The SerH locus of Tetrahymena thermophila is one of several paralogous loci with 
genes encoding variants of the major cell surface protein known as the 
immobilization antigen (i-ag). The locus is highly polymorphic, raising 
questions concerning functional equivalency and selective forces acting on its 
multiple alleles. Here, we compare the sequences and expression of SerH1, SerH3, 
SerH4, SerH5, and SerH6. The precursor i-ags are highly similar. They are rich 
in alanine, serine, threonine, and cysteine and they share nearly identical ER 
translocation and GPI addition signals. The locations of the 39 cysteines are 
highly conserved, particularly in the 3.5 central, imperfect tandem repeats in 
which 8 periodic cysteines punctuate alternating short and long stretches of 
amino acids. Hydrophobicity patterns are also conserved. Nevertheless, amino 
acid sequence identity is low, ranging from 60.7 to 82.9%. At the nucleotide 
level, from 9.7 to 26.7% of nucleotide sites are polymorphic in pairwise 
comparisons. Expression of each allele is regulated by temperature-sensitive 
mRNA stability. H mRNAs are stable at <36 degrees but are unstable at >36 
degrees. The H5 mRNA, which is less affected by temperature, has a different 
arrangement of the putative mRNA destabilization motif AUUUA. Statistical 
analysis of SerH genes indicates that the multiple alleles are neutral. 
Significantly low ratios of the rates of nonsynonymous to synonymous amino acid 
substitutions suggest that the multiple alleles are subject to purifying 
(negative) selection enforcing constraints on structure.