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    PP2D1 protein phosphatase 2C like domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 151649, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PP2D1provided by HGNC
    Official Full Name
    protein phosphatase 2C like domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:28406
    See related
    Ensembl:ENSG00000183977 AllianceGenome:HGNC:28406
    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
    C3orf48
    Summary
    Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in protein dephosphorylation. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in testis (RPKM 9.5), duodenum (RPKM 5.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PP2D1 in Genome Data Viewer
    Location:
    3p24.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (19979961..20012264, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (19984029..20016332, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (20021453..20053756, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376984 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67588 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19896761-19897348 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:19906013-19907212 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67669 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67675 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67680 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67685 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_67687 and experimental_67689 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67692 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67694 Neighboring gene EF-hand domain family member B Neighboring gene Sharpr-MPRA regulatory region 12217 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:19987470-19988071 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_67714 and experimental_67716 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19989274-19989873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19578 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67724 Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 18 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67730 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67732 Neighboring gene RAB5A, member RAS oncogene family Neighboring gene ReSE screen-validated silencer GRCh37_chr3:20044283-20044424 Neighboring gene uncharacterized LOC124909352 Neighboring gene RNA, U4 small nuclear 85, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr3.1018 Neighboring gene ribosomal protein L39 pseudogene 18 Neighboring gene SAP18 pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:20081563-20082533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19582 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67745 Neighboring gene lysine acetyltransferase 2B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19583 Neighboring gene microRNA 3135a

    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. Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets. Robertson MJ, et al. BMC Biol, 2020 Aug 19. PMID 32814578, Free PMC Article
    2. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
    3. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Xiao T, et al. Proc Natl Acad Sci U S A, 2018 Jul 31. PMID 29987050, Free PMC Article
    4. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. Oláh J, et al. J Biol Chem, 2011 Sep 30. PMID 21832049, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25449

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein serine/threonine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of MAPK cascade IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein phosphatase 2C-like domain-containing protein 1

    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_001252657.2 → NP_001239586.1  protein phosphatase 2C-like domain-containing protein 1

      See identical proteins and their annotated locations for NP_001239586.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and is protein coding.
      Source sequence(s)
      AC097635
      Consensus CDS
      CCDS58817.1
      UniProtKB/Swiss-Prot
      A8MPX8, Q96LI7
      Related
      ENSP00000373702.4, ENST00000389050.5
      Conserved Domains (1) summary
      cd00143
      Location:181 → 466
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    RNA

    1. NR_027694.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' splice pattern, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC021717, BC105097, BI463522, BI463551
      Related
      ENST00000333083.11

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      19979961..20012264 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      19984029..20016332 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_144714.3: Suppressed sequence

      Description
      NM_144714.3: 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
    A8MPX8.2 GenPept UniProtKB/Swiss-Prot:A8MPX8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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