RGD Reference Report - Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. - Rat Genome Database

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Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors.

Authors: Gruber, AR  Martin, G  Keller, W  Zavolan, M 
Citation: Gruber AR, etal., Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):183-96. doi: 10.1002/wrna.1206. Epub 2013 Nov 14.
RGD ID: 9681742
Pubmed: PMID:24243805   (View Abstract at PubMed)
PMCID: PMC4282565   (View Article at PubMed Central)
DOI: DOI:10.1002/wrna.1206   (Journal Full-text)

Expression of mature messenger RNAs (mRNAs) requires appropriate transcription initiation and termination, as well as pre-mRNA processing by capping, splicing, cleavage, and polyadenylation. A core 3'-end processing complex carries out the cleavage and polyadenylation reactions, but many proteins have been implicated in the selection of polyadenylation sites among the multiple alternatives that eukaryotic genes typically have. In recent years, high-throughput approaches to map both the 3'-end processing sites as well as the binding sites of proteins that are involved in the selection of cleavage sites and in the processing reactions have been developed. Here, we review these approaches as well as the insights into the mechanisms of polyadenylation that emerged from genome-wide studies of polyadenylation across a range of cell types and states.



Molecular Pathway Annotations    Click to see Annotation Detail View

RGD Manual Annotations


  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
CLP1Human3'-end pre-mRNA processing pathway  TAS  RGD 
CPSF1Human3'-end pre-mRNA processing pathway  TAS  RGD 
CPSF2Human3'-end pre-mRNA processing pathway  TAS  RGD 
CPSF3Human3'-end pre-mRNA processing pathway  TAS  RGD 
CPSF4Human3'-end pre-mRNA processing pathway  TAS  RGD 
CPSF6Human3'-end pre-mRNA processing pathway  TAS  RGD 
CPSF7Human3'-end pre-mRNA processing pathway  TAS  RGD 
CSTF1Human3'-end pre-mRNA processing pathway  TAS  RGD 
CSTF2Human3'-end pre-mRNA processing pathway  TAS  RGD 
CSTF2THuman3'-end pre-mRNA processing pathway  TAS  RGD 
CSTF3Human3'-end pre-mRNA processing pathway  TAS  RGD 
Clp1Mouse3'-end pre-mRNA processing pathway  ISOCLP1 (Homo sapiens) RGD 
Clp1Rat3'-end pre-mRNA processing pathway  ISOCLP1 (Homo sapiens) RGD 
Cpsf1Mouse3'-end pre-mRNA processing pathway  ISOCPSF1 (Homo sapiens) RGD 
Cpsf1Rat3'-end pre-mRNA processing pathway  ISOCPSF1 (Homo sapiens) RGD 
Cpsf2Mouse3'-end pre-mRNA processing pathway  ISOSnai3 (Mus musculus) RGD 
Cpsf2Rat3'-end pre-mRNA processing pathway  ISOSnai3 (Mus musculus) RGD 
Cpsf3Mouse3'-end pre-mRNA processing pathway  ISOCPSF3 (Homo sapiens) RGD 
Cpsf3Rat3'-end pre-mRNA processing pathway  ISOCPSF3 (Homo sapiens) RGD 
Cpsf4Mouse3'-end pre-mRNA processing pathway  ISOCPSF4 (Homo sapiens) RGD 
Cpsf4Mouse3'-end pre-mRNA processing pathway  ISOArhgef5 (Mus musculus) RGD 
Cpsf6Mouse3'-end pre-mRNA processing pathway  ISOCPSF6 (Homo sapiens) RGD 
Cpsf6Rat3'-end pre-mRNA processing pathway  ISOCPSF6 (Homo sapiens) RGD 
Cpsf7Mouse3'-end pre-mRNA processing pathway  ISOCPSF7 (Homo sapiens) RGD 
Cpsf7Rat3'-end pre-mRNA processing pathway  ISOCPSF7 (Homo sapiens) RGD 
