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    PCIF1 phosphorylated CTD interacting factor 1 [ Homo sapiens (human) ]

    Gene ID: 63935, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PCIF1provided by HGNC
    Official Full Name
    phosphorylated CTD interacting factor 1provided by HGNC
    Primary source
    HGNC:HGNC:16200
    See related
    Ensembl:ENSG00000100982 MIM:618626; AllianceGenome:HGNC:16200
    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
    CAPAM; MT-A70; hCAPAM; hPCIF1; C20orf67; PPP1R121
    Summary
    Enables RNA polymerase II C-terminal domain phosphoserine binding activity; S-adenosyl-L-methionine binding activity; and mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity. Involved in mRNA processing; negative regulation of translation; and positive regulation of translation. Located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 21.7), thyroid (RPKM 17.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PCIF1 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45934683..45948020)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47670740..47684073)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (44563322..44576659)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44519312-44520021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17954 Neighboring gene spermatogenesis associated 25 Neighboring gene neuralized E3 ubiquitin protein ligase 2 Neighboring gene cathepsin A Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44531171-44531366 Neighboring gene phospholipid transfer protein Neighboring gene Sharpr-MPRA regulatory region 14031 Neighboring gene Sharpr-MPRA regulatory region 10402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44561248-44561940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17955 Neighboring gene pre-mRNA-splicing factor cwc22-like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44562632-44563323 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44563324-44564014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44567204-44567719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44567720-44568234 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:44572602-44573801 Neighboring gene zinc finger protein 335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44603922-44604458 Neighboring gene ferritin light chain pseudogene 1

    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. LncRNA PCIF1 promotes aerobic glycolysis in A549/DDP cells by competitively binding miR-326 to regulate PKM expression. Zhong W, et al. Mol Cell Probes, 2024 Oct. PMID 39074568
    2. Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. Yu D, et al. J Biol Chem, 2022 Apr. PMID 35189146, Free PMC Article
    3. Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas. Gao S, et al. Biochim Biophys Acta Mol Basis Dis, 2022 Nov 1. PMID 35868483
    4. The Phosphorylation of PDX-1 by Protein Kinase CK2 Is Crucial for Its Stability. Klein S, et al. Pharmaceuticals (Basel), 2016 Dec 28. PMID 28036027, Free PMC Article
    5. Atlas of quantitative single-base-resolution N(6)-methyl-adenine methylomes. Koh CWQ, et al. Nat Commun, 2019 Dec 10. PMID 31822664, Free PMC Article

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA PCIF1 promotes aerobic glycolysis in A549/DDP cells by competitively binding miR-326 to regulate PKM expression.
      Title: LncRNA PCIF1 promotes aerobic glycolysis in A549/DDP cells by competitively binding miR-326 to regulate PKM expression.
    2. m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression.
      Title: m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression.
    3. The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma.
      Title: The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma.
    4. Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy.
      Title: Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy.
    5. Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas.
      Title: Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas.
    6. Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs.
      Title: Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs.
    7. The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features.
      Title: The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features.
    8. Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-beta.
      Title: Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-β.
    9. HIV reprograms host m(6)Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1.
      Title: HIV reprograms host m(6)Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1.
    10. Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima.
      Title: Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    EBI GWAS Catalog

    Description
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    EBI GWAS Catalog

    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

    Gene Ontology Provided by GOA

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

    General protein information

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    Preferred Names
    mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
    Names
    PDX-1 C terminus-interacting factor 1
    PDX1 C-terminal inhibiting factor 1
    cap-specific adenosine methyltransferase
    protein phosphatase 1, regulatory subunit 121
    NP_071387.1
    XP_011527282.1
    XP_011527283.1
    XP_016883502.1
    XP_047296324.1
    XP_054179797.1
    XP_054179798.1
    XP_054179799.1
    XP_054179800.1

    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_022104.4 → NP_071387.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase

      See identical proteins and their annotated locations for NP_071387.1

      Status: VALIDATED

      Source sequence(s)
      BC013365, BQ684226
      Consensus CDS
      CCDS13388.1
      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5
      Related
      ENSP00000361486.3, ENST00000372409.8
      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:446 → 616
      PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      45934683..45948020
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528980.4 → XP_011527282.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      See identical proteins and their annotated locations for XP_011527282.1

      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5
      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:446 → 616
      PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain

    2. XM_017028013.3 → XP_016883502.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5
      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:446 → 616
      PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain

    3. XM_011528981.4 → XP_011527283.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      See identical proteins and their annotated locations for XP_011527283.1

      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5
      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:446 → 616
      PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain

    4. XM_047440368.1 → XP_047296324.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X2

    RNA

    1. XR_936605.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      47670740..47684073
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323822.1 → XP_054179797.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5

    2. XM_054323824.1 → XP_054179799.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5

    3. XM_054323823.1 → XP_054179798.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

      UniProtKB/Swiss-Prot
      E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
      UniProtKB/TrEMBL
      B7Z5U5

    4. XM_054323825.1 → XP_054179800.1  mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X2

    RNA

    1. XR_008485291.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H4Z3.1 GenPept UniProtKB/Swiss-Prot:Q9H4Z3

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