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CPSF3 cleavage and polyadenylation specific factor 3 [ Homo sapiens (human) ]

Gene ID: 51692, updated on 8-May-2016
Official Symbol
CPSF3provided by HGNC
Official Full Name
cleavage and polyadenylation specific factor 3provided by HGNC
Primary source
HGNC:HGNC:2326
See related
Ensembl:ENSG00000119203 HPRD:05825; MIM:606029; Vega:OTTHUMG00000090415
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
Also known as
CPSF73; CPSF-73
Summary
This gene encodes a member of the metallo-beta-lactamase family. The encoded protein is a 73kDa subunit of the cleavage and polyadenylation specificity factor and functions as an endonuclease that recognizes the pre-mRNA 3'-cleavage site AAUAAA prior to polyadenylation. It also cleaves after the pre-mRNA sequence ACCCA during histone 3'-end pre-mRNA processing. [provided by RefSeq, Oct 2012]
Orthologs
Location:
2p25.1
Exon count:
19
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 2 NC_000002.12 (9423537..9473110)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (9563666..9613239)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506317 Neighboring gene ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 Neighboring gene integrin subunit beta 1 binding protein 1 Neighboring gene isoamyl acetate-hydrolyzing esterase 1 homolog Neighboring gene ADAM metallopeptidase domain 17 Neighboring gene uncharacterized LOC101929643

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Protein interactions

Protein Gene Interaction Pubs
Tat tat 73 kDa subunit of the cleavage and polyadenylation specificity factor (CPSF-73) and its homologue RC-68 repress the HIV-1 LTR promoter. The LTR region between -275 to -110 within the 5' upstream region is necessary for the CPSF-73 interaction PubMed
tat HIV-1 Tat interacts with CPSF-73 and counteracts its repressive activity on the HIV-1 LTR promoter. The N-terminal 48 amino acid residues of Tat are sufficient to mediate the interaction with CPSF-73 PubMed
tat HIV-1 Tat specifically increases the expression of the cleavage and polyadenylation specificity factor 73-kDa subunit (CPSF3), and this upregulation is an important regulatory step for both viral and cellular gene expression PubMed

Go to the HIV-1, Human Interaction Database

  • 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.
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing.
  • Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystemTransport of mature mRNAs derived from intronless transcripts require some of the same protein complexes as mRNAs derived from intron containing complexes, including TAP and Aly/Ref. However a number...
  • 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 processing, organism-specific biosystem (from WikiPathways)
    mRNA processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • 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 ...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
5'-3' exonuclease activity ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
endoribonuclease activity ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA phosphodiester bond hydrolysis, endonucleolytic IEA
Inferred from Electronic Annotation
more info
 
mRNA 3'-end processing TAS
Traceable Author Statement
more info
 
mRNA 3'-end processing by stem-loop binding and cleavage IDA
Inferred from Direct Assay
more info
PubMed 
mRNA cleavage TAS
Traceable Author Statement
more info
PubMed 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA polyadenylation TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
termination of RNA polymerase II transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
intracellular ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 
mRNA cleavage and polyadenylation specificity factor complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
Preferred Names
cleavage and polyadenylation specificity factor subunit 3
Names
cleavage and polyadenylation specific factor 3, 73kDa
mRNA 3'-end-processing endonuclease CPSF-73

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_001321833.1NP_001308762.1  cleavage and polyadenylation specificity factor subunit 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) and variant 3 both encode the same isoform (b).
    Source sequence(s)
    AA635764, BC014106, DA455023, DC420903
    Conserved Domains (5) summary
    smart00849
    Location:1158
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:209330
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:1417
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:343385
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:440646
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
  2. NM_001321834.1NP_001308763.1  cleavage and polyadenylation specificity factor subunit 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) and variant 2 both encode the same isoform (b).
    Source sequence(s)
    AA635764, BC014106, DA455023, DC420903
    Conserved Domains (5) summary
    smart00849
    Location:1158
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:209330
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:1417
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:343385
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:440646
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
  3. NM_001321835.1NP_001308764.1  cleavage and polyadenylation specificity factor subunit 3 isoform c

    Status: REVIEWED

    Source sequence(s)
    AA635764, BC014106, DA478774, DC420903
    Conserved Domains (4) summary
    smart01027
    Location:107228
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:18315
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:241283
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:338544
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
  4. NM_001321836.1NP_001308765.1  cleavage and polyadenylation specificity factor subunit 3 isoform d

    Status: REVIEWED

    Source sequence(s)
    AA635764, AC080162, BC014106, BG773037, DA455023, DC420903
    Conserved Domains (5) summary
    smart00849
    Location:30199
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:250371
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:22458
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:384426
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:481687
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
  5. NM_016207.3NP_057291.1  cleavage and polyadenylation specificity factor subunit 3 isoform a

    See identical proteins and their annotated locations for NP_057291.1

    Status: REVIEWED

    Source sequence(s)
    AA635764, BC020211, DC420903
    Consensus CDS
    CCDS1664.1
    UniProtKB/Swiss-Prot
    Q9UKF6
    Related
    ENSP00000238112, OTTHUMP00000115483, ENST00000238112, OTTHUMT00000206843
    Conserved Domains (5) summary
    smart00849
    Location:26195
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:246367
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:14454
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:380422
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:477683
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p2 Primary Assembly

    Range
    9423537..9473110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246168.1XP_005246225.1  

    UniProtKB/TrEMBL
    G5E9W3
    Conserved Domains (5) summary
    smart00849
    Location:1158
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:209330
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:1417
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:343385
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:440646
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
  2. XM_011510362.1XP_011508664.1  

    UniProtKB/TrEMBL
    G5E9W3
    Related
    ENSP00000418957, OTTHUMP00000214089, ENST00000460593, OTTHUMT00000353330
    Conserved Domains (5) summary
    smart00849
    Location:1158
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:209330
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:1417
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:343385
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:440646
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
  3. XM_005246167.3XP_005246224.1  

    Conserved Domains (5) summary
    smart00849
    Location:16185
    Lactamase_B; Metallo-beta-lactamase superfamily
    smart01027
    Location:236357
    Beta-Casp; Beta-Casp domain
    COG1236
    Location:1444
    YSH1; RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]
    pfam07521
    Location:370412
    RMMBL; RNA-metabolizing metallo-beta-lactamase
    pfam11718
    Location:467673
    CPSF73-100_C; Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 Alternate CHM1_1.1

    Range
    9493101..9542657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)