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

    Gene ID: 130367, updated on 17-Jun-2024

    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; AllianceGenome:HGNC:19953
    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
    NEW
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    Genomic context

    See SGPP2 in Genome Data Viewer
    Location:
    2q36.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222423988..222562621)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (222909191..223047956)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223288707..223427340)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene paired box 3 Neighboring gene PAX3 promoter region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171419-223171954 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171955-223172489 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223182883-223183478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12368 Neighboring gene CCDC140 long non-coding RNA Neighboring gene ring finger protein 228 Neighboring gene cancer/testis associated transcript 75 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223258471-223259068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17166 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223335177-223335698 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223335699-223336218 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223342957-223343680 Neighboring gene Nanog homeobox pseudogene 2 Neighboring gene RNA, U6 small nuclear 619, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223383170-223383762 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 49 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:223400343-223400843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12372 Neighboring gene phenylalanyl-tRNA synthetase subunit beta Neighboring gene ReSE screen-validated silencer GRCh37_chr2:223502966-223503113 Neighboring gene uncharacterized LOC105373902 Neighboring gene tripartite motif containing 60 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17167 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:223521038-223521234 Neighboring gene uncharacterized LOC124907985

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ39004

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in phospholipid dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of type B pancreatic cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in sphingolipid catabolic process TAS
    Traceable Author Statement
    more info
     
    involved_in sphingosine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sphingosine metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    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)

    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_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/TrEMBL
      Q4ZFX2
      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/TrEMBL
      Q4ZFX2
      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
      A3KPB4, Q8IWX5, Q8N8Q6
      UniProtKB/TrEMBL
      Q3B870
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      222909191..223047956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)