Last modified on 30 January 2007.

Table 1: Intron Position

The introns in Table 1 are organized by their position numbers in the 16S and 23S rRNAs. The 16S and 23S rRNA position numbers are based on the E. coli rRNA reference sequence (J01695). The intron occurs between the position number listed and the following position (e.g., the introns between position 516 and 517 are listed as 516). Table 1 has four tabular components.

The total number of introns and the number of positions with at least one intron in the 16S and 23S rRNAs are shown in Table 1A. The numbers of intron types per intron position are tabulated in Table 1B, while the numbers of introns at each rRNA position are ranked in Table 1C. This latter table contains six fields of information for each rRNA: 1) number of introns per rRNA position; 2) number of positions with that number of introns; 3) the rRNA position numbers; 4) total number of introns (field #1 × field #2); 5) the Poisson probability (see below for details); and 6) the expected number of introns for each of the observed number of introns per rRNA site.

The list of all publicly available rRNA introns, sorted by the numeric order of the intron positions, is contained in Table 1D. FIELD LIST NEEDS A COMPLETE OVERHAUL. This table has nine fields: 1) rRNA type (16S or 23S); 2) the intron position; 3) the number of documented introns occurring at that position; 4) the intron types (RNA classes) for each rRNA intron position; 5) the number of introns for each intron type for each rRNA position; 6) the length variation (minimum # - maximum #) for introns in each intron type; 7) the cell location for each intron type; 8) the number of phylogenetic groups for each intron type, (here, defined using the third column from Table 4: Phylogenetic Distribution); and 9) the organism name and accession number.

These fields in Table 1D allow for a natural dissemination of the introns that occur at each rRNA site. For example, of the 116 introns (as of December 2001) at position 516 in 16S rRNA, 55 of them are in the IC1 subgroup; these introns range from 334-1789 nucleotides in length, all occur in the nucleus, and are distributed into four distinct phylogenetic groups. 54 of the introns at position 516 are in the IE subgroup, range from 190 to 622 nucleotides in length, all occur in the nucleus, and are also distributed into four distinct phylogenetic groups, etc.

Additional information is available in a new window for each of the values in Table 1D. This information is retrieved from the relational database management system. The information for each intron entry in the new window are: 1) exon (16S or 23S rRNA); 2) intron position in the rRNA; 3) intron type (RNA class); 4) length of intron (in nucleotides); 5) cell location; 6) NCBI phylogeny; 7) organism name; 8) accession number; 9) link to structure diagram (if it is available); and 10) comment.

The highlights from Table 1 are:

  1. As of December 2001, there are 1184 publicly available introns that occur in the rRNAs, with 900 in the 16S rRNA, and 284 in 23S rRNA. These introns are distributed over 152 different positions, 84 in the 16S rRNA and 68 in 23S rRNA.
  2. Although 16S rRNA is approximately half the length of 23S rRNA, there are more than three times as many introns in 16S rRNA. However, this bias is due, at least in part, to the more prevalent sampling of 16S and 16S-like rRNAs for introns.
  3. The sampling of introns at the intron positions is not evenly distributed (1184/152 = 7.79 introns per position for a random sampling). Instead, nearly 50% (71/152) of the intron positions contain a single intron and 89% (135/152) of the intron positions contain ten or less introns. In contrast, 59% (681/1163) of the introns are located at 9% of the intron positions and the three intron positions with the most introns (943, 516, and 1516 in 16S rRNA) contain 361, or 31% (361/1163), of the rRNA introns.
  4. Table 1B compares the observed distribution of rRNA introns with the Poisson distribution for the observed number of introns. The Poisson distribution, P(x) = e-μ μxx!-1, where μ is the mean frequency of introns for positions in a particular exon and x is the target number of introns present at a particular position, allows the calculation of expected numbers of positions containing a particular number of introns. Based upon the observed raw numbers of introns in the 16S and 23S rRNAs, we expect to see no positions in 16S rRNA containing more than five introns and no positions in 23S rRNA containing more than three introns. However, thirty-five rRNA positions fall into one of those two categories. We also see both more positions without introns and fewer positions containing only one or two introns than expected. This observed distribution of rRNA introns among the available insertion positions is extremely unlikely to occur by chance.
  5. While a single intron type occurs at the majority of the intron positions, several positions have more than one intron type. A few of the positions that deserve special attention have IC1 and IE introns at the same position (16S rRNA positions 516 and 1199, and 23S rRNA position 2563). The 16S rRNA position 788 has several examples each of IC1, IIB, and I introns.

Presented as Table 1E are 16S and 23S rRNA secondary structure diagrams that show the locations for all of the known rRNA introns (as of the noted dates).