*Where a primer spans 2 exons, the junctions are indicated by a virgule.
120
Housekeeping gene
Fig. S1. Integrated AluYRa1 nucleotide sequences multiple alignment. The blue arrow indicates the AluYRa1 element and red boxes indicate 5’ and 3’ splice sites. Sequences correspond to: (1) HU: human; (2) hominoid: CH: chimpanzee; (3) Old World monkeys (OWM): JA: Japanese monkey, RH: rhesus monkey, CR: crab-eating monkey, PI: pigtail monkey, BO: bonnet monkey; MA: mandrill, AF: African green monkey, LA: langur; (4) New World monkeys (NWM): MAR: marmoset, TA: tamarin; and (5) prosimian: RL: ringtailed lemur. PPT, polypyrimidine tract.
Fig. S2. Unrooted phylogenetic trees constructed for 97 intact AluYRa1 elements of rhesus monkey and crab-eating monkey. CTSF_AluYRa1 corresponds to the Alu element integrated in the CTSF gene.
Fig. S3. Validation of AluYRa1-exonized transcripts found in the crab-eating monkey using reverse transcription-PCR. (A) V1 (450 bp) and V3 (496 bp) transcript variants were identified by validation primer 1. (B) V2 (312 bp), V3 (190 bp), and V4 (610 bp) transcript variants were identified by validation primer 2. (C) V3 (198 bp) and V5 (278 bp) transcript variants were identified by validation primer 3. (D) GAPDH (120 bp) was used as the positive control. M indicates the molecular size marker. Numbers represent crab-eating monkey tissue samples. 1: cerebellum; 2: cerebrum; 3: kidney; 4: large intestine; 5: liver; 6: lung; 7: pancreas; 8: small intestine; 9: spleen; 10: stomach; 11: testis. Reverse transcriptionPCR products were validated by sequencing analysis.
Fig. S4. Nucleotide sequence of the reverse transcription-PCR products obtained for the six transcript variants and for the GAPDH gene. RH, rhesus monkey; CR, crab-eating monkey; V1–V6, variant transcripts.
