The Complete HOXA Cluster Sequence of a Primitive Ray-Finned Fish Provides Insights into the Duplication and Evolution of HOX Clusters Within the Bony Fish Lineage
C-H. Chiu, Ken Dewar, Günter P. Wagner, Kazuhiko Takahashi, Frank Ruddle, Christina Ledje, Peter Bartsch, Jean-Luc Scemama, Edmund Stellwag, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler, Chris T. Amemiya


Supplement 6a: Heterodontus francisci A

PFC 5'-3' Number of PF, N Coordinates
(distance to 3' gene)
Sequences
Upstream of 13-a 2 6,519-6,573 (9,775 nt) GATTAAAGTTTAACCAGAGGCGTGTTTACGGTTTTACCTTGCTATTTAAACACAT
Upstream of 13-b 1 (n=16nt) 6,799-6,814 (9,496 nt) AGACATCTAGTGGGAA
Upstream of 13-c 4 8,558-8,898 (7,737 nt) ACAGAAAACAGTTTTTGTAAAATAGTCATTTAGTATTAAATATATCACTTATTATTTGGCACGTAACAGGTATATG CAATAGAGTTACAGAGTGCAATAGAAAATACTTCCCATGCAAACGATGCGGCGTTAGAGGAGAACAAATAAATGAT ATGTCTTGTTAAGGAGTGAAAATAAATTCACGTCTCGCAATTGCAAGCATTTAGAATGTATTATAGTAAAACAACT TTAATATTTAGCTTTGACATTGTACTTGTTAAATGTAAGAAACGTTGGGTTCATATAGTGTGGACAGCAGTTATAT TGCAGTGCAACAATATATTTTTTCTTGTTTTCCAGTT
Upstream of 13-d 3 13,232-13,292 (3,063 nt) GGCTAGACTGCAACTTTCAACTTGACCTTGGCCTTTAGCCGTGTCTAACCCGTATGTAAAA
13pp 4 16,136-16,285 (159 nt) TATCATCTACTTTGCATATCATGTGATCATCTCGCAGCCAATGAGGAGGCAAGTTTCAGCGACACTGGCGCGTCAA TGCTGCTAAGTCTGAGAGACTCAGTATCTCTTTTCAGTCTTAGGGGCTTTTAAAACGGCCACTAGTCTCAATGT
13-11-a 3 19,139-19,201 (10,846 nt) CTTAAACCTTGACCTTGACGAAAACTGATAGTCTTTGACCTTGACTATTAACTGCTCATGAAT
13-11-pp 6 29,795-29,916 (190 nt) TGTCAATTTCTCCAGGCATCTGGTCACATGACTGGCTTGTCCCTGCGATGTATGGAGATACATTTCCACGTCAGCT TACGTTTCCAAATTTTTACTCCGCGGATCAGCTTCAAAGAGGCAGC
11-10-a 3 34,437-43,489 (9,023 nt) TTGTTTCCTGGCTTTGAACTTCTGTTGCGCCATGGACGTCACCTCTAACCTTG
11-10-c 1 (n=18nt) 35,064-35,081 (8,396 nt) GATCAATGTCAAAGCCGC
10-9-a 8 46,403-46,773 (6,926 nt) TATTGCTGCTGAACTGTGTACATTTAAAAAAATACTTGTGTTTTCATGAAAGATGAATAAAACGTATTTGGTCGGA GTCCTTTGAGATAGGTATATGTACATTGTTTTTACTTCATTTTGTGTTCGTTTTTTTCTTACCTCATCTGTTGAGG AAGCTTCCAACAGGAATGGTAGGTTTAAAGACTGGCAATTACCGTTGCAATCTATTTAAATATTACCTAGACGGTC GTAATTTGTCTGGGCTATATAGCAATGGTGCTGTAACGTTTGTCGGCTTTTGTTGAGTTTTATGACTTGCTAGTAT ATCTGGGTTGTTGCTGTCTTGGACGAGTGGTTTCAGTTGAGCGAACAGCCACGAAGACAGAGGAAGC
