Oligonucleotides and primers used in experiments
| Target, primer names . | Primer sequences (5′ to 3′) . |
|---|---|
| Exon 16 minigenes | |
| Ex13-clone-S | GAAGACGAGCCACCTGAGCAA |
| In17-clone-As | CTAGGGGCAACCCAGCAGAG |
| Bss-S | CTCGTGTTGGTGAACATGAAGATATG |
| Bss-As | TTCACCAACACGAGAAAGCATTTTAAACCTAAAGTCC |
| DUP minigenes | |
| DUP-HindIII-S | GACACCAAGCTTGGTGCACCTGACTCC |
| DUP-XbaI-As | GATGCTTCTAGATCCACGTGCAGCTTGTCAC |
| PN-3WT-S | GATCTTTTGCATGCAATTGCATGAAGGGTTTTGCATGCAATTGCATGAAGGGTTTTGCATGCAATTGCATGAAGGGTTTA |
| PN-3WT-As | GATCTAAACCCTTCATGCAATTGCATGCAAAACCCTTCATGCAATTGCATGCAAAACCCTTCATGCAATTGCATGCAAAA |
| PN-3MU-S | GATCTTTCACGTGCAATCACGTGAAGGGTTTCACGTGCAATCACGTGAAGGGTTTCACGTGCAATCACGTGAAGGGTTTA |
| PN-3MU-As | GATCTAAACCCTTCACGTGATTGCACGTGAAACCCTTCACGTGATTGCACGTGAAACCCTTCACGTGATTGCACGTGAAA |
| mFox-2 5′ RACE | |
| mEx3-RT | GGTCAGGTTATGTTCACTGGTCTGG |
| GeneRace 5′ primer | CGACTGGAGCACGAGGACACTGA |
| 5′ Race-1-As | GAGGTGGTGGGAACGGGATGGTA |
| GeneRace 5′ nested primer | GGACACTGACATGGACTGAAGGAGTA |
| 5′ Race-2-As | AGGAGTTGTTGTTGGCTCCTGGTTAC |
| Fox-2 isoform clones | |
| mEx1A-S | CGGGCGGATGGCGGAAGG |
| mEx1F-S | GGGCGGATGGAGAAAAAGAAAAT |
| mEx1D-S | CATGGACCAGCCCAGGAAC |
| mEx1E-S | CAGCGGCTCTGCCATGATGTA |
| mEx16-As | TCACGTCACTTCAGTAGGGGGCAAAT |
| hEx1A-S | ATGGCGGAGGGCGCCCAGCCGCAGCA |
| hEx1F-S | ATGGAGAAAAAGAAAATGGTAACTCAG |
| hEx16-As | GGGGTCTCACGTCACTTCAGTAG |
| Gel shift constructs | |
| Ex16-shift-S | CAATAAGCTTTTGGAGGTTTGTATGAACTTGAAGC |
| Ex16-shift-As | GAATTCTAGACAGAAGGCGAGATGTTTGCAT |
| mFox-2-shRNA constructs | |
| sh-1A130 target | GCCTGAGCAAGCGGCCACGCAC |
| sh-1A161 target | GGCCGACGGCGGGATGCAGAAC |
| sh-1A195 target | CCGGGTTATCATGGATTCCCAG |
| sh-1A204 target | CATGGATTCCCAGCAAGGGATG |
| sh-1F14 target | AATGGTAACTCAGGGTAACCAG |
| sh-1F15 target | ATGGTAACTCAGGGTAACCAGG |
| sh-1F16 target | GGTAACTCAGGGTAACCAGGAG |
| sh-1F218 target | CTTCTTCTGGTTTATGGAGAAA |
| 5′miR30-XhoI | CAGAAGGCTCGAGAAGGTATATTGCTGTTGACAGTGAGCG |
| 3′miR30-EcoRI | CTAAAGTAGCCCCTTGAATTCCGAGGCAGTAGGCA |
| Exon 16 splicing analysis | |
| mEx17-RT | CTCCAGTAGGGACTTGCCCGTTGATGTTAAGA |
| Ex13-S | AGAGCCCACAGAAGCATGGA |
| Ex17-As | GTGTGTAGATAAGCCCTTGTCCCA |
| DUP exon E2 splicing analysis | |
| DUP-ex1-S | AAGGTGAACGTGGATGAAGTTGGT |
| DUP-ex3-As | ACAGATCCCCAAAGGACTCAAAGAAC |
| mFox-2 real-time PCR | |
| mFox-2A-rt-S | AAGCGGCCACGCACAGAG |
| mFox-2A-rt-AS | CTTGCTGGGAATCCATGATAAC |
| mFox-2F-rt-S | ATGGAGAAAAAGAAAATGGTAACTCAGG |
| mFox-2F-rt-AS | ATATTCTGTGGGAATTCCATTTTGTGG |
| mFox-2-89-rt-S | GGTCCTGAGTTATATGCAGCATCC |
| mFox-2-89-rt-AS | GACAAGGGCACAGCCGC |
| mHprt-rt-S | AGCAGTACAGCCCCAAAATGGTTA |
