Supplementary table 2: Validation set primer sequences

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Home Public data LGFUS Public Data High-Throughput Quantification of Splicing Isoforms Supplementary table 2: Validation set primer sequences

Supplementary table 2: Validation set primer sequences ⚙

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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