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    PPP2R2D protein phosphatase 2 regulatory subunit Bdelta [ Homo sapiens (human) ]

    Gene ID: 55844, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PPP2R2Dprovided by HGNC
    Official Full Name
    protein phosphatase 2 regulatory subunit Bdeltaprovided by HGNC
    Primary source
    HGNC:HGNC:23732
    See related
    Ensembl:ENSG00000175470 MIM:613992; AllianceGenome:HGNC:23732
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    B55D; MDS026; B55delta
    Summary
    Predicted to enable protein phosphatase regulator activity. Predicted to be involved in exit from mitosis. Predicted to be located in cytoplasm. Predicted to be part of protein phosphatase type 2A complex. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in pancreas (RPKM 6.3), ovary (RPKM 5.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PPP2R2D in Genome Data Viewer
    Location:
    10q26.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (131901008..131971533)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (132840100..132911782)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (133747955..133773338)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378566 Neighboring gene 60S ribosomal protein L19-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2948 Neighboring gene Sharpr-MPRA regulatory region 4393 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:133747865-133749064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133758459-133759288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133761987-133762488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133785771-133786641 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133794606-133795530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133809534-133810520 Neighboring gene uncharacterized LOC124902525 Neighboring gene BCL2 interacting protein 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133820384-133820908 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:133823019-133823543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133832958-133833629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133842692-133843192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133852590-133853427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133857569-133858086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133858087-133858604 Neighboring gene Janus kinase and microtubule interacting protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133878227-133878974 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:133881249-133881749 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11218 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11222 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11225 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133920928-133921428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133933330-133934168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133934169-133935006 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133951279-133951800 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133955152-133955999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133956000-133956846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133959409-133959910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133959911-133960410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:133960832-133961794 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:133977007-133977706 Neighboring gene JAKMIP3 antisense RNA 1

    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. Identification and functional analysis of variant haplotypes in the 5'-flanking region of protein phosphatase 2A-Bδ gene. Chen HF, et al. PLoS One, 2012. PMID 22539979, Free PMC Article
    2. An in vivo screen implicates PPP2R2D as an inhibitor of T-cell function. . Cancer Discov, 2014 Mar. PMID 24596207
    3. MicroRNA-5010-5p ameliorates high-glucose induced inflammation in renal tubular epithelial cells by modulating the expression of PPP2R2D. Choi S, et al. BMJ Open Diabetes Res Care, 2024 Mar 4. PMID 38442987, Free PMC Article
    4. PPP2R2D, a regulatory subunit of protein phosphatase 2A, promotes gastric cancer growth and metastasis via mechanistic target of rapamycin activation. Yu S, et al. Int J Oncol, 2018 Jun. PMID 29568966
    5. PPP2R2D suppresses IL-2 production and Treg function. Pan W, et al. JCI Insight, 2020 Oct 2. PMID 32897879, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MicroRNA-5010-5p ameliorates high-glucose induced inflammation in renal tubular epithelial cells by modulating the expression of PPP2R2D.
      Title: MicroRNA-5010-5p ameliorates high-glucose induced inflammation in renal tubular epithelial cells by modulating the expression of PPP2R2D.
    2. PPP2R2D suppresses IL-2 production and Treg function.
      Title: PPP2R2D suppresses IL-2 production and Treg function.
    3. Results show that PPP2R2D expression was significantly upregulated at the mRNA and protein levels in gastric cancer (GC) tissues and correlated with poor prognosis. Further evidence demonstrates an oncogenic role of PPP2R2D in GC progression and development through regulation of mTOR.
      Title: PPP2R2D, a regulatory subunit of protein phosphatase 2A, promotes gastric cancer growth and metastasis via mechanistic target of rapamycin activation.
    4. The PP2A regulatory subunit PPP2R2D inhibits T-cell proliferation and survival within tumors.
      Title: An in vivo screen implicates PPP2R2D as an inhibitor of T-cell function.
    5. The -462 G>A variant of PPP2R2D affects NF1 binding to the proximal promoter of PPP2R2D.
      Title: Identification and functional analysis of variant haplotypes in the 5'-flanking region of protein phosphatase 2A-Bδ gene.
    6. These highly related members of the same subfamily of PP2A regulatory subunits differentially regulate TGF-beta/Activin/Nodal signalling to elicit opposing biological outcomes.
      Title: Two highly related regulatory subunits of PP2A exert opposite effects on TGF-beta/Activin/Nodal signalling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, protein phosphatase 2, regulatory subunit B, delta (PPP2R2D), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

    Go to the HIV-1, Human Interaction Database

    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 enzyme-substrate adaptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase regulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein phosphatase regulator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in exit from mitosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mitotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of chromosome segregation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein phosphatase type 2A complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein phosphatase type 2A complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform
    Names
    protein phosphatase 2 regulatory subunit B, delta

    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.

    mRNA and Protein(s)

    1. NM_001291310.2 → NP_001278239.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform b

      See identical proteins and their annotated locations for NP_001278239.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an additional exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AB040974, BC047379, BQ023669
      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1
      Conserved Domains (2) summary
      COG5170
      Location:2 → 283
      CDC55; Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
      sd00039
      Location:21 → 57
      7WD40; WD40 repeat [structural motif]

    2. NM_018461.5 → NP_060931.2  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform a

      See identical proteins and their annotated locations for NP_060931.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AB040974, BC047379, BQ023669
      Consensus CDS
      CCDS73224.1
      UniProtKB/Swiss-Prot
      A8KAK0, Q5SQJ2, Q66LE6, Q9P1Y7
      Related
      ENSP00000399970.2, ENST00000455566.6
      Conserved Domains (2) summary
      COG5170
      Location:14 → 448
      CDC55; Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
      sd00039
      Location:37 → 85
      7WD40; WD40 repeat [structural motif]

    RNA

    1. NR_033191.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) includes an additional exon and uses an alternate splice site in the central region, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB040974, BC047379, BC060885, BQ023669

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      131901008..131971533
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717914.4 → XP_006717977.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X4

      Conserved Domains (2) summary
      sd00039
      Location:37 → 85
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35 → 333
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. XM_047425478.1 → XP_047281434.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    3. XM_047425475.1 → XP_047281431.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    4. XM_047425471.1 → XP_047281427.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X1

    5. XM_047425473.1 → XP_047281429.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X3

    6. XM_047425472.1 → XP_047281428.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X2

    7. XM_047425474.1 → XP_047281430.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X5

    8. XM_047425476.1 → XP_047281432.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    9. XM_047425477.1 → XP_047281433.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      132840100..132911782
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366287.1 → XP_054222262.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X4

    2. XM_054366292.1 → XP_054222267.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    3. XM_054366289.1 → XP_054222264.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    4. XM_054366286.1 → XP_054222261.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X3

    5. XM_054366285.1 → XP_054222260.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X2

    6. XM_054366288.1 → XP_054222263.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X5

    7. XM_054366290.1 → XP_054222265.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    8. XM_054366291.1 → XP_054222266.1  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X6

      UniProtKB/TrEMBL
      Q6IN90, Q6PEG1

    RNA

    1. XR_008488229.1 RNA Sequence

    2. XR_008488228.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001003656.1: Suppressed sequence

      Description
      NM_001003656.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q66LE6.1 GenPept UniProtKB/Swiss-Prot:Q66LE6

    Gene LinkOut

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