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Table 4.

Closely-Spaced (≥40 bp) and Related (>80% Homology) InvertedAlu Repeats Associated with Known Genes[i]

Locus ID[ii]		Locus description[ii]		Indent.[iii] (%)		Len.[iv] (bp)	Dist.[v] (bp)	Subfamily
Locus ID[ii]		Locus description[ii]		Indent.[iii] (%)		Len.[iv] (bp)	Dist.[v] (bp)	1st	2nd
CD orientation
D26607	Endothelial nitric oxide synthase gene	81	109	7	Sxz	Y
Y11950	PHKG2 gene, exon 16	86	180	13	Y	Sc
X64467	ALAD gene for porphobilinogen synthase	82	294	19	Jo	Jb
AP000113	GARTand AML related genomic DNA chr 21q21.1	83	301	25	Sq	Sp
AE000658	T-cell receptor α; and δ; locus	88	131	27	Sp	Sc
AE000658	T-cell receptor α; and δ; locus	83	165	28	Spqxz	Sg
L78810	ADP/ATP carrier protein (ANT 2) gene	83	296	28	Y	Sx
U62293	LIM kinase 1 (LIMK1)	86	264	30	Sz	Sc
AF042084	Heparan glucosaminyl N-deactylase/sulfotransferase	82	298	31	Sx	Sp
AJ000673	CD94 gene (NK cell receptor) exons 4, 5, and 6	87	311	31	Y	Y
D28126	ATP synthase α; subunit gene	82	298	31	Sp	Sx
M90058	Serglycin gene, exons 1, 2, and 3	82	301	31	Sp	Sg
U63721	Elastin (ELN) gene, partial cds, and LIMK1	84	263	31	Sz	Sc
AP000114	GARTand AML-related genomic DNA chr 21q21.1	81	266	32	Sg	Sc
AF030876	MeCP2 locus, X chromosome	81	306	33	Sx	Sp
AF019413	HLA class II region containing tenascin x (TEN-X)	81	126	34	Sz	Jo
Z68226	Huntington's disease region, cosmid L141A8	86	306	35	Y	Ya1
L06849	CD36 (macrophage type B scavenger receptor) gene	84	296	35	Sp	Sq
AP000152	Down's Syndrome Critical Region, chr 21q21.2	85	311	36	Sx	Sx
M31651	Sex hormone binding globulin (SHBG) gene	81	299	37	Sz	Sp
U62293	LIM kinase 1 (LIMK1)	81	295	38	Y	Sg
D87024	λ DNA for immunoglobulin light chain	84	305	39	Ya1	Y
DC orientation
AF060911	Epithelial sodium channel α; subunit, exon 3	83	297	12	Sx	Sp
AP000116	GARTand AML related genomic DNA chr 21q21.1	82	287	15	Sq	Sx
AF003529	Glypican 3 (GPC3) gene	82	212	17	Y	Sg
U29953	Pigment epithelium derived factor gene	80	310	17	Y	Sz
U80017	Basic transcription factor 2 p44 (btf2p44) gene	83	166	19	Sx	Sp
U07000	Breakpoint cluster region (BCR) gene	80	296	20	Sp	Y
AP000119	GART- and AML-related genomic DNA chr 21q21.1	82	141	34	Sg	Sxzg
U80017	Basic transcription factor 2 p44 (btf2p44) gene	95	311	35	Y	Y
AF088219	Beta (CC) chemokine gene cluster	84	302	36	Sq	Y
Z73359	BRCA2gene region	81	313	37	Sx	Sz
M27148	Alpha 2 plasmin inhibitor allele B	81	194	40	Spqxz	Spqxz

[i] Clones without a known function are not included. List is sorted according to separation distance. Minimum cutoff values used were >100 bp for length and >80% sequence identity. The maximum separation distance is 40 bp.

[ii] The Locus identification (Locus ID) number and description are taken from GenBank.

[iii] The percent identity (Ident.) between the two pairedAlu sequences = number of matched nucleotides/alignment length.

[iv] The alignment length (Len.) = number of matches + number of mismatches + total gap lengths.

[v] The total separation distance (Dist.) = b + c (see Fig.1).