Cstf1Mouse3'-end pre-mRNA processing pathway  ISOCSTF1 (Homo sapiens) RGD 
Cstf1Rat3'-end pre-mRNA processing pathway  ISOCSTF1 (Homo sapiens) RGD 
Cstf2Mouse3'-end pre-mRNA processing pathway  ISOCSTF2 (Homo sapiens) RGD 
Cstf2Rat3'-end pre-mRNA processing pathway  ISOCSTF2 (Homo sapiens) RGD 
Cstf2tMouse3'-end pre-mRNA processing pathway  ISOCSTF2T (Homo sapiens) RGD 
Cstf2tRat3'-end pre-mRNA processing pathway  ISOCSTF2T (Homo sapiens) RGD 
Cstf3Mouse3'-end pre-mRNA processing pathway  ISOCSTF3 (Homo sapiens) RGD 
Cstf3Rat3'-end pre-mRNA processing pathway  ISOCSTF3 (Homo sapiens) RGD 
FIP1L1Human3'-end pre-mRNA processing pathway  TAS  RGD 
Fip1l1Mouse3'-end pre-mRNA processing pathway  ISOFIP1L1 (Homo sapiens) RGD 
Fip1l1Rat3'-end pre-mRNA processing pathway  ISOFIP1L1 (Homo sapiens) RGD 
NUDT21Human3'-end pre-mRNA processing pathway  TAS  RGD 
Nudt21Mouse3'-end pre-mRNA processing pathway  ISONUDT21 (Homo sapiens) RGD 
Nudt21Rat3'-end pre-mRNA processing pathway  ISONUDT21 (Homo sapiens) RGD 
PABPN1Human3'-end pre-mRNA processing pathway  TAS  RGD 
PAPOLAHuman3'-end pre-mRNA processing pathway  TAS  RGD 
PAPOLBHuman3'-end pre-mRNA processing pathway  TAS  RGD 
PAPOLGHuman3'-end pre-mRNA processing pathway  TAS  RGD 
PCF11Human3'-end pre-mRNA processing pathway  TAS  RGD 
Pabpn1Rat3'-end pre-mRNA processing pathway  ISOPABPN1 (Homo sapiens) RGD 
Pabpn1Mouse3'-end pre-mRNA processing pathway  ISOPABPN1 (Homo sapiens) RGD 
PapolaRat3'-end pre-mRNA processing pathway  ISOPAPOLA (Homo sapiens) RGD 
PapolaMouse3'-end pre-mRNA processing pathway  ISOPAPOLA (Homo sapiens) RGD 
PapolbRat3'-end pre-mRNA processing pathway  ISOPAPOLB (Homo sapiens) RGD 
PapolbMouse3'-end pre-mRNA processing pathway  ISOPAPOLB (Homo sapiens) RGD 
PapolgRat3'-end pre-mRNA processing pathway  ISOPAPOLG (Homo sapiens) RGD 
PapolgMouse3'-end pre-mRNA processing pathway  ISOPAPOLG (Homo sapiens) RGD 
Pcf11Rat3'-end pre-mRNA processing pathway  ISOPCF11 (Homo sapiens) RGD 
Pcf11Mouse3'-end pre-mRNA processing pathway  ISOPCF11 (Homo sapiens) RGD 
SYMPKHuman3'-end pre-mRNA processing pathway  TAS  RGD 
SympkMouse3'-end pre-mRNA processing pathway  ISOSYMPK (Homo sapiens) RGD 
SympkRat3'-end pre-mRNA processing pathway  ISOSYMPK (Homo sapiens) RGD 
WDR33Human3'-end pre-mRNA processing pathway  TAS  RGD 
Wdr33Rat3'-end pre-mRNA processing pathway  ISOWDR33 (Homo sapiens) RGD 
Wdr33Mouse3'-end pre-mRNA processing pathway  ISOWDR33 (Homo sapiens) RGD 
CLP1HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CPSF1HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CPSF2HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CPSF3HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CPSF4HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CPSF6HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CPSF7HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CSTF1HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CSTF2HumanRNA polymerase II transcription termination pathway  TAS  RGD 
CSTF2THumanRNA polymerase II transcription termination pathway  TAS  RGD 
CSTF3HumanRNA polymerase II transcription termination pathway  TAS  RGD 
Clp1RatRNA polymerase II transcription termination pathway  ISOCLP1 (Homo sapiens) RGD 
