1. c acaatataATGGAGCGTGAGACTTCGTCATCTTCAACTCCTCCGGAGGATCTTGTTACATCGATGATCGGAAAGTTCGTCGCTGTCATGTCTA
b acaatataATGGAGCGTGAGACTTCGTCATCTTCAACTCCTCCGGAGGATCTTGTTACATCGATGATCGGAAAGTTCGTCGCTGTCTTGTCTA
a acaatataATGGAGCGTGAGACTTCGTCATCTTCAACTCCTCCGGAGGATCTTGTTACATCGATGATCGGAAAGTTCGTCGCTGTCATGTCTA
************************************************************************************** ******
c ACAACGACATACGATACGAAGGCGTTATTAGCCTTCTCAATCTGCAAGATTCGAAATTAGGTCTCCAAAACGgta-taattcgattccaaacc
b ACAACGACATACGATACGAAGGCGTTATTAGCCTTCTCAATCTGCAAGATTCGAAATTAGGTCTCCAAAACGgtaacaattcgattccaaacc
a ACAACGACATACGATACGAAGGCGTTATTAGCCTTCTCAATCTGCAAGATTCGAAATTAGGTCTCCAAAACGgtaacaattcgattccaaacc
*************************************************************************** ****************
c ctctccaagatctactgtttatgattttcttcttttcaagttcttcatatttgtttctttggtcgttgttagaatatttccgtgaaaactata
b ctctccaagatctactgtttatgattttcttcttttcaagttcttcatatttgtttctttggtcgttgttagaatatttccgtgaaaactata
a ctctccaagatctactgtttatgattttcttcttttcaagttcttcatatttgtttctttggtcgttgttagaatatttccgtgaaaactata
*********************************************************************************************
c cgtttcatatatataaaacagtatcatgtgatagattaaggcctcaaatttatgtatgcagTCGTTAGGGTTTATGGAAGAGAGGTTGAGAAT
b cgtttcatatatataaaacagtatcatgtgatagattaaggcctcaaatttatgtatgcagTCGTTAGGGTTTATGGAAGAGAGGTTGAGAAT
a cgtttcatatatataaaacagtatcatgtgatagattaaggcctcaaatttatgtatgcagTCGTTAGGGTTTATGGAAGAGAGGTTGAGAAT
c GATAATGAGCAACGAGTGTTCCAGGTTCTTAAAGAAGTTCACAGTCACATGGTATTTAGAGGAAGTGACATTAAGgttagttttcgttaattt
b GATAATGAGCAACGAGTGTTCCAGGTTCTTAAAGAAGTTCACAGTCACATGGTATTTAGAGGAAGTGACATTAAGgttagttttcgttaattt
a GATAATGAGCAACGAGTGTTCCAGGTTCTTAAAGAAGTTCACAGTCACATGGTATTTAGAGGAAGTGACATTAAGgttagttttcgttaattt
c tttgggttcaagattcctcgctagtcttcttcctagttagTTGCTTGCTGCACAAGAAACACTTTTCTTGAAGCTTAAACTGGTTATTTTAAT
b tttgggttcaagattcctcgctagtcttcttcctagttagTTGCTTGCTGCACAAGAAACACTTTTCTTGAAGCTTAAACTGGTTATTTTAAT
a tttgggttcaagattcctcgctagtcttcttcctagttagTTGCTTGCTGCACAAGAAACACTTTTCTTGAAGCTTAAACTGGTTATTTTAAT
c TGCACCAATAGCAGATAACGAAGCACACGTTACTGTGTTTAGATTTCGAGgttagttagtttagggtttgagggtcgttaatgataaatcatc
b TGCACCAATAGCAGATAACGAAGCACACGTTACTGTGTTTAGATTTCGAGgttagttagtttagggtttgagggtcgttaatgataaatcatc
a TGCACCAATAGCAGATAACGAAGCACACGTTACTGTGTTTAGATTTCGAGgttagttagtttagggtttgagggtcgttaatgataaatcatc
c tacttggttacttgctatataagataagtttttttttatataaagttatatatattcagtatttgtgacattagtttgttggtttctgtgtcc
b tacttggttacttgctatataagataagtttttttttatataaagttatatatattcagtatttgtgacattagtttgttggtttttgtgtcc
