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Table 2 Alu subfamily distribution of Alu elements bound by RNA polymerase III factors

From: Alu expression in human cell lines and their retrotranspositional potential

Alu % Total # of disease % Alu % Alu loci Pol III # Pol III
subfamilya full Alus (530,850) cases due to ade novo insertion transcriptsd bound by pol III bound Alu enrichment bound Alu with ERP
   (%)c   factorse   ≥0.10
S + J 84.5 0 (0) 66 88.4 1.0 2
Y 15.5 13 (23) 33 9.8 0.6 0
Ya5 0.63 24 (44) 0.8 1.2 2.0 0
Yb8 0.42 18 (33) 0.5 0.6 1.5 1
  1. aIncludes all subfamily variants: for example, AluYa5, AluYa5a2, AluYa8 are classified as Ya5; bnumber of Alu elements meeting full length criteria (Details in supplemental data); csubfamily distribution of the 55 de novo Alu elements reported to cause a disease [2, 15]; danalysis was performed on transcripts isolated from the Ntera2 (teratocarcinoma) cell line [11]; eanalyses were performed on the cumulative data obtained from studies on IMR-90 (normal untransformed Tert-immortalized lung fibroblast) [13], HeLa (cervical adenocarcinoma), Jurkat (T-cell leukemia), HEK 293 T (T antigen-transformed kidney) [12] and K562 (myelogenous leukemia) cells [14] (raw data and detailed analysis for each cell line included in Additional file 1: Table S3); frepresents the increase in Alu loci bound by RNA polymerase III factors relative to copy number (that is, %AluY bound/%AluY copies in the genome, detailed analysis in Additional file 1: Table S3); gnumber of Alu loci bound by RNA polymerase III factors with estimated retrotransposition potential (ERP) scores of ≥0.10. An ‘ideal’ Alu will have ERP score of 1.00.