Clp1MouseRNA polymerase II transcription termination pathway  ISOCLP1 (Homo sapiens) RGD 
Cpsf1RatRNA polymerase II transcription termination pathway  ISOCPSF1 (Homo sapiens) RGD 
Cpsf1MouseRNA polymerase II transcription termination pathway  ISOCPSF1 (Homo sapiens) RGD 
Cpsf2RatRNA polymerase II transcription termination pathway  ISOSnai3 (Mus musculus) RGD 
Cpsf2MouseRNA polymerase II transcription termination pathway  ISOSnai3 (Mus musculus) RGD 
Cpsf3RatRNA polymerase II transcription termination pathway  ISOCPSF3 (Homo sapiens) RGD 
Cpsf3MouseRNA polymerase II transcription termination pathway  ISOCPSF3 (Homo sapiens) RGD 
Cpsf4MouseRNA polymerase II transcription termination pathway  ISOArhgef5 (Mus musculus) RGD 
Cpsf4MouseRNA polymerase II transcription termination pathway  ISOCPSF4 (Homo sapiens) RGD 
Cpsf6RatRNA polymerase II transcription termination pathway  ISOCPSF6 (Homo sapiens) RGD 
Cpsf6MouseRNA polymerase II transcription termination pathway  ISOCPSF6 (Homo sapiens) RGD 
Cpsf7RatRNA polymerase II transcription termination pathway  ISOCPSF7 (Homo sapiens) RGD 
Cpsf7MouseRNA polymerase II transcription termination pathway  ISOCPSF7 (Homo sapiens) RGD 
Cstf1RatRNA polymerase II transcription termination pathway  ISOCSTF1 (Homo sapiens) RGD 
Cstf1MouseRNA polymerase II transcription termination pathway  ISOCSTF1 (Homo sapiens) RGD 
Cstf2RatRNA polymerase II transcription termination pathway  ISOCSTF2 (Homo sapiens) RGD 
Cstf2MouseRNA polymerase II transcription termination pathway  ISOCSTF2 (Homo sapiens) RGD 
Cstf2tRatRNA polymerase II transcription termination pathway  ISOCSTF2T (Homo sapiens) RGD 
Cstf2tMouseRNA polymerase II transcription termination pathway  ISOCSTF2T (Homo sapiens) RGD 
Cstf3RatRNA polymerase II transcription termination pathway  ISOCSTF3 (Homo sapiens) RGD 
Cstf3MouseRNA polymerase II transcription termination pathway  ISOCSTF3 (Homo sapiens) RGD 
FIP1L1HumanRNA polymerase II transcription termination pathway  TAS  RGD 
Fip1l1RatRNA polymerase II transcription termination pathway  ISOFIP1L1 (Homo sapiens) RGD 
Fip1l1MouseRNA polymerase II transcription termination pathway  ISOFIP1L1 (Homo sapiens) RGD 
NUDT21HumanRNA polymerase II transcription termination pathway  TAS  RGD 
Nudt21RatRNA polymerase II transcription termination pathway  ISONUDT21 (Homo sapiens) RGD 
Nudt21MouseRNA polymerase II transcription termination pathway  ISONUDT21 (Homo sapiens) RGD 
PCF11HumanRNA polymerase II transcription termination pathway  TAS  RGD 
Pcf11MouseRNA polymerase II transcription termination pathway  ISOPCF11 (Homo sapiens) RGD 
Pcf11RatRNA polymerase II transcription termination pathway  ISOPCF11 (Homo sapiens) RGD 
SYMPKHumanRNA polymerase II transcription termination pathway  TAS  RGD 
SympkRatRNA polymerase II transcription termination pathway  ISOSYMPK (Homo sapiens) RGD 
SympkMouseRNA polymerase II transcription termination pathway  ISOSYMPK (Homo sapiens) RGD 
WDR33HumanRNA polymerase II transcription termination pathway  TAS  RGD 
Wdr33RatRNA polymerase II transcription termination pathway  ISOWDR33 (Homo sapiens) RGD 
Wdr33MouseRNA polymerase II transcription termination pathway  ISOWDR33 (Homo sapiens) RGD 
Objects Annotated

