Module 7: Molecular Computing with RNA Sequences
Translational Control Elements
- Search for consensus 5' untranslated sequences: Prokaryotic mRNAs have the consensus Shine-Delgarno
sequence immediately upstream (5') of the translation initiation AUG codon (Figure of Prokaryotic 5' Untranslated Region). Eukaryotes have no such common site in the 5'
untranslated regions of their mRNAs. The HMMgene server can locate the potential start codon in vertebrate and C.elegans genes.
- Search for consensus 3' poly-A sequences: POLYAH is an algorithm which is part of the
Gene Finder site that can search
for potential poly-A regions with the AATAAA sequence in human genes. Another server wherein one can search for
3'-polyadenylation signals is at GENSCAN.
- Control of protein secretion during translation: Secretory proteins in eukaryotic cells are made with a
signal sequence which is cleaved off during passage through the endoplasmic reticular membrane. This process is
aided by a signal recognition particle (SRP) which can recognize and bind a ribosome translating a mRNA for a
secretory protein. The Signal Recognition
Particle (SRP) Database provides aligned, annotated and phylogenetically ordered sequences related to structure
and function of SRPs. (Figure of SRP Function)