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    Ppef1 protein phosphatase with EF-hand domain 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317498, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Ppef1provided by RGD
    Official Full Name
    protein phosphatase with EF-hand domain 1provided by RGD
    Primary source
    RGD:1562772
    See related
    EnsemblRapid:ENSRNOG00000027331 AllianceGenome:RGD:1562772
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable protein serine/threonine phosphatase activity. Predicted to be involved in chromatin remodeling; detection of stimulus involved in sensory perception; and regulation of transcription by RNA polymerase II. Predicted to be active in cytosol and nucleus. Orthologous to human PPEF1 (protein phosphatase with EF-hand domain 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 72.6) and Thymus (RPKM 9.2) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ppef1 in Genome Data Viewer
    Location:
    Xq14
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (37803204..37960378)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (33994503..34151704)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (35822687..35947690)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene cyclin-dependent kinase-like 5 Neighboring gene transfer RNA valine (anticodon UAC) Neighboring gene retinoschisin 1 Neighboring gene metallothionein 1F Neighboring gene phosphorylase kinase regulatory subunit alpha 2 Neighboring gene adhesion G protein-coupled receptor G2 Neighboring gene 60S ribosomal protein L15 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC125115

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables MAP kinase serine/threonine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calmodulin-dependent protein phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H2AXS140 phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables manganese ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables myosin phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoprotein phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein serine/threonine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in detection of stimulus involved in sensory perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol 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
    serine/threonine-protein phosphatase with EF-hands 1
    Names
    PPEF-1
    protein phosphatase with EF hand calcium-binding domain 1
    protein phosphatase, EF-hand calcium binding domain 1
    serine/threonine-protein phosphatase with EF-hands 1-like
    NP_001030107.1
    XP_038955765.1
    XP_038955767.1
    XP_038955768.1
    XP_063136153.1
    XP_063136154.1

    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_001034935.2 → NP_001030107.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

      See identical proteins and their annotated locations for NP_001030107.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/Swiss-Prot
      Q3SWT6
      UniProtKB/TrEMBL
      F1LNH9
      Conserved Domains (4) summary
      PTZ00183
      Location:481 → 623
      PTZ00183; centrin; Provisional
      smart00015
      Location:15 → 33
      IQ; Calmodulin-binding motif
      cd07420
      Location:116 → 442
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:558 → 626
      EF-hand_7; EF-hand domain pair

    2. NM_001434223.1 → NP_001421152.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A8I6B3D3, F1LNH9

    3. NM_001434224.1 → NP_001421153.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/Swiss-Prot
      Q3SWT6
      UniProtKB/TrEMBL
      F1LNH9

    4. NM_001434225.1 → NP_001421154.1  serine/threonine-protein phosphatase with EF-hands 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A8I6B3D3, F1LNH9

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      37803204..37960378
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063280083.1 → XP_063136153.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

      UniProtKB/Swiss-Prot
      Q3SWT6
      UniProtKB/TrEMBL
      F1LNH9

    2. XM_039099837.2 → XP_038955765.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      Related
      ENSRNOP00000095819.1, ENSRNOT00000094755.2
      Conserved Domains (4) summary
      PTZ00183
      Location:505 → 647
      PTZ00183; centrin; Provisional
      smart00015
      Location:40 → 57
      IQ; Calmodulin-binding motif
      cd07420
      Location:140 → 466
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:582 → 650
      EF-hand_7; EF-hand domain pair

    3. XM_039099840.2 → XP_038955768.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

      Related
      ENSRNOP00000055729.5, ENSRNOT00000058947.6
      Conserved Domains (4) summary
      PTZ00183
      Location:481 → 623
      PTZ00183; centrin; Provisional
      smart00015
      Location:15 → 33
      IQ; Calmodulin-binding motif
      cd07420
      Location:116 → 442
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:558 → 626
      EF-hand_7; EF-hand domain pair

    4. XM_039099839.2 → XP_038955767.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X1

      Conserved Domains (4) summary
      PTZ00183
      Location:505 → 647
      PTZ00183; centrin; Provisional
      smart00015
      Location:40 → 57
      IQ; Calmodulin-binding motif
      cd07420
      Location:140 → 466
      MPP_RdgC; Drosophila melanogaster RdgC and related proteins, metallophosphatase domain
      pfam13499
      Location:582 → 650
      EF-hand_7; EF-hand domain pair

    5. XM_063280084.1 → XP_063136154.1  serine/threonine-protein phosphatase with EF-hands 1 isoform X2

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3SWT6.1 GenPept UniProtKB/Swiss-Prot:Q3SWT6

    Gene LinkOut

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