PCIF1 Gene (Protein Coding)

Phosphorylated CTD Interacting Factor 1

GC20P045934
GIFtS:
32
See more...

Aliases for PCIF1 Gene

Aliases for PCIF1 Gene

  • Phosphorylated CTD Interacting Factor 1 2 3 5
  • PPP1R121 2 3 4
  • CAPAM 2 3 4
  • MRNA (2'-O-Methyladenosine-N(6)-)-Methyltransferase 3 4
  • Protein Phosphatase 1, Regulatory Subunit 121 2 3
  • Cap-Specific Adenosine Methyltransferase 3 4
  • PDX1 C-Terminal Inhibiting Factor 1 2 3
  • C20orf67 3 4
  • HCAPAM 3 4
  • HPCIF1 3 4
  • Protein Phosphatase 1 Regulatory Subunit 121 4
  • Cap-Specific Adenosine Methyltransferase' 2
  • Phosphorylated CTD-Interacting Factor 1 4
  • PDX-1 C Terminus-Interacting Factor 1 3
  • Chromosome 20 Open Reading Frame 67 2
  • EC 2.1.1.62 4
  • BA465L10.1 2
  • PCIF1 5

External Ids for PCIF1 Gene

Previous HGNC Symbols for PCIF1 Gene

  • C20orf67

Previous GeneCards Identifiers for PCIF1 Gene

  • GC20P043997
  • GC20P044563
  • GC20P041304

Summaries for PCIF1 Gene

GeneCards Summary for PCIF1 Gene

PCIF1 (Phosphorylated CTD Interacting Factor 1) is a Protein Coding gene.

UniProtKB/Swiss-Prot Summary for PCIF1 Gene

  • Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2'-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs (PubMed:30467178, PubMed:30487554, PubMed:31279658, PubMed:31279659). Recruited to the early elongation complex of RNA polymerase II (RNAPII) via interaction with POLR2A and mediates formation of m6A(m) co-transcriptionally (PubMed:30467178).

Additional gene information for PCIF1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCIF1 Gene

Genomics for PCIF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PCIF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCIF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCIF1

Top Transcription factor binding sites by QIAGEN in the PCIF1 gene promoter:
  • AML1a
  • COMP1
  • CREB
  • deltaCREB
  • GATA-1
  • Ik-3
  • MAZR
  • XBP-1
  • Zic3

Genomic Locations for PCIF1 Gene

Latest Assembly
chr20:45,934,674-45,948,023
(GRCh38/hg38)
Size:
13,350 bases
Orientation:
Plus strand

Previous Assembly
chr20:44,563,322-44,576,659
(GRCh37/hg19 by Entrez Gene)
Size:
13,338 bases
Orientation:
Plus strand

chr20:44,563,267-44,576,662
(GRCh37/hg19 by Ensembl)
Size:
13,396 bases
Orientation:
Plus strand

Genomic View for PCIF1 Gene

Genes around PCIF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCIF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCIF1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PCIF1 Gene

Proteins for PCIF1 Gene

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  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for PCIF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H4Z3-CAPAM_HUMAN
    Recommended name:
    mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase
    Protein Accession:
    Q9H4Z3
    Secondary Accessions:
    • E1P5P1
    • Q54AB9
    • Q9NT85

    Protein attributes for PCIF1 Gene

    Size:
    704 amino acids
    Molecular mass:
    80670 Da
    Quaternary structure:
    • Interacts with POLR2A; interacts with the phosphorylated C-terminal domain (CTD) of POLR2A.

