Table 1.

Oligonucleotides used in the SMART-HOX system

HOXAmplicon size,
bp
Accession
no.
Forward primerReverse primer5′FAM/3′TAMRA probe
A1 63 NM_005522 CGGACCATAGGATTACAACTTTCC GTCGCCGCCGCAACT TGCGCGGTCAGCGCCAA 
A4 70 NM_002141 TGGTGTACCCCTGGATGAAGA CTTAGGCTCCCCTCCGTTATAAC TCCATGTCAGCGCCGTTAACCCC 
A5 92 XM_004918 TCCCATCGCTTCCCTACCT GCTTTGGAACAGCCTACAGCTT ACCCATTGCAAAGTTCAGGGCATAAGGT 
A7 79 NM_006896 AGCTTGGAAATTCTGCTCACTTCT TCTGATGTCATGGCCAAATTTG CTCTTGCTTGCTTCTCTGGTGGGCTTC 
A9 84 U82759 GCCGGCCTTATGGCATTAA CAGGGACAAAGTGTGAGTGTCAA TGAACCGCTGTCGGCCAGAAGG 
A10 70 AF040714 CAAGAGGCAAAGAAAAGCGTTAA GTAGATGCTTGCAGAAGGAAAGG TCAAGATGTACAGCCTGCCCTCCCA 
A11 87 NM_005523 TTGAGCATGCGGGACAGTT GTACCAGATCCGAGAGCTGGAA AGGCGCTTCTCTTTGTTAATGTAGACGCTGAA 
B1 65 NM_002144 GCCATATCCTCCGCAGCAT CATAGGCCGGTGCAAAGCT CCCCTTATGGGAACGAGCAGACCG 
B3 58 NM_002146 TCACCCAGCGATGCAGAA CGAGGAATAGCCTCCGAAGA CCACCTACTACGACAACGCCGCG 
B5 71 NM_002147 TCCTTCCATGCTCCCAACTC CCACAGACACAAACATTCAGAAACA CTTCTGCTTGTCCCAAATCCGCCA 
B6 56 NM_018952 AGCATCTCCACTCTGCGTAACA AGCGTCTGGTAACGTGTGTATGTCT CCCAGCGGCCGGCGAG 
B7 61 NM_004502 TCGAGCCGAGTTCCTTCAAC CACACCCCGGAGAGGTTCT TGCACTGCGCGCCCTTTGAG 
B8 64 NM_024016 AAGCGGCGAATCGAGGTA GGAACCAGATTTTGACCTGTCTCT CGCACGCCCTGGGACTGACA 
B9 77 X16172 AACCCCTCCGCCAACTG CCAGCGTCTGGTATTTGGTGTA CACGCTCGCTCTTCCCGGAAAAA 
B13 65 NM_006361 GCTGATGCCTGCTGTCAACTAT ATTGCTTTGGCGGCTCC CCTTGGATCTGCCAGGCTCGGC 
C4 68 NM_014620 GCTGCCGGGTATAAGCTGTACT CAGTTAGCAGGTGAACCCCAAT AGCGCTTGGGTTCCCCTCCGTTA 
C5 107 NM_018953 TCTGGCATAGGTACCACATAAGGA GACACGGACAGAGCCAGACA CACAGGGAAACAGAGCAGTCCTCTAGACCA 
C6 69 NM_004503 TCAAACGTGGACCTGAAAGTCA GGCGCGTGGAGAAAGAGA TCTGGACCCCCTCCCTCACCG 
C9 66 AK000445 TCATCCTTCGATTCTGAAACCA GGTGGCCCGGGTTCTC ATTTTGACCTGCCGCTCGGTGAGAT 
C11 75 XM_012215 GCGGCCGACGAGCTT GCCTTCGTTTTTCATGAGGATCT TGCACCGGGAGTGCCTGCC 
C12 69 AF328963S2 GCGAGTTTCTGGTCAACGAGTT AAGATTCAAGCGGTCTGAGAGTTC CACACGCCAGCGCCGGAG 
C13 78 AF263466 GGCTAGCAAGTTCATCACCAAA GGTTACCTGGCGCTCAGAGA CGCATCTCCGCCACCACGAA 
D3 77 Y09980 CCACGTGATTGGCGAAATAA CCTTTGCGTGGCAGATTAATG AATTCAGCACGTCCCTTAAGAAACACGGAGT 
D4 77 NM_014621 GAGAGCAGTCTTTGGATGTACCATT TTTTAGGAAAGCAGCTTAGCAACTT AAGGAGCCGCTATCCTTAGGCAAGTTGG 
D8 74 AY014304 CTGACCAGGAAAAGAAGAATCGA TGGAACCAGATTTTTACCTGTCTCT TTCCCACGCCCTAGCCCTCACC 
D9 75 NM_014213 CCCCGAAGCGAACTGGAT GCTCAAGCGTCTGGTATTTGG CCCGGAAAAAGCGCTGTCCCTACA 
D10 102 NM_002148 CAGCAGCGCCAGCATGT TTCACTTCTCTTTTGGCCAGAGA CATGCCACCACCTAGCGCAGACA 
D13 69 NM_000523 CACTTCGGCAACGGCTACTAC CTTGAGCGCATTCTGCTGTAAG CCGTATGTCGCACGGCGTGG 
HOXAmplicon size,
bp
Accession
no.
