Mouse-Human Sequence Conservation in Selected Genomic Regions
| Genomic region[i] | Non-exonic, non-repetitive (unmasked) sequence | |||||
| Total conserved (%)[ii] | Highly conserved (%)[iii] | G+C (%)[iv] | Length (bp)[v] | Masked (%)[vi] | Reference[vii] | |
| HOXA | 99.3 | 21.3 | 50.7 | 93,211 | 15.2 | Unpublished |
| TCR | 77.8 | 7.0 | 44.0 | 77,115 | 21.0 | Koop and Hood 1994 |
| FHIT | 58.1 | 7.6 | 37.1 | 331,123 | 42.1 | Shiraishi et al. 2001 |
| CFTR | 53.2 | 4.9 | 34.9 | 247,331 | 41.3 | Ellsworth et al. 2000 |
| BTK | 49.6 | 4.9 | 41.1 | 43,504 | 41.0 | Oeltjen et al. 1997 |
| SNCA | 44.4 | 1.0 | 34.6 | 84,504 | 29.8 | Touchman et al. 2001 |
| DIST1 | 40.9 | 0.8 | 55.3 | 64,841 | 45.7 | Flint et al. 2001 |
| MECP2 | 39.7 | 5.9 | 47.8 | 59,670 | 56.9 | Reichwald et al. 2000 |
| CD4 | 35.6 | 3.3 | 51.9 | 106,531 | 50.8 | Ansari-Lari et al. 1998 |
| CECR | 21.3 | 1.8 | 45.9 | 368,778 | 52.5 | Footz et al. 2001 |
| WS region | 20.3 | 1.1 | 48.9 | 573,537 | 49.7 | This paper |
| MYO15 | 15.4 | 3.7 | 56.9 | 46,035 | 47.7 | Liang et al. 1999 |
| ERCC2 | 11.0 | 0 | 58.5 | 15,721 | 61.7 | Lamerdin et al. 1996 |
[i] Listed here are 13 genomic regions for which mouse and human genomic sequence is available for comparative analyses. In all cases except for the WS region, finished sequence was available for both mouse and human; in these cases, the name of a known (human) gene within the sequenced region is given. In the case of the WS region, the ∼1.4 Mb of finished mouse sequence was analyzed and an attempt was made to remove mouse sequence for which the orthologous human sequence was not available.
[ii] Annotated exons and sequences identified by theRepeatMasker program (using the default settings) were masked in the human sequence (or the mouse sequence in the case of the WS region). The mouse and human sequences were then aligned with theBLASTZ component of PipMaker (using the default settings). In all cases except for the WS region, the human sequence was used as the reference for the PipMakeranalysis. Shown in this column is the percentage of the non-exonic, non-repetitive sequence within a mouse-human alignment, reflecting the amount of unmasked sequence with at least moderate levels of mouse–human sequence conservation.
[iii] Percentage of the non-exonic, non-repetitive (unmasked) sequence within a gap-free mouse-human sequence alignment of ≥100 bp in length and ≥70% nucleotide identity.
[iv] Percentage of G+C nucleotides in the non-exonic, non-repetitive (unmasked) sequence.
[v] Total length (in bp) of the non-exonic, non-repetitive (unmasked) sequence.
[vi] Percentage of the entire region masked as repetitive or exonic.
[vii] All of the mouse and human genomic sequences used for the analysis summarized in this table are in GenBank. When available, a citation reporting the mouse and/or human sequence for the region is provided.