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LGFUS Public Data
High-Throughput Quantification of Splicing Isoforms
Supplementary table 2: Validation set primer sequences
Information
: Data view
| Gene name | Forward primer sequence | Reverse primer sequence | BSP 3' end perfect match sequence | Tm of 3' end perfect match sequence | ΔCt | 3’-end mispriming | Specificity for typical qRT-PCR | Forward primer sequence for template | Reverse primer sequence for template | |
| AFF3 | GGACCTCGAGTCACTGTGTGTC | ACGTGCCATCATCCTGTTGAGT | TGTC | −56.3 | >27,7 | no | yes | AGTCACTGTGGGGTGAAGACAT | ACGTGCCATCATCCTGTTGAGT | |
| APC | AGTTGGACTTAACGTATTTCTTGAGGTT | CCTGCCGACGTTTCTTTCGTTT | GTT | −101.9 | >28,4 | no | yes | TCAAACAGGAAGATGGGAGCCT | CCTGCCGACGTTTCTTTCGTTT | |
| APP | TGTGTGGCAGCGCCATTC | TGACGTTCTGCCTCTTCCCATT | TTC | −103.9 | 18,9* | no | yes | CAGCGCCATGTCCCAAAGTTTA | TGACGTTCTGCCTCTTCCCATT | |
| AXIN1 | GCACCCTCCAAGCAGAGGAC | TAGCTGCCCTTTTTGGTCAGCA | GAC | −86.9 | >24,4 | no | yes | ACCCTCCAAGCAGAGGTATGT | TAGCTGCCCTTTTTGGTCAGCA | |
| BCAS1 | AACAGTGGACCTCAACGAAGGA | GTCTTTTCTGTGGAGTCTGATGTCAT | CAT | −106.2 | >26,2 | no | yes | AACAGTGGACCTCAACGAAGGA | TCTGATGTTTGGCAGCTGGAGT | |
| BMP4 | CACTGGCCAAGTCAGGATGG | AGGCACATATTGCCCATCAGGT | GGAGCC | −2.0 | 18,5** | no | yes | AGAAAGAAAGCGAGGGAGGGAA | ACCTCTGAACGGTTGCAGTGAA | |
| BTC | AGAAAGAAAGCGAGGGAGGGAA | GGCACTACGGAATGGCTCCTA | CCC | −83.4 | >27,8 | no | yes | TTGGTCATCGGTGTCTGCACAT | ACTTTGCAGCTTGCCACCAA | |
| C11orf17 | GACGCCCTCCTGTGTCCC | ACTTTGCAGCTTGCCACCAA | GAAATATT | −6.6 | >27,6 | no | yes | GTGCTTCCTTCAGAACAATGGCTG | TCCAGGACCAAGGGATGTCTTT | |
| CASC4 | GCGTTCTCCCGGGAGAGAAATATT | TCCAGGACCAAGGGATGTCTTT | TTTGCT | −15.4 | >28,1 | no | yes | AACCACAATGGAAACCCCGGTA | TTAGAGCCATGCTGCGGATCAA | |
| CCL4 | ACCATGAAGCTCTGCGTGACT | GCTTGCTTCTTTTGGTTTGGAATTTG | TTG | −101.3 | >26,8 | no | yes | ACCATGAAGCTCTGCGTGACT | TGTAAGAAAAGCAGCAGGCGGT | |
| CHEK2 | GCTGGCTTTCGAGAGGAAAACA | AGCTCTCCCCCTTCCATCATG | ATG | −106.2 | 17,6* | no | yes | GCTGGCTTTCGAGAGGAAAACA | CTCCCCCTTCCATCAATTCCAAA | |
| DRF1 | CCTCAAAATCGAAGATGAAAGCAGATG | ATGTCTGCAAAGCTGTGGCT | AGATG | −37.9 | >27,4 | no | yes | TTTCCTGAAATTTCTTTTCTTGGACCC | ATGTCTGCAAAGCTGTGGCT | |
| DSC3 | ACCCCGTCTCGGTGAAAAATTG | TGCTTTTCACTGCAGCAGCC | AAATTG | −24.5 | 20,0* | no | yes | ACCCCGTCTCGGTGAAGAAT | TGCTTTTCACTGCAGCAGCC | |
| FANCA | TGGACACACAGAACCTTCCGA | GGTCATAACTCCTTGAGCGTTCA | CGTTCA | −8.7 | >26,6 | no | yes | TGGACACACAGAACCTTCCGA | TGGTGGAAATCCATCAGTGCGT | |
| FGFR2 | AAGGCATTGCGCGTAGTCCA | CTCCGGATGAGATGGCATCTTC | TCTTC | −37.2 | >28,2 | no | yes | AAGGCATTGCGCGTAGTCCA | ATCTTTCAACAGGCAGCGCA | |
| FN1-alt3 | CCTGATTGGAAGGAAAAAGACAGTTC | TTTGTTGCCCAACACTGGGT | ACAGTTC | −2.4 | >28,1 | no | yes | AAAGACAGACGAGCTTCCCCAA | TTTGTTGCCCAACACTGGGT | |
| FN1-EDA | TACAAACGGCCAGCAGGGAAA | GGGAGGAGGAACAGCTGGG | TGGTTA | −21.5 | >25,8 | no | yes | TACAAACGGCCAGCAGGGAAA | AGGCCGATGCTTGAATCGGTTA | |
