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SPHK2 sphingosine kinase 2 [ Homo sapiens (human) ]

Gene ID: 56848, updated on 1-Jun-2020

Summary

Official Symbol
SPHK2provided by HGNC
Official Full Name
sphingosine kinase 2provided by HGNC
Primary source
HGNC:HGNC:18859
See related
Ensembl:ENSG00000063176 MIM:607092
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

Genomic context

See SPHK2 in Genome Data Viewer
Location:
19q13.33
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (48619291..48630407)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (49122548..49133974)

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 ribosomal protein L18 Neighboring gene D-box binding PAR bZIP transcription factor Neighboring gene secretory blood group 1, pseudogene Neighboring gene carbonic anhydrase 11 Neighboring gene netrin 5

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

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
D-erythro-sphingosine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
D-erythro-sphingosine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
NAD+ kinase activity IEA
Inferred from Electronic Annotation
more info
 
Ras GTPase binding NAS
Non-traceable Author Statement
more info
PubMed 
lipid kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleosomal histone binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sphinganine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
sphingosine-1-phosphate receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
blood vessel development IEA
Inferred from Electronic Annotation
more info
 
brain development IEA
Inferred from Electronic Annotation
more info
 
cellular response to phorbol 13-acetate 12-myristate IDA
Inferred from Direct Assay
more info
PubMed 
cytokine secretion involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
female pregnancy IEA
Inferred from Electronic Annotation
more info
 
histone H2A-K5 acetylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H2B-K12 acetylation IDA
Inferred from Direct Assay
more info
PubMed 
interleukin-13 secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
interleukin-6 secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
lipid phosphorylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell growth ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of histone deacetylation IDA
Inferred from Direct Assay
more info
PubMed 
phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of apoptotic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of calcium ion import ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ceramide biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression, epigenetic IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of histone H3-K9 acetylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mast cell activation involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of mast cell degranulation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein kinase C signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of ATP biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of I-kappaB kinase/NF-kappaB signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cytochrome-c oxidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of reactive oxygen species biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
sphinganine-1-phosphate biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphinganine-1-phosphate biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
 
sphingolipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingosine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sphingosine biosynthetic process IGI
Inferred from Genetic Interaction
more info
PubMed 
sphingosine biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
sphingosine metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
sphingosine-1-phosphate receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
tumor necrosis factor secretion ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
lysosomal membrane HDA PubMed 
membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
sphingosine kinase 2
Names
sphingosine kinase type 2
NP_001191087.1
NP_001191088.1
NP_001191089.1
NP_001230805.1
NP_064511.2
XP_006723355.1
XP_011525435.1
XP_011525436.1
XP_016882497.1
XP_016882499.1

NCBI Reference Sequences (RefSeq)

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_001204158.3NP_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/Swiss-Prot
    Q9NRA0
    UniProtKB/TrEMBL
    B3KV83
    Related
    ENSP00000470092.1, ENST00000600537.5
    Conserved Domains (1) summary
    pfam00781
    Location:128262
    DAGK_cat; Diacylglycerol kinase catalytic domain
  2. NM_001204159.3NP_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
    Q9NRA0
    UniProtKB/TrEMBL
    A0A024QZH5
    Related
    ENSP00000469158.1, ENST00000598088.5
    Conserved Domains (1) summary
    pfam00781
    Location:187321
    DAGK_cat; Diacylglycerol kinase catalytic domain
  3. NM_001204160.3NP_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/Swiss-Prot
    Q9NRA0
    Related
    ENSP00000471205.1, ENST00000599748.5
    Conserved Domains (1) summary
    pfam00781
    Location:151285
    DAGK_cat; Diacylglycerol kinase catalytic domain
  4. NM_001243876.1NP_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, BI224962, DA926908, DB367710
    Consensus CDS
    CCDS74414.1
    UniProtKB/TrEMBL
    B3KV83, E9PCV4
    Related
    ENSP00000341091.4, ENST00000340932.7
    Conserved Domains (1) summary
    pfam00781
    Location:1115
    DAGK_cat; Diacylglycerol kinase catalytic domain
  5. NM_020126.5NP_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
    Q9NRA0
    UniProtKB/TrEMBL
    A0A024QZH5
    Related
    ENSP00000245222.3, ENST00000245222.9
    Conserved Domains (1) summary
    pfam00781
    Location:187321
    DAGK_cat; Diacylglycerol kinase catalytic domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    48619291..48630407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017027010.2XP_016882499.1  sphingosine kinase 2 isoform X4

    Conserved Domains (1) summary
    pfam00781
    Location:187287
    DAGK_cat; Diacylglycerol kinase catalytic domain
  2. XM_011527133.1XP_011525435.1  sphingosine kinase 2 isoform X2

    See identical proteins and their annotated locations for XP_011525435.1

    UniProtKB/Swiss-Prot
    Q9NRA0
    UniProtKB/TrEMBL
    A0A024QZH5
    Conserved Domains (1) summary
    pfam00781
    Location:187321
    DAGK_cat; Diacylglycerol kinase catalytic domain
  3. XM_006723292.1XP_006723355.1  sphingosine kinase 2 isoform X3

    See identical proteins and their annotated locations for XP_006723355.1

    UniProtKB/Swiss-Prot
    Q9NRA0
    Conserved Domains (1) summary
    pfam00781
    Location:151285
    DAGK_cat; Diacylglycerol kinase catalytic domain
  4. XM_011527134.1XP_011525436.1  sphingosine kinase 2 isoform X3

    See identical proteins and their annotated locations for XP_011525436.1

    UniProtKB/Swiss-Prot
    Q9NRA0
    Conserved Domains (1) summary
    pfam00781
    Location:151285
    DAGK_cat; Diacylglycerol kinase catalytic domain
  5. XM_017027008.1XP_016882497.1  sphingosine kinase 2 isoform X1

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