Forward primerReverse primer5′FAM/3′TAMRA probe
A1 63 NM_005522 CGGACCATAGGATTACAACTTTCC GTCGCCGCCGCAACT TGCGCGGTCAGCGCCAA 
A4 70 NM_002141 TGGTGTACCCCTGGATGAAGA CTTAGGCTCCCCTCCGTTATAAC TCCATGTCAGCGCCGTTAACCCC 
A5 92 XM_004918 TCCCATCGCTTCCCTACCT GCTTTGGAACAGCCTACAGCTT ACCCATTGCAAAGTTCAGGGCATAAGGT 
A7 79 NM_006896 AGCTTGGAAATTCTGCTCACTTCT TCTGATGTCATGGCCAAATTTG CTCTTGCTTGCTTCTCTGGTGGGCTTC 
A9 84 U82759 GCCGGCCTTATGGCATTAA CAGGGACAAAGTGTGAGTGTCAA TGAACCGCTGTCGGCCAGAAGG 
A10 70 AF040714 CAAGAGGCAAAGAAAAGCGTTAA GTAGATGCTTGCAGAAGGAAAGG TCAAGATGTACAGCCTGCCCTCCCA 
A11 87 NM_005523 TTGAGCATGCGGGACAGTT GTACCAGATCCGAGAGCTGGAA AGGCGCTTCTCTTTGTTAATGTAGACGCTGAA 
B1 65 NM_002144 GCCATATCCTCCGCAGCAT CATAGGCCGGTGCAAAGCT CCCCTTATGGGAACGAGCAGACCG 
B3 58 NM_002146 TCACCCAGCGATGCAGAA CGAGGAATAGCCTCCGAAGA CCACCTACTACGACAACGCCGCG 
B5 71 NM_002147 TCCTTCCATGCTCCCAACTC CCACAGACACAAACATTCAGAAACA CTTCTGCTTGTCCCAAATCCGCCA 
B6 56 NM_018952 AGCATCTCCACTCTGCGTAACA AGCGTCTGGTAACGTGTGTATGTCT CCCAGCGGCCGGCGAG 
B7 61 NM_004502 TCGAGCCGAGTTCCTTCAAC CACACCCCGGAGAGGTTCT TGCACTGCGCGCCCTTTGAG 
B8 64 NM_024016 AAGCGGCGAATCGAGGTA GGAACCAGATTTTGACCTGTCTCT CGCACGCCCTGGGACTGACA 
B9 77 X16172 AACCCCTCCGCCAACTG CCAGCGTCTGGTATTTGGTGTA CACGCTCGCTCTTCCCGGAAAAA 
B13 65 NM_006361 GCTGATGCCTGCTGTCAACTAT ATTGCTTTGGCGGCTCC CCTTGGATCTGCCAGGCTCGGC 
C4 68 NM_014620 GCTGCCGGGTATAAGCTGTACT CAGTTAGCAGGTGAACCCCAAT AGCGCTTGGGTTCCCCTCCGTTA 
C5 107 NM_018953 TCTGGCATAGGTACCACATAAGGA GACACGGACAGAGCCAGACA CACAGGGAAACAGAGCAGTCCTCTAGACCA 
C6 69 NM_004503 TCAAACGTGGACCTGAAAGTCA GGCGCGTGGAGAAAGAGA TCTGGACCCCCTCCCTCACCG 
C9 66 AK000445 TCATCCTTCGATTCTGAAACCA GGTGGCCCGGGTTCTC ATTTTGACCTGCCGCTCGGTGAGAT 
C11 75 XM_012215 GCGGCCGACGAGCTT GCCTTCGTTTTTCATGAGGATCT TGCACCGGGAGTGCCTGCC 
C12 69 AF328963S2 GCGAGTTTCTGGTCAACGAGTT AAGATTCAAGCGGTCTGAGAGTTC CACACGCCAGCGCCGGAG 
C13 78 AF263466 GGCTAGCAAGTTCATCACCAAA GGTTACCTGGCGCTCAGAGA CGCATCTCCGCCACCACGAA 
D3 77 Y09980 CCACGTGATTGGCGAAATAA CCTTTGCGTGGCAGATTAATG AATTCAGCACGTCCCTTAAGAAACACGGAGT 
D4 77 NM_014621 GAGAGCAGTCTTTGGATGTACCATT TTTTAGGAAAGCAGCTTAGCAACTT AAGGAGCCGCTATCCTTAGGCAAGTTGG 
D8 74 AY014304 CTGACCAGGAAAAGAAGAATCGA TGGAACCAGATTTTTACCTGTCTCT TTCCCACGCCCTAGCCCTCACC 
D9 75 NM_014213 CCCCGAAGCGAACTGGAT GCTCAAGCGTCTGGTATTTGG CCCGGAAAAAGCGCTGTCCCTACA 
D10 102 NM_002148 CAGCAGCGCCAGCATGT TTCACTTCTCTTTTGGCCAGAGA CATGCCACCACCTAGCGCAGACA 
D13 69 NM_000523 CACTTCGGCAACGGCTACTAC CTTGAGCGCATTCTGCTGTAAG CCGTATGTCGCACGGCGTGG 

Amplicons were verified and validated by cloning and sequencing. Amplicon sequences were interrogated by BLAST33 analysis and aligned with the specific accession number.