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SGPP2 sphingosine-1-phosphate phosphatase 2 [ Homo sapiens (human) ]

Gene ID: 130367, updated on 12-Oct-2019

Summary

Official Symbol
SGPP2provided by HGNC
Official Full Name
sphingosine-1-phosphate phosphatase 2provided by HGNC
Primary source
HGNC:HGNC:19953
See related
Ensembl:ENSG00000163082 MIM:612827
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
SPP2; SPPase2
Summary
The protein encoded by this gene is a transmembrane protein that degrades the bioactive signaling molecule sphingosine 1-phosphate. The encoded protein is induced during inflammatory responses and has been shown to be downregulated by the microRNA-31 tumor suppressor. Alternative splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2016]
Expression
Broad expression in thyroid (RPKM 13.7), esophagus (RPKM 12.0) and 18 other tissues See more
Orthologs

Genomic context

See SGPP2 in Genome Data Viewer
Location:
2q36.1
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (222423988..222562621)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223288771..223427342)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene paired box 3 Neighboring gene PAX3 promoter region Neighboring gene coiled-coil domain containing 140 Neighboring gene cancer/testis associated transcript 75 Neighboring gene Nanog homeobox pseudogene 2 Neighboring gene RNA, U6 small nuclear 619, pseudogene Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 49 Neighboring gene phenylalanyl-tRNA synthetase subunit beta Neighboring gene tripartite motif containing 60 pseudogene Neighboring gene uncharacterized LOC105373902 Neighboring gene RRAS2 pseudogene 2 Neighboring gene monoacylglycerol O-acyltransferase 1

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

Pathways from BioSystems

  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Sphingolipid Metabolism, organism-specific biosystem (from WikiPathways)
    Sphingolipid Metabolism, organism-specific biosystemThe sphingolipid metabolites and genes (with the gene abbreviations shown in boxes, or enzyme names where gene names are ambiguous) are given for the condensation of serine and palmitoyl-CoA to form ...
  • Sphingolipid de novo biosynthesis, organism-specific biosystem (from REACTOME)
    Sphingolipid de novo biosynthesis, organism-specific biosystemThe main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
  • Sphingolipid metabolism, organism-specific biosystem (from KEGG)
    Sphingolipid metabolism, organism-specific biosystem
    Sphingolipid metabolism
  • Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
    Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...
  • Sphingolipid metabolism, conserved biosystem (from KEGG)
    Sphingolipid metabolism, conserved biosystem
    Sphingolipid metabolism
  • Sphingolipid signaling pathway, organism-specific biosystem (from KEGG)
    Sphingolipid signaling pathway, organism-specific biosystemSphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) ...
  • Sphingolipid signaling pathway, conserved biosystem (from KEGG)
    Sphingolipid signaling pathway, conserved biosystemSphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) ...
  • sphingosine and sphingosine-1-phosphate metabolism, organism-specific biosystem (from BIOCYC)
    sphingosine and sphingosine-1-phosphate metabolism, organism-specific biosystemIn this pathway, ceramide, the breakdown product of sphingomyelin, is metabolized by ceramidase to generate : SPHINGOSINE, which has been shown to be produced during the early stages of apoptosis; : ...

General gene information

Markers

Homology

Clone Names

  • FLJ39004

Gene Ontology Provided by GOA

Function Evidence Code Pubs
sphingosine-1-phosphate phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
sphingosine-1-phosphate phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
regulation of type B pancreatic cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
 
sphingosine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
sphingosine-1-phosphate phosphatase 2
Names
sphingosine 1-phosphate phosphohydrolase 2
sphingosine-1-phosphatase 2
sphingosine-1-phosphate phosphotase 2

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.

mRNA and Protein(s)

  1. NM_001320833.2NP_001307762.1  sphingosine-1-phosphate phosphatase 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' end compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AC097461, AK314322, BC114513, BU676534
    UniProtKB/Swiss-Prot
    Q8IWX5
    Conserved Domains (2) summary
    COG0671
    Location:1108
    PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]
    cd03388
    Location:1105
    PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...
  2. NM_001320834.2NP_001307763.1  sphingosine-1-phosphate phosphatase 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b)
    Source sequence(s)
    AC097461, AC112718, AK096323, BU676534
    UniProtKB/Swiss-Prot
    Q8IWX5
    Conserved Domains (2) summary
    COG0671
    Location:1108
    PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]
    cd03388
    Location:1105
    PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...
  3. NM_152386.4NP_689599.2  sphingosine-1-phosphate phosphatase 2 isoform a

    See identical proteins and their annotated locations for NP_689599.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AC097461, AF542512, AK314322, BU676534
    Consensus CDS
    CCDS2453.1
    UniProtKB/Swiss-Prot
    Q8IWX5
    Related
    ENSP00000315137.7, ENST00000321276.8
    Conserved Domains (1) summary
    cd03388
    Location:84233
    PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    222423988..222562621
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017003355.1XP_016858844.1  sphingosine-1-phosphate phosphatase 2 isoform X1

    UniProtKB/Swiss-Prot
    Q8IWX5
    Conserved Domains (2) summary
    COG0671
    Location:1108
    PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]
    cd03388
    Location:1105
    PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...
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