Table 2.

CNSs Identified Through the Comparative Approach

Position
Length (bp)
Striped bass
Pufferfish
Zebrafish a
Zebrafish b
Horn shark
Human
Mouse
Over 95%
Literature
New/similar homebox binding sites
1 kb upstream 13 63 86 73 82 78 79 80 1 × 19 NF-1 (Rossi et al. 1988)
Imm. upstream 13 188 83 65 63 66 75 71 0 New
13-11 192 89 26 60 68 67 2 × 10 New
Imm. upstream 11 230 89 66 68 63 70 71 5 × 7-28 New
11-10 121 96 84 85 64 63 2 × 6-8 New
Imm. upstream 10 391 92 86 66 68 70 68 2 × 8-25 New
10-9 a 96 95 86 63 66 61 65 2 × 6-7 Abd B (Ekker et al. 1994); RNA pol. II cap signal (Bucher 1990)
10-9 b 95 98 98 89 81 79 73 72 1 × 24 Murine homeotic proteins b.s. (Catron et al. 1993)
Imm. upstream 9 191 94 87 63 56 69 61 63 2 × 5-6 Target sequences chicken CdxA (Margalit et al. 1993)
9-7 a 62 100 98 92 72 78 79 79 2 × 11-15 Abd B (Ekker et al. 1994)
9-7 b 276 96 93 71 71 70 69 3 × 6-11 c-ETS-1 protein b.s. (Woods et al. 1992)
Imm. upstream 7 185 95 88 79 78 78 3 × 9-14 HoxA7 enhancer regulatory element, H. sapiens (Knittel et al. 1995)
7-5 163 81 78 77 78 81 81 2 × 8-11 H8/7-6 FCS (Kim et al. 2000)
Imm. upstream 5 529 93 84 69 38 76 76 8 × 6-39 RARE (box c and box d), H. sapiens, M. musculus (Odenwald et al. 1989)
5-4 a 280 99 94 77 82 83 83 7 × 9-33 Pax b.s., (Epstein et al. 1994); Ultrabithorax b.s. (Ekker et al. 1991); target sequences of chicken CdxA homeobox gene (Margalit et al. 1993)
5-4 b 63 97 98 83 83 81 83 2 × 9-19 Dof b.s. (Yanagisawa and Schmidt, 1999)
5-4 c 209 95 93 67 71 69 69 5 × 8-15 NF of C-EBP family (Grange et al. 1991)
5-4 d 239 92 89 81 84 79 78 7 × 7-24 RARE (HoxA4 promoter, H. sapiens, Doerksen et al. 1996)
Imm. upstream 4 83 100 100 89 91 78 76 3 × 6-30 RARE (HoxA4 promoter, H. sapiens, Doerksen et al. 1996)
4-3 a 78 91 69 76 72 66 2 × 6-7 Dof b.s. (Yanagisawa and Schmidt, 1999)
4-3 b 480 87 67 71 66 63 5 × 6-10 New
4-3 c 51 93 72 80 75 73 2 × 6-10 New
4-3 d 136 96 76 76 66 65 4 × 8-12 New
Imm. upstream 3 235 86 90 82 73 79 6 × 7-13 New
3-2 a 476 79 61 66 60 0 New
3-2 b 189 93 72 81 68 69 67 5 × 6-9 New
Imm. upstream 2 382 89 64 78 77 77 77 8 × 8-43 HoxA2 promoter, M. musculus (Tan et al. 1992)
2-1 190 93 61 72 72 3 × 10-11 RARE, M. musculus (Frasch et al. 1995) New
Imm. upstream 1 352 78 60 59 64 61 2 × 6-8 RARE, M. musculus (Frasch et al. 1995) New
Total
6233

[i] Column 1: position of CNS in the tilapia HoxA cluster. Column 2: length in bp of the CNS. Columns 3-9: percentage identity of the corresponding CNSs in the other genomes examined. Column 10: number (x) of occurrences and length in # of bp of highly conserved sequences with over 95% identity among all species. Column 11: reference for previously described CNSs in Hox clusters. Column 12: newly suggested CNSs, and reference for known binding sites that show a similar sequence.