| mHprt-rt-AS | TCAAGGGCATATCCAACAACAAAC |
| Target, primer names . | Primer sequences (5′ to 3′) . |
|---|---|
| Exon 16 minigenes | |
| Ex13-clone-S | GAAGACGAGCCACCTGAGCAA |
| In17-clone-As | CTAGGGGCAACCCAGCAGAG |
| Bss-S | CTCGTGTTGGTGAACATGAAGATATG |
| Bss-As | TTCACCAACACGAGAAAGCATTTTAAACCTAAAGTCC |
| DUP minigenes | |
| DUP-HindIII-S | GACACCAAGCTTGGTGCACCTGACTCC |
| DUP-XbaI-As | GATGCTTCTAGATCCACGTGCAGCTTGTCAC |
| PN-3WT-S | GATCTTTTGCATGCAATTGCATGAAGGGTTTTGCATGCAATTGCATGAAGGGTTTTGCATGCAATTGCATGAAGGGTTTA |
| PN-3WT-As | GATCTAAACCCTTCATGCAATTGCATGCAAAACCCTTCATGCAATTGCATGCAAAACCCTTCATGCAATTGCATGCAAAA |
| PN-3MU-S | GATCTTTCACGTGCAATCACGTGAAGGGTTTCACGTGCAATCACGTGAAGGGTTTCACGTGCAATCACGTGAAGGGTTTA |
| PN-3MU-As | GATCTAAACCCTTCACGTGATTGCACGTGAAACCCTTCACGTGATTGCACGTGAAACCCTTCACGTGATTGCACGTGAAA |
| mFox-2 5′ RACE | |
| mEx3-RT | GGTCAGGTTATGTTCACTGGTCTGG |
| GeneRace 5′ primer | CGACTGGAGCACGAGGACACTGA |
| 5′ Race-1-As | GAGGTGGTGGGAACGGGATGGTA |
| GeneRace 5′ nested primer | GGACACTGACATGGACTGAAGGAGTA |
| 5′ Race-2-As | AGGAGTTGTTGTTGGCTCCTGGTTAC |
| Fox-2 isoform clones | |
| mEx1A-S | CGGGCGGATGGCGGAAGG |
| mEx1F-S | GGGCGGATGGAGAAAAAGAAAAT |
| mEx1D-S | CATGGACCAGCCCAGGAAC |
| mEx1E-S | CAGCGGCTCTGCCATGATGTA |
| mEx16-As | TCACGTCACTTCAGTAGGGGGCAAAT |
| hEx1A-S | ATGGCGGAGGGCGCCCAGCCGCAGCA |
| hEx1F-S | ATGGAGAAAAAGAAAATGGTAACTCAG |
| hEx16-As | GGGGTCTCACGTCACTTCAGTAG |
| Gel shift constructs | |
| Ex16-shift-S | CAATAAGCTTTTGGAGGTTTGTATGAACTTGAAGC |
| Ex16-shift-As | GAATTCTAGACAGAAGGCGAGATGTTTGCAT |
| mFox-2-shRNA constructs | |
| sh-1A130 target | GCCTGAGCAAGCGGCCACGCAC |
| sh-1A161 target | GGCCGACGGCGGGATGCAGAAC |
| sh-1A195 target | CCGGGTTATCATGGATTCCCAG |
| sh-1A204 target | CATGGATTCCCAGCAAGGGATG |
| sh-1F14 target | AATGGTAACTCAGGGTAACCAG |
| sh-1F15 target | ATGGTAACTCAGGGTAACCAGG |
| sh-1F16 target | GGTAACTCAGGGTAACCAGGAG |
| sh-1F218 target | CTTCTTCTGGTTTATGGAGAAA |
| 5′miR30-XhoI | CAGAAGGCTCGAGAAGGTATATTGCTGTTGACAGTGAGCG |
| 3′miR30-EcoRI | CTAAAGTAGCCCCTTGAATTCCGAGGCAGTAGGCA |
| Exon 16 splicing analysis | |
| mEx17-RT | CTCCAGTAGGGACTTGCCCGTTGATGTTAAGA |
| Ex13-S | AGAGCCCACAGAAGCATGGA |
| Ex17-As | GTGTGTAGATAAGCCCTTGTCCCA |
| DUP exon E2 splicing analysis | |
| DUP-ex1-S | AAGGTGAACGTGGATGAAGTTGGT |
| DUP-ex3-As | ACAGATCCCCAAAGGACTCAAAGAAC |
| mFox-2 real-time PCR | |
| mFox-2A-rt-S | AAGCGGCCACGCACAGAG |
| mFox-2A-rt-AS | CTTGCTGGGAATCCATGATAAC |
| mFox-2F-rt-S | ATGGAGAAAAAGAAAATGGTAACTCAGG |
| mFox-2F-rt-AS | ATATTCTGTGGGAATTCCATTTTGTGG |
| mFox-2-89-rt-S | GGTCCTGAGTTATATGCAGCATCC |
| mFox-2-89-rt-AS | GACAAGGGCACAGCCGC |
| mHprt-rt-S | AGCAGTACAGCCCCAAAATGGTTA |
| mHprt-rt-AS | TCAAGGGCATATCCAACAACAAAC |