In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs (mRNAs) have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs in order to facilitate gene expression patterns.

These tracks can elucidate RNA processing by identifying RNA molecules that interact with specific RBPs. They were developed using assays that first purify mRNA-RBP complexes and then separate the complexes to identify the target mRNAs bound to specific RBPs. The mRNAs can be identified by methods including sequencing, microarrays, and SAGE.

The tracks in this supertrack contain two forms of information: genes whose transcripts were bound by the given RBP (such as SUNY RIP GeneSt) and approximate location of the RBP binding site in the mRNA sequence (such SUNY RIP Tiling and SUNY RIP-seq).

Please note:

RIP input tracks (both array and sequencing based) were created for use in downstream informatic analysis to produce RBP specific RIP tracks. Low abundance RNA that is undetectable in the input samples may be proportionally enriched to the point of detection in the RIPs. This may be confusing to some users expecting to see RIP as a subset of input. Users seeking information on total RNA should examine the "expression" RNA-seq tracks produced by other ENCODE groups.

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