a tacttggttacttgctatataagataagtttttttttatataaagttatatatattcagtatttgtgacattagtttgttggtttttgtgtcc
************************************************************************************* *******
c atatgtttcagtcagtcgaagttctctctctgccgccaccagCTAGGCATAATTCTGCTATAGGGCACGTAGGTAGCTTGATTACTACCGAAG
b atatgtttcagtcagtcgaagttctctctctgccgccaccagCTAGGCATAATTCTGCTATAGGGCACGTAGGTAGCTTGATTACTACCGAAG
a atatgtttcagtcagtcgaagttctctctctgccgccaccagCTAGGCATAATTCTGCTATAGGGCACGTAGGTAGCTTGATTACTACCGAAG
c ACGTGAGGATTGAGGGGGTTATCAGCCATGTTAAATTTCATGATTCGATGATATTCATGAAGAATTgtgagaacctttttttcctgatttcta
b ACGTGAGGATTGAGGGGGTTATCAGCCATGTTAAATTTCATGATTCGATGATATTCATGAAGAATTgtgagaacctttttttcctgatttcta
a ACGTGAGGATTGAGGGGGTTATCAGCCATGTTAAATTTCATGATTCGATGATATTCATGAAGAATTgtgagaacctttttttcctgatttcta
c ttctactaataaataaatatatatataatgttgattcattttaatttacagGTATGTGTTATGGTACTGAGGGGAGGACGAAGAGAAGACGTT
b ttctactaataaataaatatatatataatgttgattcattttaatttacagGTATGTGTTATGGTACTGAGGGGAGGACGAAGAGAAGACGTT
a ttctactaataaataaatatatatataatgttgattcattttaatttacagGTATGTGTTATGGTACTGAGGGGAGGACGAAGAGAAGACGTT
c CAATAGTAGCTTGCAATCAATTAGCTGGTTCAATCCACTTCAAATTCAGAGACATTAAAgtacgtggaccaatacttactcatgcatacatat
b CAATAGTAGCTTGCAATCAATTAGCTGGTTCAATCCACTTCAAATTCAGAGACATTAAAgtacgtggaccaatacttactcatgcatacatat
a CAATAGTAGCTTGCAATCAATTAGCTGGTTCAATCCACTTCAAATTCAGAGACATTAAAgtacgtggaccaatacttactcatgcatacatat
c ttgattaattagtttgtgtactgtacaatttacgatcaatctacaatttacagGCTCTCGAAATCATCTTTGTTCGGGAACTTCTACACAATG
b ttgattaattagtttgtgtactgtacaatttacgatcaatctacaatttacagGCTCTCGAAATCATCTTTGTTCGGGAACTTCTACACAATG
a ttgattaattagtttgtgtactgtacaatttacgatcaatctacaatttacagGCTCTCGAAATCATCTTTGTTCGGGAACTTCTACACAATG
c ATGATCGTGAGTTTGCTGATCAGTTTCCTCTACTAAGTAGATCACACATTTGTCATCGCCAAGGTGGCGTCTGAtagtctcatgccaaggcac
b ATGATCGTGAGTTTGCTGATCAGTTTCCTCTACTAAGTAGATCACACATTTGTCATCGCCAAGGTGGCGTCTGAtagtctcatgccaaggcac
a ATGATCGTGAGTTTGCTGATCAGTTTCCTCTACTAAGTAGATCACACATTTGTCATCGCCAAGGTGGCGTCTGAtagtctcatgccaaggcac
c agcctctttcacatgata
b agcctctttcacatgata
a agcctctttcacatgata
******************
Supplemental Figure 1: Clustal alignment of the RIBONUCLEOPROTEIN genes present in each homologous region a-c. The initiation codon is in green text, the termination codon is in red text, exons are uppercase orange letters and introns are in a lowercase purple font. The untranslated regions are lowercase black script. Identical nucleotides among a-c are indicated with an asterisk below them. The RNP encoded by homologous region b produces a cDNA that differs from those of regions a and c by a single base in the first exon (A(regions a,c)→T(region b)).

