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

Gene ID: 362269, updated on 11-Apr-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
Ensembl: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 methylation; 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, Apr 2022]
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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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
  • 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 modification 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
    ENSRNOP00000023202.5, ENSRNOT00000023202.6
    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
    Related
    ENSRNOP00000077698.1
    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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