18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10889 Neighboring gene Sharpr-MPRA regulatory region 2382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49130943-49131443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10890 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10893 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14904 Neighboring gene D-box binding PAR bZIP transcription factor Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:49147372-49148073 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49148074-49148774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49148775-49149475 Neighboring gene secretory blood group 1, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10897 Neighboring gene carbonic anhydrase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49166921-49167422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49167423-49167922 Neighboring gene netrin 5

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. Down-regulation of sphingosine kinase 2 (SphK2) increases the effects of all-trans-retinoic acid (ATRA) on colon cancer cells. Chu JH, et al. Biomed Pharmacother, 2014 Oct. PMID 25455157
  2. Metabolic Adaptation of Airway Smooth Muscle Cells to an SPHK2 Substrate Precedes Cytostasis. Blais-Lecours P, et al. Am J Respir Cell Mol Biol, 2020 Jan. PMID 31247144, Free PMC Article
  3. Decreased S1P and SPHK2 are involved in pancreatic acinar cell injury. Xiao J, et al. Biomark Med, 2019 Jun. PMID 31157539
  4. Sphingosine kinase 2: a controversial role in arthritis. Xu T, et al. Rheumatol Int, 2014 Jul. PMID 23881266
  5. In vitro and in vivo roles of sphingosine kinase 2 during dengue virus infection. Al-Shujairi WH, et al. J Gen Virol, 2019 Apr. PMID 30869582

See all (114) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Sphingosine kinase 2 and p62 regulation are determinants of sexual dimorphism in hepatocellular carcinoma.
    Title: Sphingosine kinase 2 and p62 regulation are determinants of sexual dimorphism in hepatocellular carcinoma.
  2. YTHDF1-mediated sphingosine kinase 2 upregulation alleviates bupivacaine-induced neurotoxicity via the PI3K/AKT axis.
    Title: YTHDF1-mediated sphingosine kinase 2 upregulation alleviates bupivacaine-induced neurotoxicity via the PI3K/AKT axis.
  3. The accumulation of sphingosine kinase 2 disrupts the DNA damage response and promotes resistance to genotoxic agents.
    Title: The accumulation of sphingosine kinase 2 disrupts the DNA damage response and promotes resistance to genotoxic agents.
  4. Accumulation of sphingosine kinase 2 protein induces malignant transformation in oral keratinocytes associated with stemness, autophagy, senescence, and proliferation.
    Title: Accumulation of sphingosine kinase 2 protein induces malignant transformation in oral keratinocytes associated with stemness, autophagy, senescence, and proliferation.
  5. Inhibition of Sphingosine Kinase 2 Results in PARK2-Mediated Mitophagy and Induces Apoptosis in Multiple Myeloma.
    Title: Inhibition of Sphingosine Kinase 2 Results in PARK2-Mediated Mitophagy and Induces Apoptosis in Multiple Myeloma.
  6. Sphingosine kinase 2 regulates insulin receptor trafficking in hepatocytes.
    Title: Sphingosine kinase 2 regulates insulin receptor trafficking in hepatocytes.
  7. miR-153-3p Attenuates the Development of Gastric Cancer by Suppressing SphK2.
    Title: miR-153-3p Attenuates the Development of Gastric Cancer by Suppressing SphK2.
  8. Enzymatic independent role of sphingosine kinase 2 in regulating the expression of type I interferon during influenza A virus infection.
    Title: Enzymatic independent role of sphingosine kinase 2 in regulating the expression of type I interferon during influenza A virus infection.
  9. Loss of sphingosine kinase 2 protects against cisplatin-induced kidney injury.
    Title: Loss of sphingosine kinase 2 protects against cisplatin-induced kidney injury.
  10. Upregulated flotillins and sphingosine kinase 2 derail AXL vesicular traffic to promote epithelial-mesenchymal transition.
    Title: Upregulated flotillins and sphingosine kinase 2 derail AXL vesicular traffic to promote epithelial-mesenchymal transition.
Submit: New GeneRIF Correction See all GeneRIFs (84)