2. gatcggtgttcgattagaaaacaaaaagcaagtgtttgttttgtaaaaaaactaATGGCATACTTAAGCTTCAAGTCTAATATGGAACGTACACCACGCGAGTCAAACACTCCTTGTCCGCCTCCCCAACCATCTCCGTCGTTGTTTTCTTCACTACCAGATGACATCGTTTTGAATATCTTGGCTCGCATATCTACTTCCTACTACCAAACGCTCTCTCTTGTCTCCAAGACCTTCCGTTTGCTCATCCTCTCCAAGGAGCTCGACATGGAACGTTCCTACCTTGGAACCCGAAAACCATGTGTTTATGTCTGCCTTCAATCTCCCACCCATCCTTTTGATCGTAGATGGTTCGGTCTCTGGATAAAACCCTATGATCATCAGCCCCTAACCCATTGGACGATCGACATCAAGTGTACCGGACATTGGTTGCTACCGATGCCCTCTCCCTATTCTCGTTGCTTACAAATAGTCCACGAAACTGTTGGTTCAGAAACATACGAAATCGGTGGACAAAACATGACACCCTCGACTGACGTATGGGTCTATGATAAGCTCATTGGCAAACAACGCAAAGCTCCTAGCATGATGGTGGCTCGTAAGAACGCCTTTACGTGCGTCCTTGATGGAAAACTATATGTAATGGGAGGATGTGAAGCGGATGAATCTACTCATTGGGCTGAAGTTTTCGACCCAAAGACTCAAACTTGGGAAGCATTGCCGGATCCTGGAGTTGAGCTCCGGTACTCTTCAGTAAAGAATATCCAAACGAAGCAAGGAAAAGTGTACGTGAGGAGCAATAAGAAGAACTTTGTTTACCTTATAAAAGAGTGTATGTGGGAAGTTGCCGAGGAAAACTTGGGTGAGAGTACCTGTGAGATAGAGAATGTATGCTACTGTTATAGTAATAAAAGATACTGGTGGTATGACGCAAAGTGTGAAGAGTGGAGATTAGTCAAAGGTGTGAGTGGACTTTACGAGTATTATAAAACTGATTCTGAAATAGGTAATTATGGTGGAAAACTTGTTGTCTTTTGGGACCGTGCGGTGTCTCGTTTAACCGCAACCAAAGAAATTTGGTGTGCTATGATTTCTCTTGAAAAGGGACATGATGGTGAAATCTGGGGTCACATCGAATGGCTTGATGCTGTGCTTATAGCCCCTCGGTCGTATGCACTCTCACATTGTATGGACTTCTTGCAATAAttaaccatatcttttttgctttgatttttttcaatcttttttattttatttttt|t|ttgca|g|cttaaaactt|ata|attca|a|ttagttttaatcagaactatatat|atta|ttgatatatatagttttcttttttcggtcatgttttttattttatattttatttatatctaggtaataccagtaattcgttattatttcatcgggtatcgtttgctttattgtatt|tatgaagcttgatgggctaaattcaatttttttttatgtttttgtttttatttaagtttt C
Supplemental Figure 2: Illumina poly(A) tags identify a series of polyadenylation sites downstream of the experimentally derived annotation for the CTG10 F-BOX. A) Depiction of At4g19330 as currently annotated and the experimentally determined transcript above it (DQ666277). B) Below these are the locations of individual Illumina sequence tags, generated as paired end reads, using a technique designed to indicate the 3’UTR/poly(A) junction (Green = forward read). C) These Poly(A) tags (PATs) are presented in the genomic sequence below them as upright bars. The presentation of the genomic sequence is color-coded based on the current annotation in TAIR (purple text for introns; orange for coding sequences) but uses uppercase letters to denote the experimentally determined ORF. Both the start codon (commencing in the long intron) and the legitimate stop codon (ending in the sixth intron) are underlined. The site of the T-DNA insertion into the intronless DQ is represented by the underlined, black, inverted triangle. A
DQ666277 B

3. A B C
