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    Pcif1 phosphorylated CTD interacting factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362269, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Pcif1provided by RGD
    Official Full Name
    phosphorylated CTD interacting factor 1provided by RGD
    Primary source
    RGD:1310800
    See related
    EnsemblRapid:ENSRNOG00000016870 AllianceGenome:RGD:1310800
    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
    Also known as
    RGD1310800
    Summary
    Predicted to enable RNA polymerase II C-terminal domain phosphoserine binding activity; S-adenosyl-L-methionine binding activity; and mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity. Predicted to be involved in mRNA processing; negative regulation of translation; and positive regulation of translation. Predicted to be located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human PCIF1 (phosphorylated CTD interacting factor 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 120.2), Thymus (RPKM 108.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pcif1 in Genome Data Viewer
    Location:
    3q42
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (174033471..174046403)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (153614147..153627079)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (161343883..161356815)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene neuralized E3 ubiquitin protein ligase 2 Neighboring gene cathepsin A Neighboring gene phospholipid transfer protein Neighboring gene phosphorylated CTD interacting factor 1 like 1 Neighboring gene zinc finger protein 335 Neighboring gene matrix metallopeptidase 9

    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 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. PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression. Sendinc E, et al. Mol Cell, 2019 Aug 8. PMID 31279659, Free PMC Article
    2. Identification of the m(6)Am Methyltransferase PCIF1 Reveals the Location and Functions of m(6)Am in the Transcriptome. Boulias K, et al. Mol Cell, 2019 Aug 8. PMID 31279658, Free PMC Article
    3. Cap-specific, terminal N(6)-methylation by a mammalian m(6)Am methyltransferase. Sun H, et al. Cell Res, 2019 Jan. PMID 30487554, Free PMC Article
    4. Cap-specific terminal N (6)-methylation of RNA by an RNA polymerase II-associated methyltransferase. Akichika S, et al. Science, 2019 Jan 11. PMID 30467178
    5. Human phosphorylated CTD-interacting protein, PCIF1, negatively modulates gene expression by RNA polymerase II. Hirose Y, et al. Biochem Biophys Res Commun, 2008 May 2. PMID 18294453

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II C-terminal domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II C-terminal domain phosphoserine binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables S-adenosyl-L-methionine binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in intercellular bridge IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intercellular bridge ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
    Names
    PDX1 C-terminal inhibiting factor 1
    NP_001102075.1
    XP_038961470.1

    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_001108605.1 → NP_001102075.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase

      See identical proteins and their annotated locations for NP_001102075.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474005
      UniProtKB/TrEMBL
      A0A8I5Y7T8, A6JXC6, D4A417
      Related
      ENSRNOP00000104112.1, ENSRNOT00000163183.1
      Conserved Domains (2) summary
      cd00201
      Location:47 → 77
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam12237
      Location:445 → 615
      PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain

    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_086021.1 Reference GRCr8

      Range
      174033471..174046403
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105542.2 → XP_038961470.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      UniProtKB/TrEMBL
      A0A8I5Y7T8
      Conserved Domains (2) summary
      cd00201
      Location:64 → 94
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam12237
      Location:462 → 632
      PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain
    Nucleotide Protein Strain
    Heading Accession and Version

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