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    Pphln1 periphilin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 366975, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Pphln1provided by RGD
    Official Full Name
    periphilin 1provided by RGD
    Primary source
    RGD:1306207
    See related
    EnsemblRapid:ENSRNOG00000022778 AllianceGenome:RGD:1306207
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in negative regulation of gene expression, epigenetic; positive regulation of DNA methylation-dependent heterochromatin formation; and protein localization to heterochromatin. Predicted to be located in Golgi apparatus and cytosol. Predicted to be active in nucleoplasm. Orthologous to human PPHLN1 (periphilin 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 106.1), Thymus (RPKM 93.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pphln1 in Genome Data Viewer
    Location:
    7q35
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (126418042..126509430)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (124538594..124629985)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (134602109..134693807)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene YY1 associated factor 2 Neighboring gene uncharacterized LOC134479778 Neighboring gene uncharacterized LOC108351532 Neighboring gene zinc finger CCHC-type and RNA binding motif containing 1 Neighboring gene prickle planar cell polarity protein 1 Neighboring gene uncharacterized LOC100911384 Neighboring gene uncharacterized LOC103692964

    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. Periphilin is a novel interactor of synphilin-1, a protein implicated in Parkinson's disease. Soehn AS, et al. Neurogenetics, 2010 May. PMID 19730898
    2. GENE SILENCING. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells. Tchasovnikarova IA, et al. Science, 2015 Jun 26. PMID 26022416, Free PMC Article
    3. Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2. Tchasovnikarova IA, et al. Nat Genet, 2017 Jul. PMID 28581500, Free PMC Article
    4. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Process Evidence Code Pubs
    involved_in constitutive heterochromatin formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of gene expression, epigenetic ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization to heterochromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    periphilin-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_001108992.1 → NP_001102462.1  periphilin-1

      See identical proteins and their annotated locations for NP_001102462.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474027
      UniProtKB/TrEMBL
      A0A0G2K2G1, A6K7T2, D4A9M4
      Conserved Domains (1) summary
      pfam11488
      Location:338 → 394
      Lge1; Transcriptional regulatory protein LGE1

    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_086025.1 Reference GRCr8

      Range
      126418042..126509430
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017595022.2 → XP_017450511.1  periphilin-1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K2G1, A6K7T2, D4A9M4
      Conserved Domains (1) summary
      pfam11488
      Location:338 → 394
      Lge1; Transcriptional regulatory protein LGE1

    2. XM_006242236.5 → XP_006242298.1  periphilin-1 isoform X3

      UniProtKB/TrEMBL
      A0A0G2K2G1
      Conserved Domains (1) summary
      pfam11488
      Location:290 → 366
      Lge1; Transcriptional regulatory protein LGE1

    3. XM_039079695.2 → XP_038935623.1  periphilin-1 isoform X4

      UniProtKB/TrEMBL
      A0A0G2K2G1
      Related
      ENSRNOP00000087331.2, ENSRNOT00000098702.2
      Conserved Domains (1) summary
      pfam11488
      Location:271 → 347
      Lge1; Transcriptional regulatory protein LGE1

    4. XM_006242235.4 → XP_006242297.1  periphilin-1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A300, B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:222 → 298
      Lge1; Transcriptional regulatory protein LGE1

    5. XM_039079698.2 → XP_038935626.1  periphilin-1 isoform X8

      UniProtKB/TrEMBL
      B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:203 → 279
      Lge1; Transcriptional regulatory protein LGE1

    6. XM_039079705.2 → XP_038935633.1  periphilin-1 isoform X14

    7. XM_063264060.1 → XP_063120130.1  periphilin-1 isoform X1

      UniProtKB/TrEMBL
      A6K7T2, D4A9M4
      Related
      ENSRNOP00000052548.2, ENSRNOT00000055688.4

    8. XM_063264061.1 → XP_063120131.1  periphilin-1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6B6J6
      Related
      ENSRNOP00000097952.1, ENSRNOT00000102144.2

    9. XM_063264062.1 → XP_063120132.1  periphilin-1 isoform X5

      UniProtKB/TrEMBL
      A0A8I6A7X8, A6K7T3

    10. XM_063264063.1 → XP_063120133.1  periphilin-1 isoform X6

      UniProtKB/TrEMBL
      A6K7T4

    11. XM_063264067.1 → XP_063120137.1  periphilin-1 isoform X12

    12. XM_006242230.3 → XP_006242292.2  periphilin-1 isoform X3

      UniProtKB/TrEMBL
      A0A0G2K2G1
      Conserved Domains (1) summary
      pfam11488
      Location:290 → 366
      Lge1; Transcriptional regulatory protein LGE1

    13. XM_039079700.2 → XP_038935628.1  periphilin-1 isoform X10

      UniProtKB/TrEMBL
      B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:176 → 252
      Lge1; Transcriptional regulatory protein LGE1

    14. XM_006242233.3 → XP_006242295.2  periphilin-1 isoform X7

      UniProtKB/TrEMBL
      A0A8I6A300, B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:222 → 298
      Lge1; Transcriptional regulatory protein LGE1

    15. XM_063264064.1 → XP_063120134.1  periphilin-1 isoform X8

    16. XM_063264066.1 → XP_063120136.1  periphilin-1 isoform X11

    17. XM_039079699.2 → XP_038935627.1  periphilin-1 isoform X9

      UniProtKB/TrEMBL
      B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:183 → 259
      Lge1; Transcriptional regulatory protein LGE1

    18. XM_039079702.2 → XP_038935630.1  periphilin-1 isoform X10

      UniProtKB/TrEMBL
      B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:176 → 252
      Lge1; Transcriptional regulatory protein LGE1

    19. XM_063264065.1 → XP_063120135.1  periphilin-1 isoform X10

    20. XM_063264068.1 → XP_063120138.1  periphilin-1 isoform X13

    21. XM_039079701.2 → XP_038935629.1  periphilin-1 isoform X10

      UniProtKB/TrEMBL
      B2GV12
      Conserved Domains (1) summary
      pfam11488
      Location:176 → 252
      Lge1; Transcriptional regulatory protein LGE1

    RNA

    1. XR_010053024.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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