The protein encoded by this gene binds to CLP1 to form pre-mRNA cleavage factor IIm. The encoded protein is necessary for efficient Pol II transcription termination and may be involved in degradation of the 3' product of polyA site cleavage. [provided by RefSeq, Oct 2016] See more...

Aliases for PCF11 Gene

Aliases for PCF11 Gene

  • PCF11 Cleavage And Polyadenylation Factor Subunit 2 3 5
  • Pre-MRNA Cleavage Complex II Protein Pcf11 3 4
  • Pre-MRNA Cleavage Complex 2 Protein Pcf11 3 4
  • KIAA0824 2 4
  • PCF11, Cleavage And Polyadenylation Factor II Subunit, Homolog (S. Cerevisiae) 2
  • PCF11, Cleavage And Polyadenylation Factor Subunit, Homolog (S. Cerevisiae) 2
  • PCF11, Cleavage And Polyadenylation Factor Subunit, Homolog 3
  • PCF11p Homolog 3
  • PCF11 5

External Ids for PCF11 Gene

Previous GeneCards Identifiers for PCF11 Gene

  • GC11P085194
  • GC11P084407
  • GC11P083090
  • GC11P082594
  • GC11P082545
  • GC11P082868
  • GC11P079165

Summaries for PCF11 Gene

Entrez Gene Summary for PCF11 Gene

  • The protein encoded by this gene binds to CLP1 to form pre-mRNA cleavage factor IIm. The encoded protein is necessary for efficient Pol II transcription termination and may be involved in degradation of the 3' product of polyA site cleavage. [provided by RefSeq, Oct 2016]

GeneCards Summary for PCF11 Gene

PCF11 (PCF11 Cleavage And Polyadenylation Factor Subunit) is a Protein Coding gene. Diseases associated with PCF11 include Amyotrophic Lateral Sclerosis 4, Juvenile and Oculopharyngeal Muscular Dystrophy. Among its related pathways are Processing of Capped Intronless Pre-mRNA and Tat-mediated elongation of the HIV-1 transcript. Gene Ontology (GO) annotations related to this gene include mRNA binding and RNA polymerase II complex binding.

UniProtKB/Swiss-Prot Summary for PCF11 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCF11 Gene

Genomics for PCF11 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCF11 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 PCF11 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCF11

Top Transcription factor binding sites by QIAGEN in the PCF11 gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • E47
  • GATA-3
  • Tal-1
  • YY1

Genomic Locations for PCF11 Gene

Latest Assembly
chr11:83,156,988-83,187,451
(GRCh38/hg38)
Size:
30,464 bases
Orientation:
Plus strand

Previous Assembly
chr11:82,868,173-82,898,493
(GRCh37/hg19 by Entrez Gene)
Size:
30,321 bases
Orientation:
Plus strand

chr11:82,868,030-82,898,493
(GRCh37/hg19 by Ensembl)
Size:
30,464 bases
Orientation:
Plus strand

Genomic View for PCF11 Gene

Genes around PCF11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCF11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCF11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCF11 Gene

Proteins for PCF11 Gene

  • Protein details for PCF11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94913-PCF11_HUMAN
    Recommended name:
    Pre-mRNA cleavage complex 2 protein Pcf11
    Protein Accession:
    O94913
    Secondary Accessions:
    • A6H8W7
    • O43671
    • Q6P0X8

    Protein attributes for PCF11 Gene

    Size:
    1555 amino acids
    Molecular mass:
    173050 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC03107.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAC03107.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA74847.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PCF11 Gene

neXtProt entry for PCF11 Gene

Post-translational modifications for PCF11 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibodies for research

  • Abcam antibodies for PCF11
  • Boster Bio Antibodies for PCF11

No data available for DME Specific Peptides for PCF11 Gene

Domains & Families for PCF11 Gene

Gene Families for PCF11 Gene

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

Protein Domains for PCF11 Gene

InterPro:
Blocks:
  • Regulation of nuclear pre-mRNA protein

Suggested Antigen Peptide Sequences for PCF11 Gene

GenScript: Design optimal peptide antigens:
  • Pre-mRNA cleavage complex II protein Pcf11 (PCF11_HUMAN)
  • PCF11 protein (Q0D2H7_HUMAN)
genes like me logo Genes that share domains with PCF11: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCF11 Gene

Function for PCF11 Gene

Molecular function for PCF11 Gene

UniProtKB/Swiss-Prot Function:
Component of pre-mRNA cleavage complex II.

