Table 2.

Noncoding sequences conserved between the orthologous mammalian SCN1A, SCN2A, and SCN3A genes

CNS	Locus	Location	Length (bp)	% Identity Human/Mouse	% Identity Human/Chicken	Coordinates
CNS1c	SCN1A	5′	213	75	-	chr2:166,842,083-166,842,296
CNS2a	SCN1A	5′	526	81	67	chr2:166,830,939-166,831,465
CNS3ac	SCN1A	5′	404	83	54b	chr2:166,809,777-166,810,181
CNS4a	SCN1A	5′	142	91	42	chr2:166,809,487-166,809,629
CNS5c	SCN1A	5′	200	88	-	chr2:166,808,083-166,808,283
CNS6d	SCN1A	5′	161	85	-	chr2:166,800,604-166,800,765
CNS7d	SCN1A	Intron 11	113	90	83	chr2:166,725,531-166,725,644
CNS8c	SCN1A	Intron 11	265	82	-	chr2:166,724,939-166,725,204
CNS9c	SCN1A	Intron 20	195	85	63b	chr2:166,691,462-166,691,657
CNS10	SCN1A	Intron 20	609	86	64b	chr2:166,689,133-166,689,742
CNS11	SCN1A	Intron 20	365	85	59b	chr2:166,685,142-166,685,507
CNS12	SCN2A	Intron 16	310	85	64	chr2:166,046,497-166,046,807
CNS13	SCN2A	Intron 16	204	82	57	chr2:166,046,115-166,046,319
CNS14	SCN2A	Intron 16	299	86	76	chr2:166,039,754-166,040,053
CNS15	SCN2A	Intron 12	341	90	-	chr2:166,010,303-166,010,604
CNS16	SCN2A	Intron 5	346	79	58	chr2:165,991,994-165,992,340
CNS17	SCN2A	Intron 5	175	84	52	chr2:165,991,605-165,991,780
CNS18ac	SCN2A	5′	592	81	58b	chr2:165,975,883-165,976,475
CNS19ac	SCN2A	5′	335	79	55b	chr2:165,921,347-165,921,682
CNS20c	SCN2A or 3A	5′	189	80	-	chr2:165,911,346-165,911,535
CNS21d	SCN2A or 3A	5′	153	80	-	chr2:165,909,714-165,909,867
CNS22	SCN2A or 3A	5′	448	88	71b	chr2:165,907,878-165,908,326
CNS23d	SCN2A or 3A	5′	271	78	-	chr2:165,898,175-165,898,446
CNS24ac	SCN3A	5′	597	81	61b	chr2:165,885,613-165,886,210
CNS25c	SCN3A	5′	190	89	-	chr2:165,882,665-165,882,855
CNS26	SCN3A	5′	301	79	-	chr2:165,881,079-165,881,380
CNS27	SCN3A	5′	250	84	-	chr2:165,875,531-165,875,781
CNS28d	SCN3A	Intron 10	202	93	-	chr2:165,825,443-165,825,645
CNS29	SCN3A	Intron 16	564	80	66b	chr2:165,804,405-165,804,969
CNS30d	SCN3A	Intron 16	212	90	56	chr2:165,802,407-165,802,619
CNS31d	SCN3A	Intron 16	210	86	57b	chr2:165,802,029-165,802,239
CNS32c	SCN3A	Intron 16	1031	78	52b	chr2:165,801,700-165,802,731
CNS33d	SCN3A	3′	248	80	-	chr2:165,737,238-165,737,486

^aCNS corresponds to a noncoding exon: CNS2, SCN1A exon 1a; CNS3, SCN1A exon 1b; CNS4, SCN1A exon 1f; CNS18, SCN2A exon 1c; CNS19, SCN2A exon 1a; CNS24, SCN3A exon 1a

^bChicken homology does not extend the entire length of the CNS

^cCNS identified by WebMCS only

^dCNS identified by phastCon only