TTCCTCTACTAAGTAGATCACACATTTGTCATCGCCAAGGTGGCGTCTGAtagtctcatgccaaggcacagcctctttcacatgataattagagacgacgagagaagaagtattagagaggctgctccttgatttgtgtagaataaaacatatacctaattattaatggatttacatggtttttctacgtgtgcattatttggttgactccaattatttaacaattgcatatttgtctcaggtctcatttagcaactaggtaatgtaggaatttaaatagctctataacctactttttaattgtttttttggtgaaacttttttctcataacatggttttttttttttttttggtttaacggatatc|ttc|tcgt|a|aca|t|atgttcttctca|catgttaacactaaagcagacacaagaaaacaaattagtacgttacgttgttgcatgtgttattttgatggctaactggaaaaatacaagtcgttgtgattagccatccaatgggcctctaaaaataatgacttggtaaaactagacaacccaaaatcacaaaacaaatattctcttcttctattaagtaaaaaaaaaaatcttattaaaatctggtttaaatgtttgttcattcaaataaataatggagtgtattttagaatcaaataaaaaaaaactttatcaaatgatttatttggtagataacaaccaaatcttgagctaaaaagggtgaaaaaatattgagaattttgttaataagtaaatagttatggttttgactgggtataggagatatatctaggctggtgaaaaaaaaaagaaaaaaaaggatatatctaggctttaaaatattcacatgcatacaatcagattttcatcggtgttcgataagaaaacaaaaagcaagtgtttgttttgtaaaaaactaatggcatacttaagcttcaagtctaatatggaaccaccacggggatataggagatatatctaggctggtgaaaaacagaaaagcaaaaaaaaaggagagttaatctaggctggtgaaaaaaaaaaggatatatctaggctataaaatattcacatgcatacaataagattttgatcggtgttcgattagaaaacaaaaagcaagtgtttgttttgtaaaaaaactaatggcatacttaagcttcaagtctaatatggaacgtacaccacgcgagtcaaacactccttgtccgcctccccaaccatctccgtcgttgttttcttcactaccagatgacatcgttttgaatatcttggctcgcatatctacttcctactaccaaacgctctctcttgtctccaagaccttccgtttgctcatcctctccaaggagctcgacatggaacgttcctaccttggaacctgaaaaccatgtgtttatgtctgccttcaatctcccacccatccttttgatcgtagatggttcggtctctggataaaaccctatgatcatcagcccctaacccattggacgatcgacatcaagtgtaccggacattggttgctaccgatgccctctccctattctcgttgcttacaaatagTCCACGAAACTGTTGGTTCAGAAACATACGAAATCGGTGGACAAAACATGACACCCTCGACTGACGTATGGGTCTATGATAAGCTCATTGGCAAACAACGCAAAGCTCCTAGCATGATGGTGGCTCGTAAGAACGCCTTTACGTGCGTCCTTGATGGAAAACCAAACACATTAGACtaa
Supplemental Figure 3: Illumina poly(A) tags identify a polyadenylation cluster downstream of the experimentally derived annotation for At4G A) At4g19260 as currently annotated and the experimentally determined transcript below it. B) Below these are the locations of individual Illumina sequence tags, generated as paired end reads, using a technique designed to indicate the 3’UTR/poly(A) junction (Green = forward read). C) These Poly(A) tags (PATs) are presented in the genomic sequence below them as upright bars. The presentation of the genomic sequence is color-coded based on the current annotation in TAIR (purple text for introns; orange for coding sequences) but uses uppercase letters to denote the experimentally determined ORF. The legitimate stop codon (ending in the sixth intron of the current annotation, underlined and in red text) is followed by PATs whereas the stop codon in the current annotation is not (at least in seed cDNA). The blue “C” above is the end of the grey region of homology between regions a and c in figures 1B, D.