Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

Table 2 TE effect on the mouse transcriptome

RE	Total	Intronic	TE in introns of UCSC annotated genes^a	TE in introns of non-annotated genes^a	TE exonization in UCSC annotated genes^a	TE exonization in non-annotated genes^a
B1	506,528	331,015 (65%)	189,268	141,747	134 (0.07%)	96 (0.07%)
MIR	116,355	66,597 (63%)	41,853	24,744	27 (0.06%)	14 (0.06%)
B2	338,642	215,264 (63%)	118,646	96,618	81 (0.07%)	80 (0.08%)
B4	345,646	216,550 (66%)	119,827	96,723	62 (0.05%)	72 (0.07%)
ID	45,955	30,285 (57%)	18,022	12,263	8 (0.04%)	3 (0.02%)
L1	820,434	457,705 (56%)	181,292	276,413	102 (0.07%)	189 (0.07%)
L2	56,518	34,923 (62%)	18,963	15,960	9 (0.05%)	5 (0.03%)
CR1	11,812	7,167 (61%)	3,779	3,388	0 (0%)	1 (0.03%)
LTR	756,324	396,226 (52%)	156,690	239,536	72 (0.05%)	243 (0.1%)
DNA	124,202	75,200 (60%)	40,428	34,772	11 (0.02%)	19 (0.05%)
Total	3,122,416	1,830,932 (58%)	888,768	942,164	506 (0.06%)	722 (0.08%)

Insertions of transposed elements (TEs) within the mouse genome. The different classes of the examined TEs are shown in the left column. 'Total' (second column) indicates the overall amount of each TE within the human and mouse genomes. 'Intronic' (third column) indicates the number of TEs within intronic regions, and the percentage of TEs within introns relative to the total amount of TEs is shown in parentheses. The fourth and fifth columns show the number of TEs within introns of University of California, Santa Cruz (UCSC) knownGene list (version mm6) and those inserted within genes not listed within UCSC knownGene list. The sixth and seventh columns show the numbers of exonized TEs within the UCSC knownGene list and those exonized within genes not listed within UCSC knownGene list. In brackets are indicated the percentage of exonized TEs. The lower row shows the total number of all TEs. ^aGene annotation is based on the annotations of the known gene list in the UCSC genome browser (version hg17). LTR, long terminal repeat; MIR, mammalian interspersed repeat; RE, retroelement.

ISSN: 1474-760X