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
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
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 histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables lipid kinase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding NAS
Non-traceable Author Statement
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 blood vessel development IEA
Inferred from Electronic Annotation
more info
  
involved_in brain development IEA
Inferred from Electronic Annotation
more info
  
involved_in cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to phorbol 13-acetate 12-myristate IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in female pregnancy IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of cell growth ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cytokine production involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of interleukin-13 production ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of interleukin-6 production ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of mast cell activation involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of mast cell degranulation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of tumor necrosis factor production ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of ATP biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of canonical NF-kappaB signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of cytochrome-c oxidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of reactive oxygen species biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in sphinganine-1-phosphate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphinganine-1-phosphate biosynthetic process IDA
Inferred from Direct Assay
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in sphingosine-1-phosphate receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription initiation-coupled chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
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
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum 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
  
located_in lysosomal membrane HDA PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of nucleosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
sphingosine kinase 2
NP_001191087.1
NP_001191088.1
NP_001191089.1
NP_001230805.1
NP_064511.2

NCBI Reference Sequences (RefSeq)

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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.

Genomic

  1. NG_029867.1 RefSeqGene

    Range
    5216..16115
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001204158.3 → NP_001191087.1  sphingosine kinase 2 isoform b

    See identical proteins and their annotated locations for NP_001191087.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AK122735, AK300541, DB367710
    Consensus CDS
    CCDS59404.1
    UniProtKB/TrEMBL
    B3KV83
    Related
    ENSP00000470092.1, ENST00000600537.5
    Conserved Domains (1) summary
    pfam00781
    Location:128 → 262
    DAGK_cat; Diacylglycerol kinase catalytic domain

  2. NM_001204159.3 → NP_001191088.1  sphingosine kinase 2 isoform a

    See identical proteins and their annotated locations for NP_001191088.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 both encode the same isoform (a).
    Source sequence(s)
    AC022154, AF245447, AL136701, DB053266
    Consensus CDS
    CCDS12727.1
    UniProtKB/Swiss-Prot
    A0T4C8, B4DU87, Q9BRN1, Q9H0Q2, Q9NRA0, Q9NWU7
    UniProtKB/TrEMBL
    B3KV83
    Related
    ENSP00000469158.1, ENST00000598088.5
    Conserved Domains (1) summary
    pfam00781
    Location:187 → 321
    DAGK_cat; Diacylglycerol kinase catalytic domain

  3. NM_001204160.3 → NP_001191089.1  sphingosine kinase 2 isoform c

    See identical proteins and their annotated locations for NP_001191089.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    BC010671
    Consensus CDS
    CCDS59405.1
    UniProtKB/TrEMBL
    M0R344
    Related
    ENSP00000471205.1, ENST00000599748.5
    Conserved Domains (1) summary
    pfam00781
    Location:151 → 285
    DAGK_cat; Diacylglycerol kinase catalytic domain

  4. NM_001243876.2 → NP_001230805.1  sphingosine kinase 2 isoform d

    See identical proteins and their annotated locations for NP_001230805.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an exon in the coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK122735, DA926908, DB367710
    Consensus CDS
    CCDS74414.1
    UniProtKB/TrEMBL
    E9PCV4
    Related
    ENSP00000341091.4, ENST00000340932.7
    Conserved Domains (2) summary
    PLN02958
    Location:1 → 175
    PLN02958; diacylglycerol kinase/D-erythro-sphingosine kinase
    PHA03247
    Location:149 → 310
    PHA03247; large tegument protein UL36; Provisional

  5. NM_020126.5 → NP_064511.2  sphingosine kinase 2 isoform a

    See identical proteins and their annotated locations for NP_064511.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 3 both encode the same isoform (a).
    Source sequence(s)
    BC006161
    Consensus CDS
    CCDS12727.1
    UniProtKB/Swiss-Prot
    A0T4C8, B4DU87, Q9BRN1, Q9H0Q2, Q9NRA0, Q9NWU7
    UniProtKB/TrEMBL
    B3KV83
    Related
    ENSP00000245222.3, ENST00000245222.9
    Conserved Domains (1) summary
    pfam00781
    Location:187 → 321
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    48619506..48630405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    51613990..51624887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NRA0.2 GenPept UniProtKB/Swiss-Prot:Q9NRA0

Gene LinkOut

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