10-9-b 2 47,562-47,662 (5,767 nt) GTGATTTAGGTAGTTTCATGTTGTTGGGGCTCAAGTCTATCTCTACAACACGAAACTGCCTGAATTACTGCAGTTA TAGTCTTCGCCAGTGAGTTCTGTCG
10-9-c 1 (n=21nt) 48,332-48,352 (4,997 nt) GCAAGGCCTCGGTTATGATCA
10-9-d 2 52,913-52,992 (416 nt) TTTTATGTGAAGGTTAACGGTTTTAAGGTGTTCGTTAAAAAAAACGAGCATCTGATGGGAAGATTGATTATGATAT AAAA
10-9pp 10 53,088-53,301 (242 nt) CTTTGCATAAAAACATACGGAGTTGCTATATAAAATTATGTCTATAAAAGATTGACTCTGTTACAAGCTGCGGATT GATTTATATTTTATTGTTGTTTTTTGAATCACGTGAGTAACTTAGCCAATGGCATGGAAGTGCTTCTGCACCATAT TAGTAGACTGTACTTGTCGCGGCGGTAAGTTGTTACATTGAAATCTGCTCTTTCATATTTTC
9-7-a 2 56,999-57,039 (5,339 nt) ATAAAAGAAAATGACTGCTGTAAGCGTTTATGGGGTGTAAA
9-7-b 8 57,233-57,438 (5,105 nt) GACGCCCTCTGTTGTTGCAGATGGAACTTCAAAGACTAAACTGGGAGACTTGCAATAAAATGAAGGGTCTGGCAAG CCGTCTGGTATTCAGGTTTTAATGAGTTTACAACTGTCCAGCTACAATCAGTATTTTTCCAGAGAAGGCGATCCAT TTGTTTTGTCTGGCTGCCTAGACAAAAGGGTCTGCGGAAATAACGACCTTTATT
9-7-pp 9 62,153-62,338 (185 nt) ACCACCTGTGATGTGGAATGCTATTGGGGGACGGGATCACATGGTCGGGTCACGTGAATAGAAATAAGTCGGACTG AAGGAAAATGGGTGTTTGGTGTAAATCGGGGGTGTAATGCTGCCATATATCACGCTATCTCGTAAAACCGACACTG AAGAGCCTTGGCCAACAAATCACCAGACAAAATT
7-6-a 9 66,475-66,640 (5,462 nt) ATGGGGAAATGTCATAAATCCGTTGTTGTTTTATGAAAATTTACAACTTTGCAATAGAACTTTACGAGTTGTTCGG TTTTTCCATTGGCCGCTGAAAGTCATGTGGAGTGTAACCGTGAACATGAACTTTTTATAATTTCCCTTGCGACTAT AGAGCTGCATTCTT
7-6pp 10 71,722-71,914 (215 nt) TGTTTGTAACTTTGCTAGCTCAGTCGCCGGATCTCCAGGGAGTTTTTTGAACCAGAGTCAGTTTCTATTGGCCAGA GACTGATCAGCTGGTTATATTTGCTGCTGTCGCTTTGGCGCTCGGCCATCCTGAAACAAACCACCTCGATGACTAC TAATAGCTAAACCACATTGTGTACTAATACATAACAAATCA
6-5pp 9 74,586-74,780 (219 nt) AGTGCACGGATTTACCTCTAGAGGTCATCAGCGAGAATTTACGACTGGACAACAAAAGCACGTGATTCCAAGTCGT ACCCCATATTTGGGCGCCTACGTAGGAGGGAACGAAGTACATGTCCCAGTCATTTCCATAATTCATCATAAATTGT GCAGGGTGCTAGACGCACAAGCGACCAAGAGCCACAAATCAAG
5-4-a 4 76,427-76,535 (11,435 nt) TGTGTTGCACTCTGCAAACAAGTATATGTACGTGTTAGTGTTGCTAAATGTCAAAATAGCTCCAAGCTTGCAATAC GTATTTAATTTCAGGCCATTGTCTTCTGTAATT
