Markup | Genome Research

Table 1.

Comparison of Alignments of Mouse Naip Paralogs[i]

		Naip1 [ii]		Naip2 [iii]		Naip3 [iv]		Naip5 [v]		Naip6 [vi]		Naip7 [vii]
		align	ident	align	ident	align	ident	align	ident	align	ident	align	ident
Naip1 [ii]	—	—	36	78	46	82	48	80	37	79	45	77
Naip2 [iii]	46	81	—	—	34	81	49	75	36	80	44	73
Naip3 [iv]	67	80	37	79	—	—	46	72	46	78	34	85
Naip5 [v]	27	80	21	76	17	77	—	—	63	95	78	94
Naip6 [vi]	29	80	22	77	24	80	86	94	—	—	100	97
Naip7 [vii]	28	80	21	75	15	85	86	96	82	98	—	—

[i] The genomic sequence for each Naip gene locus was aligned with each other Naip locus (see Methods). The similarities between these alignments are expressed in terms of the percentage of the gene named in the column head that appears in a local alignment with the gene named in the row head (column labeled “align”) and of the percentage of sequence identity within those local alignments (column labeled “ident”). Because of the differences in the overall length of the different Naipgenes, it is important for the reader to confine their comparisons to looking for trends within a column. In this way, one can see the relationships among the different families of Naip genes. For example, by looking in the Naip1 column, one can see that it most resembles Naip3, because of the extensive proportion of Naip1 that aligns with Naip3. On this basis, one can also see that Naip1 is more closely related to Naip2 and Naip3 than it is toNaip5, Naip6, or Naip7. The parameters used in generating the local alignments prohibit little variation in the percent identity of the alignments. An exception to this is seen in the homologies among the Naip5/6/7 family, in which the percent identities typically exceed 90%.

[ii] Bases 6546-51581 of GenBank no. AF242432.

[iii] Bases 68968-128492 of GenBank no. AF131205.

[iv] Bases 56706-117791 of GenBank no. AF242431 and 1-2335 of GenBank no. AF242432.

[v] Bases 140365-165807 of GenBank no. AF131205.

[vi] Bases 22-34589 of GenBank no. AF242431.

[vii] Bases 5565-34032 of GenBank no. AF242433.