136
Alternatively Spliced Genes
Tab. 1
(
continued
)
Acce.#
Protein name
Yeast homolog
(SGD ORF)
Motifs
Cal. MWt
Spliced mRNP/EJC proteins
AF048977
SRm160
PWI, RS
93 519
Q13838
UAP56
SUB2 (YDL084W)
DExD, Helicase
48 991
PJC4525
RNPS1
1 RRM, Ser-rich
34 208
NM
005782
Aly
YRA1 (YDR381W)
1 RRM
26 861
Q9Y5S9
Y14
1 RRM
19 889
P50606
Magoh
Mago
nashi
17 164
Source
: (Adapted with permission from Zhou, Z., Licklider, L.J., Gygi, S.P., Reed, R. (2002)
Comprehensive proteomic analysis of the human spliceosome,
Nature
419
(6903), 182–185).
Note
: A. snRNP proteins. B. Non-snRNP spliceosomal proteins. C. Late-acting spliceosomal proteins.
In each list, spliceosomal proteins are grouped by their structural motifs. Corresponding GenBank
accession numbers are shown (Acce#), together with their yeast homologs (as SGD open reading
frame, SGD ORF), sequence motifs, and calculated molecular weight (Cal. Mwt).
COLD: cold shock RNA-binding domain; Cyclophilin: cyclophilin type peptidyl–prolyl cis–trans
isomerase; DEATH: domain found in proteins involved in cell death; DExD: DExD/H-like helicases
superfamily; DSRM: double-stranded RNA-binding motif; ERM: ezrin/radixin/moesin family motif;
fSAP: functional spliceosome-associated protein; FF: two conserved F residues; G domain:
GTP-binding domain that contains a P-loop motif; GYF: contains conserved G-T-F residues; HAT:
Half-A-TPR (tetratrico-peptide repeat); Gly-rich: peptide sequences rich in G, R, S residues; HELICc:
helicase superfamily c-terminal domain; KH: hnRNP K homology RNA-binding domain; MIF4G:
middle domain of eukaryotic initiation factor 4G; NOP: putative snoRNA binding domain; NUDIX:
mutT-like domain; PABP: poly-adenylate binding protein, unique domain; PP2A: protein phosphatase
2A repeat; PWI: domain in splicing factors; RED: protein with extensive stretch of alternating R and E
or D; RRM: RNA recognition motif; RS: arginine–serine-rich domains; SKIP: conserved domain found
in chromatinic proteins; Sm: snRNP Sm proteins; SWAP: suppressor-of-white-apricot splicing
regulator; TUDOR: a domain present in several RNA-binding proteins; TyrKc: tyrosine kinase,
catalytic domain; UBQ: ubiquitin homologs; Ubox: modi±ed RING ±nger domain; WD40s: WD40
repeats, structural repeats of the beta propeller domain; WW: domain with 2 conserved W residues,
interacting with proline-rich polypeptides; ZF: Zinc ±nger domain.
whereas
the
U12-type
of
spliceosome
involves U11, U12, and U4atac/U6atac,
with both sharing U5snRNP. Although
nucleotide sequences of U11, U12, and
U4atac/U6atac snRNAs are different from
their counterparts in the spliceosomes
for U2-type introns, the predicted sec-
ondary structures of the corresponding
snRNAs have striking similarity (Fig. 3a).
In
addition,
the
speci±c
interactions
between the spliceosomal snRNAs and
pre-mRNA substrates also appear to be
highly similar, as shown in Fig. 3(b). Both
U2-
and
U12-types
of
introns
can
be
found in the same genes. There is ev-
idence suggesting that the two types of
spliceosomes may interact and share some
protein components in addition to the
common U5snRNP. The evolutionary ori-
gins of these two types of spliceosomes
remain largely speculative.
U12-class introns contain more con-
served sequences at the 5
0
ss. The
se-
quences around branch sites of the U12-
class introns are also highly conserved with
the TCCTTAA
C (the underlined A as the
branch site) consensus signal located ap-
proximately10to20nucleotidesupstream
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