Pseudogenes for human U2 small nuclear RNA do not have a fixed site of 3' truncation

We present the sequences of five additional human U2 pseudogenes which are very similar to the U2.13 pseudogene reported previously [Van Arsdell et al. (1981) Cell 26, 11-17]. All six U2 pseudogenes preserve the 5' end of the mature U2 snRNA sequence, and all six are flanked by nearly perfect direct repeats that differ in sequence and range in length from 16 to 21 base pairs. The 3' ends of the six U2 pseudogenes are truncated at five different sites between position 33 and 82, and in two cases the 3' end of the pseudogene overlaps the downstream direct repeat by 5 or 6 base pairs. The structure of these six U2 pseudogenes contrasts with that of four human U3 pseudogenes [Bernstein et al. (1983) Cell 32, 461-472] all of which are identically truncated at position 69 or 70, and appear to be derived from a self-primed 74 base reverse transcript of U3 snRNA. Comparison of the U2 and U3 pseudogenes suggests a model for their generation in which the 3' end of the pseudogene is always truncated relative to the initial cDNA template.