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Aliases for PCF11 Gene

Aliases for PCF11 Gene

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

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. Among its related pathways are mRNA surveillance pathway and Formation of HIV elongation complex in the absence of HIV Tat. GO annotations related to this gene include mRNA binding and RNA polymerase II core binding.

UniProtKB/Swiss-Prot for PCF11 Gene

  • Component of pre-mRNA cleavage complex II.

Additional gene information for PCF11 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCF11 Gene

Genomics for PCF11 Gene

Regulatory Elements for PCF11 Gene

Enhancers for PCF11 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11H083155 1.4 ENCODE dbSUPER 42.4 +2.4 2442 8 HNRNPUL1 HDGF PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1 PCF11 ANKRD42 LOC100506282 ENSG00000254676 RAB30-AS1 RAB30 ENSG00000254551 SNORA70E ENSG00000254522 ENSG00000254698
GH11H082899 1.7 FANTOM5 ENCODE dbSUPER 29.7 -256.0 -256033 3.8 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 PCF11 DDIAS ENSG00000254676 PRCP ENSG00000254551 ANKRD42 RAB30 RPL7AP54
GH11H083042 1.3 Ensembl ENCODE dbSUPER 21.5 -112.7 -112715 2.9 GTF2F1 TBP KLF1 JUN ETV1 CHD4 FEZF1 FOSL1 HIC1 GTF3C2 PCF11 RAB30 ENSG00000254676 ENSG00000254551 RAB30-AS1 PRCP SNORA70E GC11M083042
GH11H083006 1.6 Ensembl ENCODE dbSUPER 15.5 -149.2 -149172 2.4 ARNT ARID4B DMAP1 ZNF766 SP5 JUNB ZNF592 KAT8 SMARCA4 RCOR2 PCF11 DDIAS ENSG00000254551 ENSG00000254676 ENSG00000254698 SNORA70E ENSG00000254522 RAB30 RAB30-AS1 GC11M082975
GH11H083284 1.2 ENCODE 18 +128.8 128759 3.4 HDGF PKNOX1 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 CCDC90B PCF11 ENSG00000255234 ENSG00000254676 GC11M083251
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCF11 on UCSC Golden Path with GeneCards custom track

Promoters for PCF11 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000042784 1012 4801 HNRNPUL1 HDGF PKNOX1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1

Genomic Locations for PCF11 Gene

Genomic Locations for PCF11 Gene
chr11:83,156,988-83,187,451
(GRCh38/hg38)
Size:
30,464 bases
Orientation:
Plus strand
chr11:82,868,030-82,898,493
(GRCh37/hg19)

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; Positions=712; 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};

neXtProt entry for PCF11 Gene

Post-translational modifications for PCF11 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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
  • Predicted secreted proteins

Protein Domains for PCF11 Gene

Suggested Antigen Peptide Sequences for PCF11 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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 core binding IBA --
GO:0003729 mRNA binding IBA --
genes like me logo Genes that share ontologies with PCF11: view
genes like me logo Genes that share phenotypes with PCF11: view

miRNA for PCF11 Gene

miRTarBase miRNAs that target PCF11

Clone Products

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

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 --
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 IBA,TAS --
GO:0006378 mRNA polyadenylation IBA --
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

Unigene Clusters for PCF11 Gene

PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae):
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
PCF11

Expression for PCF11 Gene

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

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, PaxDb, MaxQB, and MOPED for PCF11 Gene



Protein tissue co-expression partners for PCF11 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCF11 Gene:

PCF11

SOURCE GeneReport for Unigene cluster for PCF11 Gene:

Hs.128959

Evidence on tissue expression from TISSUES for PCF11 Gene

  • Nervous system(4.6)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with PCF11: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 33 34
  • 98.53 (n)
dog
(Canis familiaris)
Mammalia PCF11 33 34
  • 95.2 (n)
cow
(Bos Taurus)
Mammalia LOC510604 33
  • 92.47 (n)
PCF11 34
  • 88 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pcf11 33
  • 91.69 (n)
mouse
(Mus musculus)
Mammalia Pcf11 33 16 34
  • 91.59 (n)
oppossum
(Monodelphis domestica)
Mammalia PCF11 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PCF11 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves PCF11 33 34
  • 74.93 (n)
lizard
(Anolis carolinensis)
Reptilia PCF11 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.10887 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.8613 33
zebrafish
(Danio rerio)
Actinopterygii pcf11 33 34
  • 58.44 (n)
Dr.18893 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6287 33
fruit fly
(Drosophila melanogaster)
Insecta CG10228 35
  • 43 (a)
Pcf11 34
  • 14 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea pcf-11 34
  • 26 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PCF11 34 36
  • 25 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 15 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5693 33
Species where no ortholog for PCF11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for PCF11 Gene

No data available for Paralogs for PCF11 Gene

Variants for PCF11 Gene

Sequence variations from dbSNP and Humsavar for PCF11 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs864309498 Uncertain significance 83,169,558(+) AGAGG(-/T)TTGAT nc-transcript-variant, reference, frameshift-variant
rs1000001182 -- 83,167,726(+) TGTGA(A/G)CCATC intron-variant, nc-transcript-variant, reference, synonymous-codon
rs1000033007 -- 83,185,189(+) ATAAA(A/C)AATAT nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1000124480 -- 83,164,603(+) ATAGG(C/T)CAGGC intron-variant
rs1000328338 -- 83,171,592(+) TTTAA(C/T)CCATT intron-variant

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)

Relevant External Links for PCF11 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCF11

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

Disorders for PCF11 Gene

Relevant External Links for PCF11

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCF11

No disorders were found for PCF11 Gene.

No data available for MalaCards , 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 60
  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 60
  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 60
  4. Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation. (PMID: 28112733) Hendriks IA … Nielsen ML (Nature structural & molecular biology 2017) 4 60
  5. Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators. (PMID: 27880917) St-Denis N … Gingras AC (Cell reports 2016) 3 60

Products for PCF11 Gene

Sources for PCF11 Gene

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