Spliceosome



Gene
 
BCLAF1 (BCL2-associated transcription factor 1)
 
CASC3 (cancer susceptibility candidate 3)
 
DDX1 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 1)
 
DDX5 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 5)
 
EWSR1 (Ewing sarcoma breakpoint region 1)
 
GFI1 (growth factor independent 1 transcription repressor)
 
HNRNPD (heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa))
 
MELK (maternal embryonic leucine zipper kinase)
 
PDGFRA (platelet-derived growth factor receptor, alpha polypeptide)
 
PPP1R8 (protein phosphatase 1, regulatory (inhibitor) subunit 8)
 
PTBP1 (polypyrimidine tract binding protein 1)
 
SOX2 (SRY (sex determining region Y)-box 2)
 
SPI1 (spleen focus forming virus (SFFV) proviral integration oncogene spi1)
 
SRSF1 (serine/arginine-rich splicing factor 1)
 
SRSF3 (serine/arginine-rich splicing factor 3)
 
THRAP3 (thyroid hormone receptor associated protein 3)
 
THRB (Thyroid Hormone Receptor, Beta)
 
USB1 (U6 snRNA biogenesis 1)
 
USP15 (ubiquitin specific peptidase 15)
 
WRAP53 (WD repeat containing, antisense to TP53)
 
YBX1 (Y box binding protein 1)
 

Protein domains in BCLAF1L and BCLAF1S isoforms.

from : BCLAF1 (BCL2-associated transcription factor 1)
 


Diagram of conserved motifs among DEAD box RNA helicase family proteins.
from : DDX1 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 1)
 


Domain structure of p68 RNA helicase. Functional sequence motifs are marked.

from : DDX5 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 5)
 


from : EWSR1 (Ewing sarcoma breakpoint region 1)
 


Figure 1. GFI1 protein (from Möröy and Khandanpour).

from : GFI1 (growth factor independent 1 transcription repressor)
 


Structure of HNRNPD (AUF1) proteins; RBD1-2, RNA binding domains; Q, glutamine rich element; HNS, Exon 2, 19 amino acids; Exon 7, 49 amino acids.
from : HNRNPD (heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa))
 


A schematic representation of the domain structure of NIPP1 and its interactor binding sites. The FHA-domain (red) binds the indicated interactors via a phosphorylated TP dipeptide motif. NIPP1 binds PP1 via the indicated RVXF-motif and via a C-terminal binding site (green). EED and RNA binding sites are colored blue and orange, respectively. Known phosphorylation sites are indicated in black (in vivo validated) or grey (in vitro data).

from : PPP1R8 (protein phosphatase 1, regulatory (inhibitor) subunit 8)
 


Schematic representation of PTBP1 protein structure. Each RNA recognition motif (RRM) has different binding affinity for pyrimidine-rich sequences on mRNA. The N-terminal domain encloses partially overlapping nuclear localisation (NLS) and export signals (NES). Blue boxes representing RRMs are not drawn to scale.

from : PTBP1 (polypyrimidine tract binding protein 1)
 


from : SPI1 (spleen focus forming virus (SFFV) proviral integration oncogene spi1)
 


Schematic diagram of SF2/ASF protein. SF2/ASF has a modular structure with two RNA recognition motifs (RRM) that provide RNA-binding specificity and one arginine/serine-rich domain (RS), involved in protein-protein interactions that facilitate recruitment of the spliceosome. The RS domain acts also as a nuclear localization signal, controlling the subcellular localization of SF2/ASF. The protein can be phosphorilated in Ser residues in the C-terminal RS domain.

from : SRSF1 (serine/arginine-rich splicing factor 1)
 


Diagram of protein structure of SRSF3. The numbers below the diagram are the amino acid positions in SRSF3 protein. SRSF3 has an RNA recognition motifs (RRM) in the N-terminus and an arginine/serine-rich domain (RS) at the C-terminus. RRM motif identifies and binds specific RNA sequences. RS domain interacts with other proteins and facilitates recruitment of the spliceosomal components. The serine residues of the RS domain can be phosphorylated.

from : SRSF3 (serine/arginine-rich splicing factor 3)
 


Schematic illustrating four human USP15 isoforms. The domain structure is shown for the reference sequence protein (USP15-203) and three alternative isoforms according to Ensembl. DUSP, domain present in ubiquitin-specific proteases; UBL, ubiquitin-like fold; UCH, ubiquitin carboxyl-terminal hydrolase. The cysteine motifs that form the zinc-binding site are shown in purple and the amino acids comprising the catalytic triad are shown in red. The approximate location of nuclear export sequences (triangles) and a putative nuclear localisation signal (inverted triangle) are shown above isoform USP15-203. Differences in amino acid sequence between isoforms are shown in light blue. The UCH is absent in isoform USP15-202, but USP15-201, USP15-203 and USP15-204 are predicted to be catalytically active.

from : USP15 (ubiquitin specific peptidase 15)
 


USP15 and the paralogs USP4 and USP11.The highly similar domain structure is illustrated for USP15 (NP_006304.1), USP4 (NP_003354.2) and USP11 (NP_004642.2). The degree of identity (Id) or similarity (Sim) was derived using ClustalW (EMBL-EBI); note that the indicated UCH homology includes the internal UBL domain. Overall, USP15 shares 56.9% identity (71.2% similarity) with USP4, and 42.4% identity (60.2% similarity) with USP11.

from : USP15 (ubiquitin specific peptidase 15)
 


Structural and functional organization of YB-1. YB-1 is composed by three domains: N-terminal Ala/Pro rich (AP) domain, cold shock domain (CSD) and the C-terminal domain (CTD) containing clusters of positively and negatively charged amino acids. Indicated are some known molecular partners of YB-1 and sites of their interactions (from Sorokin et al., 2005). The arrow indicates proteasomal cleavage sites.

from : YBX1 (Y box binding protein 1)
 


Contributor(s)
Written Sep 2020 Jean-Loup Huret
Citation
This paper should be referenced as such :
Huret JL. Spliceosome. Atlas Genet Cytogenet Oncol Haematol. September 2020
URL : https://www.chromosomesincancer.eu/biocell/page.aspx?id=42