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

Gene ID: 63935, updated on 11-Apr-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 methylation; negative regulation of translation; and positive regulation of translation. Located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 21.7), thyroid (RPKM 17.5) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45934683..45948020)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47670740..47684073)
105.20220307 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. 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
  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. Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy. Wang L, et al. EMBO J, 2023 Jan 16. PMID 36514940, Free PMC Article
  4. HIV reprograms host m(6)Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1. Zhang Q, et al. Nat Commun, 2021 Sep 20. PMID 34545078, Free PMC Article
  5. Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-β. Tartell MA, et al. Proc Natl Acad Sci U S A, 2021 Jul 20. PMID 34266951, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression.
    Title: m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. PCIF1 depletion leads to loss of m6Am RNA modification from the transcriptional-start-sites of mRNAs
    Title: Atlas of quantitative single-base-resolution N(6)-methyl-adenine methylomes.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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)

Genotypes

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 modification IDA
Inferred from Direct Assay
more info
 PubMed 
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_2023_10

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

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

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

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

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

  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

Gene LinkOut

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