Splicing cleanup i)

jambomber's version from 2015-05-09 15:45


Question Answer
How small can exons get before they are skipped in vivo50nt and below tend to be skipped
give an example of a small exon7nt exon in NCAM muscle protein. Strong consensus splice sites
How do 5' and 3' most exons get selected? Interactions of 5'methyl cap and 3' polya sequences with splicing machinery
What is special about splicing as a regulatory mechanism?Highly species specific, patterns evolve very rapidly
Outline iCLip 30sec UV lyse cell digest RNA IP and Rev transcriptase. RT enzymes stall @ location of corss links
What did Jernej Ule show about hRNPC?Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements. Guards transcriptome from deleterious exons
Why are Alus a potential problem for Splicing ?Highly abundnat-10% genome. Contain a poly A linker which in antisense resembles a cryptic 3'SS
Where has rcursive splicing been seen?Saw tooth patterns from RNA seq data in neuronal genes with introns 4kb minimum
How might we detect recursive splicing events?Even though no exon occurs exon definition is still necessary- the necessary sequences therefore ought to be present
How many putative ESE and ESS families did Zhang ID2000 and 974
What did Zhang compare 5' UTR in intronless genes with pseudo exons
The exon is the initial unit of reognition- although this does not relieve problem ofsplice site selection
What proportion of salient info is used as ESEs/ ESS's?50%
What flaws did ZHang point out in Fairbrother?Weak splice sites favours alternatively spliced exons, Confounding presence of req for protein coding limits sequences available
How did Zhang circumvent past problems?Examine sequence enrichment in non coding exons

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