(A) Analysis of a primate-specific snoRT. Upper panel: localization of the snoRT. A Blat search with the human ACA58 snoRNA sequence (hosted in the gene UBAPL2) localizes a close copy in the human TMEM48 gene. The Dog Alignment Net track of the UCSC Genome Browser shows two syntheny levels. Level 1 corresponds to the dog TMEM48 gene, but Level 2 corresponds to the dog ACA48 orthologue in the UBAPL2 gene. The Chimpanzee Alignment Net track shows complete syntheny with the human TMEM48 gene (unpublished data). Lower panel: characterization of the primate-specific ACA58 snoRT and determination of the insertion point. The “view alignment details of parts of net within browser window” tool of Dog Net track (Level 1) gives the alignment of the synthenic portions of the human and dog genomes (schematized on upper panel). Examination of the human sequence allows recognition of the polyA tail [(A)n] and the TSD (green arrows) and precise localization of the snoRT insertion point at one extremity of the TSD (lower panel). The detailed alignment is given in the Figure S1, section 13.
(B) Description of the three types of snoRTs. The upper drawing shows the structure of the parental snoRNA HG. Blue and red boxes represent exons and the snoRNA sequence, respectively. The drawings below show the structures of Type 1–3 snoRTs. The partial snoRNA downstream intronic segment included in Type-2 retroposons is indicated by a green line.
(C) Duplication of U17A in the cow U17 HG and structure of a cow snoRT. U17 sequences and exons are represented by red and blue rectangles, respectively (not to scale). The duplicated segment is indicated by horizontal arrows. A similar duplication is found in the armadillo U17 HG gene, with an additional 430-bp insertion indicated by the black arrowhead. The structure of a cow snoRT containing U17C and U17 HG exons is shown below. This retroposon (chr19:44122615–44123602) is located in an intron of the TBCD gene in the sense orientation and is composed of the U17C sequence and downstream intron in addition to the duplicated copies of exon 2 and exon 3. Black horizontal arrows indicate the TSD. The vertical arrow indicates the position of a consensus polyadenylation signal located 16 bp upstream of the genomic polyA tail. See Figure S3, section 9 for sequence.
(D) Insertion of a SINE element and a snoRT at a common site. In certain cases, genomic alignments with an outlier species with no snoRT show that the snoRT (black box) and another nonautonomous mobile element such as a SINE (yellow box) are inserted at a common site, creating a triplication of the insertion site (green arrows).

(A) Rat-specific U17 retroposon and its corresponding insertion site in the mouse genome. This retroposon, located in an intron of the Pdia3 gene in the sense orientation, is part of a rat-specific insertion containing a full-length ID sequence and the U17 snoRNA copy (green and blue letters, respectively), embedded in 90-bp and 113-bp sequences of unknown origin. The triplicated target site is boxed. Sequences shown are chr3:108128544–108129247 (rat) and chr2:121165874–121165955 (mouse).
(B) Rat-specific U109 scaRT. This perfect copy of rat U109 is inserted in an extragenic region within an RnERVK8 repeat. Alignment with a typical RnERVK8 element precisely delineates the insertion site and the TSD (boxed). At a different genomic location, an ID element is inserted at the same position, with the same TSD. Note that the ID sequences from A and B display 90/93 nt identity. Sequences shown are: RnERVK8: chr12:18586394–18586560; U109 retroposon: chr7:118265612–118265946; and ID retroposon: chr8:18564189–18564463.

(A) The human U99 HG. This figure, redrawn from a UCSC Genome Browser screen, shows results of the alignment of a rhesus-specific U99 snoRT with the human genome (Blat Search track), and the position of the human U99 snoRNA gene and of human spliced ESTs. For clarity, only 4/45 spliced ESTs in this window are shown. The human sequence orthologous to the retroposon starts at the 5′ end of U99 and ends at the 3′ end of six ESTs, like BU564879. The corresponding transcription unit, the U99HG (RefSeq gene LOC751071), resides in an intron of the C11orf44 gene in the antisense orientation. The BE967121 EST corresponds to the C11orf48 gene, but the others were erroneously included in the Hs.9061 (C11orf48) UniGene cluster. Window shown: chr11:62,189,300–62,190,050 (hg18).
(B) The human U104/ACA62 HG. This UCSC screen copy shows the alignment of selected ESTs from the Hs.405444 UniGene cluster and of a rhesus-specific ACA62 snoRT with the human genome. The position of the U104 and ACA62 snoRNAs is also shown. The asterisks indicate the presence of a polyA tail in the EST sequences. The presumptive U104 ACA62 HG is larger than the UniGene cluster and overlaps the 3′ UTR of the TEX2 gene in the antisense orientation. The lower track shows the lack of conservation of the HG outside of the snoRNA sequences.