Figure 5

Multiple valid ARFs in TR-segments. (A) Frequency of valid ARFs (i.e., an ORF without stop codons) for all 6 possible reading frames for 4437 TR-repeated segments ORFs from JGI N. vectensis proteome. The average frequency of valid ARFs in any of the alternative frames is 0.375. The frequencies of all reading frames were normalized so that the original frame (ORF +1, 100%). (B) For each of the 4437 TR-proteins, number of valid ORFs (including the original frame). For example, there are 800 TR-proteins with 4 valid ORFs (including ORF +1). (C) Over-represented and under-represented amino acids for all three ORFs (ORF +1 indicates the original ORF). (D) A scheme for a repeat segment in which each reading frame translates to a nearly identical protein (differing only at the beginning and end of the sequence). In this example, the reverse complement frames are also valid (i.e., do not encounter a stop codon) throughout the sequence. The arrows indicate the directionality of the transcript.