scholarly journals A native RNA secondary structure controls alternative splice-site selection and generates two human growth hormone isoforms.

1992 ◽  
Vol 267 (21) ◽  
pp. 14902-14908 ◽  
Author(s):  
P.A. Estes ◽  
N.E. Cooke ◽  
S.A. Liebhaber
1987 ◽  
pp. 97-112 ◽  
Author(s):  
JAMES L. MANLEY ◽  
JONATHAN C.S. NOBLE ◽  
XIN-YUAN FU ◽  
HUI GE

2003 ◽  
Vol 278 (20) ◽  
pp. 18241-18248 ◽  
Author(s):  
Ute Raffetseder ◽  
Björn Frye ◽  
Thomas Rauen ◽  
Karsten Jürchott ◽  
Hans-Dieter Royer ◽  
...  

2018 ◽  
Author(s):  
Hannes Bretschneider ◽  
Shreshth Gandhi ◽  
Amit G Deshwar ◽  
Khalid Zuberi ◽  
Brendan J Frey

AbstractMotivationAlternative splice site selection is inherently competitive and the probability of a given splice site to be used also depends strongly on the strength of neighboring sites. Here we present a new model named Competitive Splice Site Model (COSSMO), which explicitly models these competitive effects and predict the PSI distribution over any number of putative splice sites. We model an alternative splicing event as the choice of a 3’ acceptor site conditional on a fixed upstream 5’ donor site, or the choice of a 5’ donor site conditional on a fixed 3’ acceptor site. We build four different architectures that use convolutional layers, communication layers, LSTMS, and residual networks, respectively, to learn relevant motifs from sequence alone. We also construct a new dataset from genome annotations and RNA-Seq read data that we use to train our model.ResultsCOSSMO is able to predict the most frequently used splice site with an accuracy of 70% on unseen test data, and achieve an R2 of 60% in modeling the PSI distribution. We visualize the motifs that COSSMO learns from sequence and show that COSSMO recognizes the consensus splice site sequences as well as many known splicing factors with high specificity.AvailabilityOur dataset is available from http://cossmo.deepgenomics.com.Contactfrey@deepgenomics.comSupplementary informationSupplementary data are available at Bioinformatics online.


2018 ◽  
Vol 34 (13) ◽  
pp. i429-i437 ◽  
Author(s):  
Hannes Bretschneider ◽  
Shreshth Gandhi ◽  
Amit G Deshwar ◽  
Khalid Zuberi ◽  
Brendan J Frey

1988 ◽  
Vol 8 (5) ◽  
pp. 2042-2051
Author(s):  
K Wiebauer ◽  
J J Herrero ◽  
W Filipowicz

The report that human growth hormone pre-mRNA is not processed in transgenic plant tissues (A. Barta, K. Sommergruber, D. Thompson, K. Hartmuth, M.A. Matzke, and A.J.M. Matzke, Plant Mol. Biol. 6:347-357, 1986) has suggested that differences in mRNA splicing processes exist between plants and animals. To gain more information about the specificity of plant pre-mRNA processing, we have compared the splicing of the soybean leghemoglobin pre-mRNA with that of the human beta-globin pre-mRNA in transfected plant (Orychophragmus violaceus and Nicotiana tabacum) protoplasts and mammalian (HeLa) cells. Of the three introns of leghemoglobin pre-mRNA, only intron 2 was correctly and efficiently processed in HeLa cells. The 5' splice sites of the remaining two introns were faithfully recognized, but correct processing of the 3' sites took place only rarely (intron 1) or not at all (intron 3); cryptic 3' splice sites were used instead. While the first intron in human beta-globin pre-mRNA was not spliced in transfected plant protoplasts, intron 2 processing occurred at a low level, indicating that some mammalian introns can be recognized by the plant intron-splicing machinery. However, excision of intron 2 proved to be incorrect, involving the authentic 5' splice site and a cryptic 3' splice site. Our results indicate that the mechanism of 3'-splice-site selection during intron excision differs between plants and animals. This conclusion is supported by analysis of the 3'-splice-site consensus sequences in animal and plant introns which revealed that polypyrimidine tracts, characteristic of animal introns, are not present in plant pre-mRNAs. It is proposed that an elevated AU content of plant introns is important for their processing.


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