Phenotypes From GWAS Catalog for PCF11 Gene

Gene Ontology (GO) - Molecular Function for PCF11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II complex binding IBA 21873635
GO:0003729 mRNA binding IBA 21873635
genes like me logo Genes that share ontologies with PCF11: view
genes like me logo Genes that share phenotypes with PCF11: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCF11

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCF11 Gene

Localization for PCF11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCF11 Gene

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 PCF11 gene
Compartment Confidence
nucleus 5
mitochondrion 4
cytosol 2
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCF11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IBA 21873635
GO:0005739 mitochondrion IDA --
GO:0005849 mRNA cleavage factor complex IBA,NAS 11060040
genes like me logo Genes that share ontologies with PCF11: view

Pathways & Interactions for PCF11 Gene

genes like me logo Genes that share pathways with PCF11: view

Pathways by source for PCF11 Gene

Gene Ontology (GO) - Biological Process for PCF11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006378 mRNA polyadenylation IBA 21873635
GO:0006379 mRNA cleavage NAS 11060040
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with PCF11: view

No data available for SIGNOR curated interactions for PCF11 Gene

Drugs & Compounds for PCF11 Gene

No Compound Related Data Available

Transcripts for PCF11 Gene

mRNA/cDNA for PCF11 Gene

4 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
7 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 PCF11

Alternative Splicing Database (ASD) splice patterns (SP) for PCF11 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16
SP1: - - - -
SP2: -
SP3:
SP4:
SP5:
SP6: -

Relevant External Links for PCF11 Gene

GeneLoc Exon Structure for
PCF11

Expression for PCF11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCF11 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

Protein differential expression in normal tissues from HIPED for PCF11 Gene

This gene is overexpressed in Brain (28.8), Cerebrospinal fluid (14.0), and Peripheral blood mononuclear cells (9.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCF11 Gene



Protein tissue co-expression partners for PCF11 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCF11

SOURCE GeneReport for Unigene cluster for PCF11 Gene:

Hs.128959

Evidence on tissue expression from TISSUES for PCF11 Gene

  • Nervous system(4.7)
  • Liver(4.2)
  • Skin(2.2)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with PCF11: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCF11 Gene

Orthologs for PCF11 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PCF11 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PCF11 29 30
  • 98.53 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PCF11 29 30
  • 95.2 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LOC510604 29
  • 92.47 (n)
PCF11 30
  • 88 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pcf11 29
  • 91.69 (n)
Mouse
(Mus musculus)
Mammalia Pcf11 29 16 30
  • 91.59 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PCF11 30
  • 81 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PCF11 30
  • 79 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PCF11 29 30
  • 74.93 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PCF11 30
  • 68 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.8613 29
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.10887 29
Zebrafish
(Danio rerio)
Actinopterygii pcf11 29 30
  • 58.44 (n)
OneToOne
Dr.18893 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6287 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG10228 31
  • 43 (a)
Pcf11 30
  • 14 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea pcf-11 30
  • 26 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PCF11 30 32
  • 25 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 15 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.5693 29
Species where no ortholog for PCF11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • 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)

Evolution for PCF11 Gene

ENSEMBL:
Gene Tree for PCF11 (if available)
TreeFam:
Gene Tree for PCF11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCF11: view image
Alliance of Genome Resources:
Additional Orthologs for PCF11

Paralogs for PCF11 Gene

No data available for Paralogs for PCF11 Gene

Variants for PCF11 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCF11 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs116099331 Benign: not provided 83,168,850(+) G/A
NM_015885.4(PCF11):c.2515G>A (p.Gly839Ser)
MISSENSE
rs140586284 Benign: not provided 83,177,140(+) A/G
NM_015885.4(PCF11):c.3813A>G (p.Glu1271=)
SYNONYMOUS
rs141549874 Benign: not provided 83,168,988(+) C/T
NM_015885.4(PCF11):c.2653C>T (p.Pro885Ser)
MISSENSE
rs17144735 Benign: not provided 83,181,167(+) T/C
NM_015885.4(PCF11):c.4143T>C (p.His1381=)
SYNONYMOUS
rs864309498 Uncertain Significance: Acute megakaryoblastic leukemia; Mediastinal germ cell tumor 83,169,557(+) GT/G
NM_015885.4(PCF11):c.3225del (p.Phe1075fs)
FRAMESHIFT

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PCF11 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 PCF11 Gene

Variant ID Type Subtype PubMed ID
esv33531 CNV loss 17666407

Variation tolerance for PCF11 Gene

Residual Variation Intolerance Score: 9.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.15; 75.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCF11 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCF11
Leiden Open Variation Database (LOVD)
PCF11

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCF11 Gene

Disorders for PCF11 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PCF11 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search PCF11 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PCF11

genes like me logo Genes that share disorders with PCF11: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCF11 Gene

Publications for PCF11 Gene

  1. Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors. (PMID: 11060040) de Vries H … Keller W (The EMBO journal 2000) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4
  4. Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells. (PMID: 30585729) Abbasi S … Schild-Poulter C (Journal of proteome research 2019) 3
  5. Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination. (PMID: 30819644) Kamieniarz-Gdula K … Proudfoot NJ (Molecular cell 2019) 3

Products for PCF11 Gene

Sources for PCF11 Gene