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PCF11 PCF11 cleavage and polyadenylation factor subunit [ Homo sapiens (human) ]

Gene ID: 51585, updated on 12-Oct-2019

Summary

Official Symbol
PCF11provided by HGNC
Official Full Name
PCF11 cleavage and polyadenylation factor subunitprovided by HGNC
Primary source
HGNC:HGNC:30097
See related
Ensembl:ENSG00000165494 MIM:608876
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 13.1), spleen (RPKM 12.7) and 25 other tissues See more
Orthologs

Genomic context

See PCF11 in Genome Data Viewer
Location:
11q14.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (83157095..83187451)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (82868137..82896836)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene C1D nuclear receptor corepressor pseudogene 5 Neighboring gene BCAS2 pseudogene 1 Neighboring gene uncharacterized LOC100506282 Neighboring gene PCF11 antisense RNA 1 Neighboring gene ankyrin repeat domain 42 Neighboring gene CDC28 protein kinase regulatory subunit 1B pseudogene 4 Neighboring gene ribosomal protein L32 pseudogene 24

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cleavage of Growing Transcript in the Termination Region, organism-specific biosystem (from REACTOME)
    Cleavage of Growing Transcript in the Termination Region, organism-specific biosystemThis section includes the cleavage of both polyadenylated and non-polyadenylated transcripts. In the former case polyadenylation has to precede transcript cleavage, while in the latter case there is ...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Processing of Capped Intronless Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intronless Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Processing of Intronless Pre-mRNAs, organism-specific biosystem (from REACTOME)
    Processing of Intronless Pre-mRNAs, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3' processing consists of two steps: The mRNA is first cleaved ...
  • RNA Polymerase II Transcription, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription, organism-specific biosystem
    RNA Polymerase II Transcription
  • RNA Polymerase II Transcription Termination, organism-specific biosystem (from REACTOME)
    RNA Polymerase II Transcription Termination, organism-specific biosystemThe detailed annotation of this section will be completed in the next release.
  • mRNA 3'-end processing, organism-specific biosystem (from REACTOME)
    mRNA 3'-end processing, organism-specific biosystemThe 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3'-end processing consists of two steps: (i) the mRNA is first ...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0824

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II complex binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA cleavage NAS
Non-traceable Author Statement
more info
PubMed 
mRNA polyadenylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
termination of RNA polymerase II transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
termination of RNA polymerase II transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA cleavage factor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA cleavage factor complex NAS
Non-traceable Author Statement
more info
PubMed 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
pre-mRNA cleavage complex 2 protein Pcf11
Names
PCF11, cleavage and polyadenylation factor subunit, homolog
PCF11p homolog
pre-mRNA cleavage complex II protein Pcf11

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_051805.1 RefSeqGene

    Range
    5037..35357
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001346413.2NP_001333342.1  pre-mRNA cleavage complex 2 protein Pcf11 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AP000873
  2. NM_001346414.2NP_001333343.1  pre-mRNA cleavage complex 2 protein Pcf11 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
    Source sequence(s)
    AP000873
  3. NM_001346415.2NP_001333344.1  pre-mRNA cleavage complex 2 protein Pcf11 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses two alternate in-frame splice junctions compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to variant 1.
    Source sequence(s)
    AP000873
  4. NM_015885.4NP_056969.2  pre-mRNA cleavage complex 2 protein Pcf11 isoform 3

    See identical proteins and their annotated locations for NP_056969.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AP000873, BC146778, DB053362
    Consensus CDS
    CCDS44689.1
    UniProtKB/Swiss-Prot
    O94913
    Related
    ENSP00000298281.4, ENST00000298281.8
    Conserved Domains (1) summary
    cd03562
    Location:19130
    CID; CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    83157095..83187451
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001747905.1 RNA Sequence

  2. XR_001747906.1 RNA Sequence

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