    Three dimensional structures from OCA and Proteopedia for PCIF1 Gene

neXtProt entry for PCIF1 Gene

Protein Expression for PCIF1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PCIF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PCIF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCIF1 Gene

Domains & Families for PCIF1 Gene

Gene Families for PCIF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PCIF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PCIF1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ61655, highly similar to Phosphorylated CTD-interacting factor 1 (B7Z5U5_HUMAN)
  • Phosphorylated CTD-interacting factor 1 (PCIF1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H4Z3

UniProtKB/Swiss-Prot:

CAPAM_HUMAN :
  • The WW domain is sufficient for direct and specific interaction with the phosphorylated CTD of RNAPII largest subunit.
  • Belongs to the CAPAM family.
Domain:
  • The WW domain is sufficient for direct and specific interaction with the phosphorylated CTD of RNAPII largest subunit.
Family:
  • Belongs to the CAPAM family.
genes like me logo Genes that share domains with PCIF1: view

Function for PCIF1 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for PCIF1 Gene

UniProtKB/Swiss-Prot Function:
Cap-specific adenosine methyltransferase that catalyzes formation of N(6),2'-O-dimethyladenosine cap (m6A(m)) by methylating the adenosine at the second transcribed position of capped mRNAs (PubMed:30467178, PubMed:30487554, PubMed:31279658, PubMed:31279659). Recruited to the early elongation complex of RNA polymerase II (RNAPII) via interaction with POLR2A and mediates formation of m6A(m) co-transcriptionally (PubMed:30467178).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyladenosine) in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-(N(6),2'-O-dimethyladenosine) in mRNA + H(+) + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:22744, Rhea:RHEA-COMP:11518, Rhea:RHEA-COMP:11519, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:85958, ChEBI:CHEBI:85959; EC=2.1.1.62; Evidence={ECO:0000269|PubMed:30467178, ECO:0000269|PubMed:30487554, ECO:0000269|PubMed:31279658, ECO:0000269|PubMed:31279659};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=3.5 uM for m7GpppAm {ECO:0000269|PubMed:30467178}; KM=82 nM for m7GpppAm oligonucleotide {ECO:0000269|PubMed:31279658}; KM=33.4 nM for m7GpppAm capped mRNA {ECO:0000269|PubMed:31279659}; KM=28 uM for m7GpppA {ECO:0000269|PubMed:30467178}; KM=630 uM for m7GpppA oligonucleotide {ECO:0000269|PubMed:31279658}; KM=208 nM for m7GpppAm dinucleotide {ECO:0000269|PubMed:31279659}; Note=Kcat is 0.036 min(-1) for m7GpppAm capped mRNA (PubMed:31279659). Kcat is 0.34 min(-1) for m7GpppAm dinucleotide (PubMed:31279659). {ECO:0000269|PubMed:31279659};

Enzyme Numbers (IUBMB) for PCIF1 Gene

Phenotypes From GWAS Catalog for PCIF1 Gene

Gene Ontology (GO) - Molecular Function for PCIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0008168 methyltransferase activity IEA --
GO:0016422 mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity IEA,IDA 30467178
GO:0016740 transferase activity IEA --
GO:0099122 RNA polymerase II C-terminal domain binding IEA,IDA 18294453
genes like me logo Genes that share ontologies with PCIF1: view
genes like me logo Genes that share phenotypes with PCIF1: view

Animal Models for research

miRNA for PCIF1 Gene

miRTarBase miRNAs that target PCIF1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCIF1

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCIF1 Gene

Localization for PCIF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCIF1 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PCIF1 gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 4
cytosol 2
plasma membrane 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (3)
  • Microtubules (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 18294453
GO:0005654 nucleoplasm IDA --
GO:0015630 microtubule cytoskeleton IDA --
GO:0045171 intercellular bridge IDA --
genes like me logo Genes that share ontologies with PCIF1: view

Pathways & Interactions for PCIF1 Gene

PathCards logo

SuperPathways for PCIF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCIF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006417 NOT regulation of translation IDA 31279658
GO:0010923 negative regulation of phosphatase activity IDA 19389623
GO:0017148 negative regulation of translation IDA 31279659
GO:0032259 methylation IEA --
GO:0045727 positive regulation of translation IMP 30467178
genes like me logo Genes that share ontologies with PCIF1: view

