Oligonucleotides used in the SMART-HOX system
| HOX . | Amplicon size, bp . | Accession no. . | Forward primer . | Reverse primer . | 5′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 |
| HOX . | Amplicon size, bp . | Accession no. . | Forward primer . | Reverse primer . | 5′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.