I have a gene sequence with first start codon (ATG) beginning at 446th nucleotide. Then what is the use of first 445 nucleotides? Do those nucleotides play any role in the functioning/expression of that gene?
Long 5' UTRs are not uncommon and are frequently seen in developmentally regulated genes. These UTRs can have secondary structures, like stem-loops, which may control translation or mRNA stability. These UTRs could also be the targets of micro RNAs. The function of a 5' UTR is likely to be very gene specific. This is an area of research that is still very much unexplored.
Eukaryotic mRNAs usually have three distinct segments: 5' untranslated region (UTR), coding sequence (CDS) or open reading frame (ORF), and 3' UTR. 5' UTR is responsible for assembly of the elongation-competent 80S ribosome complex. Theoretically, very short 5' UTR is enough to assemble the 80S ribosome in vitro. However, we have some needs to regulate the ribosomal assembly in spatiotemporal manner to respond to a conditional change in cells and tissues. To do this, various trans-acting factors (e.g., RNA-binding proteins) participate in this process as a negative and positive regulators. In addition, possible secondary structure in 5'UTR is very important for the ribosomal assembly. It could affect general translation initiation pathway called scanning model. In some specific cases, for example, Internal ribosome entry site (IRES) elements, this elements can directly (or indirectly) recruit the ribosome onto the mRNAs. 3' UTR is usually involved in mRNA stability, subcellular localization, and in some cases, translational regulation. Therefore, conditional extension of 3' UTR can confer some novel and critical cis-elements for fate of mRNAs such as AU-rich elements, miRNA-binding sites, etc.
Lots of regulation elements could hide in 5'UTR, high GC for methylation regulation, enhancer sites, etc. If your gene is not the super crucial building block one, you may find it has more than one TSS, then you could have more than one protein.
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