No data available for Pathways by source and SIGNOR curated interactions for PCIF1 Gene

Drugs & Compounds for PCIF1 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for PCIF1 Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for PCIF1 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCIF1

Alternative Splicing Database (ASD) splice patterns (SP) for PCIF1 Gene

No ASD Table

Relevant External Links for PCIF1 Gene

GeneLoc Exon Structure for
PCIF1

Expression for PCIF1 Gene

Products:

  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCIF1 Gene

mRNA expression in normal human tissues for PCIF1 Gene
mRNA expression by GTEx for PCIF1 GenemRNA expression by BioGPS for PCIF1 Gene

Protein differential expression in normal tissues from HIPED for PCIF1 Gene

This gene is overexpressed in Breast (18.2), Peripheral blood mononuclear cells (8.4), and Lymph node (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCIF1 Gene



Protein tissue co-expression partners for PCIF1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCIF1

SOURCE GeneReport for Unigene cluster for PCIF1 Gene:

Hs.472856

mRNA Expression by UniProt/SwissProt for PCIF1 Gene:

Q9H4Z3-CAPAM_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for PCIF1 Gene

  • Muscle(4.4)
  • Pancreas(4.4)
  • Liver(4.3)
  • Nervous system(3.6)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with PCIF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCIF1 Gene

Orthologs for PCIF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCIF1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PCIF1 30 31
  • 99.91 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PCIF1 30 31
  • 92.12 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PCIF1 30 31
  • 92.04 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Pcif1 30
  • 90 (n)
Mouse
(Mus musculus)
 Mammalia Pcif1 30 17 31
  • 89.9 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia PCIF1 31
  • 87 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PCIF1 30 31
  • 78.73 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PCIF1 31
  • 81 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia pcif1 30
  • 69.27 (n)
Str.2070 30
Zebrafish
(Danio rerio)
 Actinopterygii pcif1 30 31
  • 67.37 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta CG11399 30 31
  • 56.97 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP011933 30
  • 53.6 (n)
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.3903 30
Species where no ortholog for PCIF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PCIF1 Gene

ENSEMBL:
Gene Tree for PCIF1 (if available)
TreeFam:
Gene Tree for PCIF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCIF1: view image

Paralogs for PCIF1 Gene

No data available for Paralogs for PCIF1 Gene

Variants for PCIF1 Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PCIF1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PCIF1 Gene

Variant ID Type Subtype PubMed ID
esv8950 CNV gain 19470904
nsv517296 CNV loss 19592680
nsv833990 CNV loss 17160897
nsv833991 CNV loss 17160897

Variation tolerance for PCIF1 Gene

Residual Variation Intolerance Score: 13.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.99; 36.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCIF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCIF1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCIF1 Gene

Disorders for PCIF1 Gene

Additional Disease Information for PCIF1

Genetic Association Database
(GAD)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for PCIF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCIF1 Gene

Publications for PCIF1 Gene

  1. PCIF1, a novel human WW domain-containing protein, interacts with the phosphorylated RNA polymerase II. (PMID: 12565871) Fan H … Hirose Y (Biochemical and biophysical research communications 2003) 2 3 4 23
  2. Human phosphorylated CTD-interacting protein, PCIF1, negatively modulates gene expression by RNA polymerase II. (PMID: 18294453) Hirose Y … Ohkuma Y (Biochemical and biophysical research communications 2008) 3 4 23
  3. Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase. (PMID: 30467178) Akichika S … Suzuki T (Science (New York, N.Y.) 2019) 3 4
  4. Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase. (PMID: 30487554) Sun H … Yi C (Cell research 2019) 3 4
  5. Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome. (PMID: 31279658) Boulias K … Greer EL (Molecular cell 2019) 3 4

ExternalLinks

View latest publications for PCIF1 gene in Mastermind

Products for PCIF1 Gene

  • Addgene plasmids for PCIF1

Sources for PCIF1 Gene