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

Gene ID: 63935, updated on 9-Sep-2025
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, Jul 2025]
Expression
Ubiquitous expression in ovary (RPKM 21.7), thyroid (RPKM 17.5) and 25 other tissues See more
Orthologs
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See PCIF1 in Genome Data Viewer
Location:
20q13.12
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45934683..45948020)
RS_2025_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

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

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)

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

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

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 binding IEA
Inferred from Electronic Annotation
more info
  
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 
enables mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
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 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
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

NEW Try the new Transcript table

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_2025_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
    Related
    ENSP00000574091.1, ENST00000904032.1
    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: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
    Related
    ENSP00000574099.1, ENST00000904040.1
    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: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
    Related
    ENSP00000574098.1, ENST00000904039.1
    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: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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