5-4-b 5 76,648-76,710 (11,214 nt) GTATGACTTTGCACGAACTCCAATAAGTGGCTCTTAGCGCAGCGTCAATGTATGTTTTTTGTG
5-4-c 13 77,569-77,832 (10,293 nt) AAAGTTATAATCAATAAACTTTTATACACCTCAGTTCCGGCTTTATGACATTTGGGTGCCAAATGAATAGGGTTTT GTCTATGAATTAGATCGTAAAATCATCCATAGCACAGACTGATAGCCTCACTGGCTATAAAAAATCACGTGGTGTC ATTAAAGTAAGTTTTATGGTTTTGGGGAGTTGACAACCAACAGTATATTCTACATAACATATAATCTCACTGACGC TGGACTTCATTTGGTTCCTTTGCAGATTGCGTGTGC
5-4-d 4 81,957-82,012 (5,905 nt) ATCTGCACACTCTGCGACTCACCAGCAGAGCTCGCTTTAGACCAAGTTCACAGTCA
5-4-e 13 82,457-82,716 (5,404 nt) TACAACTGTAGGTCAAAAAGTTGAGGGTCAAAAGTTTACGTTTTGCACGACTTGTAATCATCTGCTCAGACAGAGT TTGATGTCAATGTTATAGCGCGATCTTGACTATCAGCACAAAAGATAAAATAGCTTTGAGTTACTCGTGTATCATA CTATGGACTCCAGGTGAACCCGAGCGACTGAACGACCTCAATTACTGACGAAAGGAAAGAAAAAAAATATTCTTTT CATGATCGAGACACGTTGTATTTCATCTTGAA
5-4-f 12 84,830-85,048 (3,032 nt) TGACCTGGGCAAAACACCCTGGTATTTGAAAGAGCACTATAGGCCTTTTAGAAATGGCTAAGTCCAAGGCCGAGGT GAAATTCAGGTCACCGCGTCTAACAAATATGAAAATGTCGCCTCACGAATGGCACGCCTTGTTACTTAACAAAGAC TGTCAATGTATAAGATTAATAAGAAACAAAACGCACACGGTGTCACTTTTCGGTCACTTCCAAACTT
5-4-g 5 85,618-85,689 (2,244 nt) CTTGCAGTAAAAATGTCAAATGTAAAAGCAGGCGAGGTATCACTTGGGGGTCCTGGCTCCATCTCTGTTTAT
4-3-a 5 91,111-91,190 (15,251 nt) GAATCATTAATCACCTCATTCAATAAATACTTCTTTGTATACTTCAACAGCAAGTCTGAAGGGCGTTCTTTTGGAA AAGT
4-3pp 9 106,192-106,356 (170 nt) AGTAAGATGGATTTGTACCATTTCGCCATTATGGTTTTGTTTCTTGTAACCCCAGGTCTACCCGAAGAGGCCATTG GAAGAAAAGAGTCACGTGACACAGGGCGCCAATGTTATTCTATAAGGGTGTCAAGACCCTGTCAGTTTGCGAAATA AATATTGGGAAAC
3-2-a 5 113,693-113,795 (558 nt) GTGTCAAAACTTTGAAGATTAATGGATTACTTTGTTAATGACTCTAGGCGTCAGATTTAGGTGCAAGATGATTTGT GAGGTGCAAGTCGTCTTCGTGACAGTC
3-2pp 11 113,960-114,181 (291 nt) GCTGGCCTTGAATGAGGCGTTTCTCTCCGACTTTTTGGATCAATCACATAGACAGTGCCTTCTTTTGATTAAACCC CAAATTGTCATTGGGCAGACGCAATCATGTGACAGCGAATTCGGTCCAATTTCAACCTTGTCTCCATGAATTCAAT AGTTTAATAGTAGCACGGTCCCCATACGGCTGTAATCAGTGAATTAGAAAAAAAAAACAGCAGCGATATT
2-1-a 16 117,382-117,518 (2,791 nt) ATCCCTTTTATGAATGAGAATGTCATCAAATGGATCAATCGCAGCAGTACATAACAAAAAAACATCTTACGTATTT GCTTGGACCGGGGAACCCCTGTCAGCTTGAAACTTGTAGGCGTTGAGTCGTAATTCATTTT