In prokaryotes, one gene codes for one protein. Eukaryotes used a much more elaborate mechanism to increase sequence diversity and to enable themselves to produce newer proteins.

Alternative promoter usage

Several exons are involved to code for a single protein. Any one of the several exons can used to initiate the expression. The choice of the initiating exon could generate a different isoform of the same protein. In other words, alternative usage of promoters results in proteins with different isoforms.

Alternative splicing

RNA splicing is a precisely regulated co- and post- transcriptional process (occurring prior to mRNA translation) that removes introns and joins exons in a primary transcript.

During RNA splicing, exons can either be retained in the mature message or targeted for removal in different combinations to create a diverse array of mRNAs from a single pre-mRNA, a process referred to as alternative RNA splicing (tissue and cell specific).

There are four known modes of alternative splicing:

1. Alternative selection of promoters:
This is the only method of splicing which can produce an alternative N-terminus domain in proteins. In this case, different sets of promoters can be spliced with certain sets of other exons.
2. Alternative selection of cleavage/polyadenylation sites:
This is the only method of splicing which can produce an alternative C-terminus domain in proteins. In this case, different sets of polyadenylation sites can be spliced with the other exons.
3. Intron retaining mode
In this case, instead of splicing out an intron, the intron is retained in the mRNA transcript. However, the intron must be properly encoding for amino acids. The intron's code must be properly expressible, otherwise a stop codon or a shift in the reading frame will cause the protein to be non-functional.
4. Exon cassette mode:
In this case, certain exons are spliced out to alter the sequence of amino acids in the expressed protein.mRNA editing

…~15 % of disease-causing mutations involve misregulation of alternative splicing (missplicing)…

Exon order is not conserved. It cam be scrambled. A technique used in alternative promotor usage.

Trans-splicing vs. Cis-splicing

Splicing prepares pre-mRNA in eukaryotes to produce mature mRNA. This mature messenger RNA is then prepared to undergo translation as part of protein synthesis to produce proteins. When the exons are in the SAME RNA transcript, it is called cis-splicing.

Trans-splicing is a form of splicing that joins two exons that are not within the same RNA transcript.

Exonic splicing enhancers (ESEs) – pre-mRNA cis-acting elements

ESEs are discrete sequences within exons that promote both constitutive and regulated splicing. The precise mechanism by which ESEs facilitate the assembly of splicing complexes has been controversial. However, recent studies have provided insights into this question and have led to a new model for ESE function. Other recent work has suggested that ESEs are comprised of diverse sequences and occur frequently within exons. Ominously, these latter studies predict that many human genetic diseases linked to mutations within exons might be caused by the inactivation of ESEs.

Exon sequence enhancers prediction - http://rulai.cshl.edu/tools/ESE/

Alternative splicing database project - http://www.ebi.ac.uk/asd/index.html