| FN1-EDB | CATACCCGCCGAATGTAGGAC | ACAGAGTTGCCCACGGTAACAA | CTGGG | −23.6 | >28,1 | no | yes | TCCGGGACTCAATCCAAATGC | ACAGAGTTGCCCACGGTAACAA | |
| FN1-intron | ACTATTGAAGGCTTGCAGCCCA | CAGTTGGTGCAGGAATAGTGGTTA | CCTAC | −32.7 | >26,0 | no | yes | ACTATTGAAGGCTTGCAGCCCA | TGCAGCTCTGCAGTGTCTTCTT | |
| GATA3 | CGGTCCAGCACAGTCTGCA | ACGAGCTGTTCTTGGGGAAGT | GTCTGCA | 5.2 | 17.3 | yes | yes | AAAATGAACGGACAGAACCGGC | ACGAGCTGTTCTTGGGGAAGT | |
| INSR | GGTTTTCGTCCCCAGGCC | ATAGCCCGTGAAGTGTCGCAA | AGGCC | −20.4 | >27,9 | no | yes | CGTCCCCAGAAAAACCTCTTCA | ATAGCCCGTGAAGTGTCGCAA | |
| LIG3 | GAGCCGGAGAGGCAGGGT | TTGGGCACCACTTTGCCAAT | CAGGGT | −9.0 | 22.0 | yes | yes | TCACGTGCCACCTACCTTGTTT | TTGGGCACCACTTTGCCAAT | |
| MCL1 | CGAGACGGCCTTCCAAGGAT | TGCCACTTGCTTTTCTGGCT | GGAT | −62.9 | >27,6 | no | yes | AAGGACAAAACGGGACTGGCT | TGCCACTTGCTTTTCTGGCT | |
| NRG1 | AATGGCCAGCTTCTACAAGGC | GTCATGCAGCTTTTTCCGCTGT | AGGC | −47.3 | 16,0* | no | yes | CCAGCTTCTACAAGCATCTTGGG | GTCATGCAGCTTTTTCCGCTGT | |
| PCSK6 | CCAGCAACAGGAAGTGAAACGA | CGTAGCTGGCGTAGGAATCCAG | CAG | −88.4 | >33,8 | no | yes | TGAAATGGCTCCAGCAACAGGA | AGGATGGTGACCACCACGTTTT | |
| PLD1 | AGCATTGACAGCACCTCCAATAC | TGGATGAAGTGACGTGCCACA | ATAC | −72.2 | 14,6** | no | yes | TCTTTCACCCGTCCAGTGAGT | TGGATGAAGTGACGTGCCACA | |
| POLB | TCACCGACATGCTCACAGAAAA | GCAATTTTTGTTCCTACTCCAGGC | AAAA | −76.4 | 18.0 | yes | yes | ACGTGAGCCAAGCTATCCACAA | GCAATTTTTGTTCCTACTCCAGGC | |
| POLI | GGCTCAAACTAAGGACAAGAGTCC | TGAAGGAATAGGGCACTGACGA | TCC | −97.7 | >27,5 | no | yes | TGAGTTTGTGCTAATCCTTATTTATGCTTC | TGAAGGAATAGGGCACTGACGA | |
| PTPN13 | CCTGGGCAAGCATATGTTCTAGATG | AATTGCAGCATGGTGGCTGA | ATG | −106.2 | 28.2 | no | yes | GGAAACTCTTCATCCCAAGTACCC | AATTGCAGCATGGTGGCTGA | |
| SHMT1 | AAGCTGATCATCGCAGGAACCA | GTGCCACAGCAACCCCTT | CCTT | −61.2 | >27,9 | no | yes | AAGCTGATCATCGCAGGAACCA | GCCAGTCTTGGGATCCACACTT | |
| SLIT2 | ACCTGTATTGTGACTGCCACCT | AGCCATAAATGACTGGTGACCAC | CAC | −84.6 | 16,3*** | no | yes | ACCTGTATTGTGACTGCCACCT | TGACTGGTGACCTTCTTCCTCA | |
| STIM1 | TCCCTTGTCCATGCAGTCCC | TCATGGCATTGAGAGCCTCGT | CCC | −83.4 | 20,5* | no | yes | ATGCAGTATGCTGCCTGGCT | TCATGGCATTGAGAGCCTCGT | |
| SYK | AGGGAAAGAAGTTCGACACGCT | TTGGGCAGGGGAGGACGC | CGC | −60.6 | 20,8** | no | yes | AGGGAAAGAAGTTCGACACGCT | TTATTCCACCCGCTGACCAAGT | |
| SYNE2 | ACTACAGCGCACTGTCAGGTAA | TTTATAAGGGGTGCTGGACGCA | GGTAA | −38.6 | 19,4* | no | yes | ACAGCGCACTGTCAGATGTAGA | TTTATAAGGGGTGCTGGACGCA | |
| UTRN | TCGGGTCGAACAGCAAAAGGT | TGAGGAGATTGTGAGGGGGTC | GTC | −86.9 | >27,9 | no | yes | TCGGGTCGAACAGCAAAAGGT | TGCTCTGGCCACATACTGATGA | |
| VLDLR | GGATGTGAATACCTATGCCTGCCA | TGCTGTGGTCACATTGATCCTTTG | CTTTG | −33.7 | >25,8 | no | yes | GGATGTGAATACCTATGCCTGCCA | GTCACATTGATCCCTCCAGGAACT | |
| * 5'-end mispriming observed | ||||||||||
| ** signal due to primer-dimers | ||||||||||
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