Genes (Rattus norvegicus)
Clp1  (cleavage factor polyribonucleotide kinase subunit 1)
Cpsf1  (cleavage and polyadenylation specific factor 1)
Cpsf2  (cleavage and polyadenylation specific factor 2)
Cpsf3  (cleavage and polyadenylation specific factor 3)
Cpsf6  (cleavage and polyadenylation specific factor 6)
Cpsf7  (cleavage and polyadenylation specific factor 7)
Cstf1  (cleavage stimulation factor subunit 1)
Cstf2  (cleavage stimulation factor subunit 2)
Cstf2t  (cleavage stimulation factor subunit 2, tau variant)
Cstf3  (cleavage stimulation factor subunit 3)
Fip1l1  (factor interacting with PAPOLA and CPSF1)
Nudt21  (nudix hydrolase 21)
Pabpn1  (poly(A) binding protein, nuclear 1)
Papola  (poly (A) polymerase alpha)
Papolb  (poly(A) polymerase beta)
Papolg  (poly(A) polymerase gamma)
Pcf11  (PCF11 cleavage and polyadenylation factor subunit)
Sympk  (symplekin scaffold protein)
Wdr33  (WD repeat domain 33)

Genes (Mus musculus)
Clp1  (CLP1, cleavage and polyadenylation factor I subunit)
Cpsf1  (cleavage and polyadenylation specific factor 1)
Cpsf2  (cleavage and polyadenylation specific factor 2)
Cpsf3  (cleavage and polyadenylation specificity factor 3)
Cpsf4  (cleavage and polyadenylation specific factor 4)
Cpsf6  (cleavage and polyadenylation specific factor 6)
Cpsf7  (cleavage and polyadenylation specific factor 7)
Cstf1  (cleavage stimulation factor, 3' pre-RNA, subunit 1)
Cstf2  (cleavage stimulation factor, 3' pre-RNA subunit 2)
Cstf2t  (cleavage stimulation factor, 3' pre-RNA subunit 2, tau)
Cstf3  (cleavage stimulation factor, 3' pre-RNA, subunit 3)
Fip1l1  (factor interacting with PAPOLA and CPSF1)
Nudt21  (nudix hydrolase 21)
Pabpn1  (poly(A) binding protein, nuclear 1)
Papola  (poly (A) polymerase alpha)
Papolb  (poly (A) polymerase beta (testis specific))
Papolg  (poly(A) polymerase gamma)
Pcf11  (PCF11 cleavage and polyadenylation factor subunit)
Sympk  (symplekin)
Wdr33  (WD repeat domain 33)

Genes (Homo sapiens)
CLP1  (cleavage factor polyribonucleotide kinase subunit 1)
CPSF1  (cleavage and polyadenylation specific factor 1)
CPSF2  (cleavage and polyadenylation specific factor 2)
CPSF3  (cleavage and polyadenylation specific factor 3)
CPSF4  (cleavage and polyadenylation specific factor 4)
CPSF6  (cleavage and polyadenylation specific factor 6)
CPSF7  (cleavage and polyadenylation specific factor 7)
CSTF1  (cleavage stimulation factor subunit 1)
CSTF2  (cleavage stimulation factor subunit 2)
CSTF2T  (cleavage stimulation factor subunit 2 tau variant)
CSTF3  (cleavage stimulation factor subunit 3)
FIP1L1  (factor interacting with PAPOLA and CPSF1)
NUDT21  (nudix hydrolase 21)
PABPN1  (poly(A) binding protein nuclear 1)
PAPOLA  (poly(A) polymerase alpha)
PAPOLB  (poly(A) polymerase beta)
PAPOLG  (poly(A) polymerase gamma)
PCF11  (PCF11 cleavage and polyadenylation factor subunit)
SYMPK  (symplekin scaffold protein)
WDR33  (WD repeat domain 33)


Additional Information