Table 2.

U2OS SVA H2D mneoI recovered insertions^a

No.	Clone	Breakpointb	Strand	Gene	TSDc	EN site	Poly(A) length (nt)	Structure (domain)/size (kb)d	Untemplated 5′ nt	TSS
1	1	chr1:115,782,912			AAAAGTGCATGGTT	TTTT/AT	∼58	FL/3.6	G	CMV (AGATCT …)
2	3	chr14:55,150,391	Antisense	SAMD4A	AAAAAGACTCCTGTGCC	TTTT/AA	∼22	FL/3.6	G	CMV (AGATCT …)
3	4	chr11:9,115,342	Sense	FLJ46111	AGAAAGGCCTCA	TTCT/GA	∼33	5′-TR (VNTR)/2.5		Unknown
4	5	chr16:20,914,555	Sense	LYRM1	GAAAAATCCG	TTTC/AA	∼72	5′-TR (VNTR)/3.0		Unknown
5	6	chr20:22,763,381			GAAAAACAAAAGCC	TTTC/AA	∼34	FL/3.6	G	CMV (AGATCT …)
6	7	chr1:8,360,967			AAACACCATGAGG	GTTT/AA	∼46	FL/3.6	G	CMV (AGATCT …)
7	10	chr9:132,538,944			AAAGGAGCGTGTGC	CTTT/AC	∼23	5′-INV(20 nt), 761-nt deletion (VNTR)/2.8		CMV (TCTCT …)
8	11	chr1:48,497,863			AAAAATTTACC	TTTT/AA	∼154	5′-TR (VNTR)/2.6	CC	Unknown
9	12	chr12:121,914,401	Antisense	KDM2B	AAAACTAACTGAAACAAA	TTTT/AA	∼81	FL/3.6		Unknown
10	13	chr6:37,611,066	Sense	MDGA1	AAAAAAAAA	TTTT/GA	∼93	FL/3.6	G	CMV (AGATCT …)

^aSVA neomycin resistance retrotransposition assays were carried out as described in Materials and Methods. SVA H2D was cotransfected with ORF1 and ORF2 on separate plasmids. Insertion breakpoints were recovered using inverse PCR (3′ breakpoint) and PCR using a primer positioned in the 5′ flank and an internal SVA primer (5′ breakpoint). TSD, target site duplication; EN, endonuclease; nt, nucleotide(s); TSS, transcriptional start site; FL, full length; TR, truncated; CMV, cytomegalovirus; VNTR, variable number of tandem repeats.

^bAccording to (GRCh37/hg19).

^cThe underlined sequence represents microhomology at the site of inversion presumably used as a primer in the second priming reaction.

^dSize indicates the entire insertion [SVA +spliced mneoI + poly(A) tail]. The size of the spliced mneoI cassette to the SV40 poly(A) signal (AATAAA) is 1.3 kb.Beginning with the first nt (+1), the CMV TSS is 5′-TCAGATCTCT…-3′.