5`-UTR sequences were defined as the mRNA region spanning from the cap site to the starting codon (excluded), whereas 3`-UTR sequences were defined as the mRNA region spanning from the stop codon (excluded) to poly(A) starting site.

    The 5´-and 3`-UTR of eukariotic mRNAs are known to play a crucial role in:

    Several regulatory signals have already been identified in 5´-and 3`-UTR sequences, usually corresponding to short oligonucleotide tracts, also able to fold in specific secondary structures, which are protein binding sites for various regulatory protein.[2]

    Feature Of 3`end UTR (trailer)

   A variety of oligonucleotides can be made to cover possible alternative codones, especially at third base position.(These oligonucleotides are used to pair with an mRNA or genomic DNA products that include the sequance of the corresponding gene.)

   Most eokaryotic mRNAs have a sequence of poliadenylic acid at the 3`end. This therminal stretch of A residues is often described as the poly(A) tail.(The poly(A) sequence is not coded in the DNA, but is edded to the RNA in the nucleus after transcribtion)

   The addition of poly(A) tail is catalized by the enzyme poly(A) polymerase, which adds ~200 A residues to the free 3`-OH end of the mRNA. The poly(A) track of both nuclear RNA and mRNA are associated with a protein, the poly(A) binding protein (PABP). Related forms of this protein is found in many eukaryotes.

   One PABP monomer of ~70kD is bound every 10-20 base of poly(A) tail. Thus a common feature in many or most eukaryot is the 3`end of the mRNA consist of a stretch of poly(A) bound to a large mass of protein.

   The removal of the poly(A) tail does seem to cause degradation of certain mRNAs; stability of mRNA is likely to be connected with poly(A), although the relationship remains to be defined. Thus the ability of poly(A) to protect mRNA against degradation, and requires binding of the PABP.

   The poly(A) region of mRNA can base pair with oligo(U) or oligo(dT) and this reaction can be used to isolate poly(A) mRNA. The most convenient technique is to immoblize the oligo (U or dT) on a solid support material. Then when an RNA population is applied to the column, only the poly(A) RNA is retained. It can be retrieved by treating the column with a solution that breaks the bonding to release the RNA.[1]

    Feature Of 5`end UTR (leader)

    5`end UTR is controlling mRNA translation initiation with harpin and ribosome entry sites.
    5`end UTR can accurately regulate the amound of protein synthesised from a specific mRNA.[3]
    REFERENCES :  

1. Lewin B, Genes 6.addition

2. Pesole G, Grillo G, Liuni S, Licciulli F, Mignone F, Gissi G, Saccone C. UTRdb and UTR site:specialized databases of sequences and functional elements of 5`and 3`untranslated regions of eukariotic mRNAs. Update 2002.

3. Meijer H.A, Thomas A.M control of eukaryotic protein synthesis by open reading frames in 5`-untranslated region of an mRNA.

4. Pesole G, Grillo G, Larizza A, Liuni S The untranslated regions of eukaryotic mRNAs: structure, function, evolution and bioinformatic tools for their analysis.