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Home Public data LGFUS Public Data High-Throughput Quantification of Splicing Isoforms Supplementary table 4: Validated set primer sequences permalink
Supplementary table 4: Validated set primer sequences ⚙
Information : Data view
Gene name Alternative splicing event type Isoform Forward primer sequence Reverse primer sequence location SNP
AFF3 cassette exon Long TGTGGAATTTCAGTCATCAGCCAG   chr2:99994403-99994426  
AFF3 cassette exon Long   TCTCGTTCTTTCCTCCGTAATGC chr2:99991782-99991804  
AFF3 cassette exon Short CCACCATGGACAGCTTCGACTTA   chr2:100087331-100087353  
AFF3 cassette exon Short   TGCATTTCTATCTGGTTCATAGACACA chr2:99991802-99991826 chr2:100087296-100087297  
APC cassette exon Long AGCCTCTGCCTTGTACAGTTCC   chr5:112228301-112228322  
APC cassette exon Long   TCAAGTGCAGCCATCTTGCCA chr5:112255229-112255249  
APP cassette exon Long ACACAGAAGAGTACTGCATGGC   chr21:26294218-26294239  
APP cassette exon Long   TTTAACAGGATCTCGGGCAAGAGG chr21:26291547-26291570  
APP cassette exon Short TGTGTGGCAGCGCCATTC   chr21:26294201-26294215 chr21:26276659-26276661  
APP cassette exon Short   TGTTCATTCTCATCCCCAGGTGTC chr21:26276589-26276612 rs34725003
AXIN1 cassette exon Long GACATGGAGCTCTCCGAGACA   chr16:281193-281213  
AXIN1 cassette exon Long   TACGCCACAACGATGCTGTCA chr16:279543-279563  
AXIN1 cassette exon Short GCACCCTCCAAGCAGAGGAC   chr16:283489-283505 chr16:279606-279608  
AXIN1 cassette exon Short   ACGCCACAACGATGCTGTCA chr16:279544-279563  
BCAS1 cassette exon Long AATGGGAAAGACTCCAGCTGCC   chr20:52007380-52007401  
BCAS1 cassette exon Long   TTCTGTGGTGCTCCTGTTGGTT chr20:52003577-52003598  
BCAS1 cassette exon Short GGCGTTTCTCAGACAAATGACATC   chr20:52016852-52016870 chr20:52003637-52003641  
BCAS1 cassette exon Short   TTCTGTGGTGCTCCTGTTGGTT chr20:52003577-52003598  
BCMP11 cassette exon Long CACAGTTTCTTCCAACCTTGCCA   chr7:16884704-16884726  
BCMP11 cassette exon Long   TACCCAAGTGATGTCATCTCCCCA chr7:16879967-16879990 rs55900499
BCMP11 cassette exon Short AGCACTGGCCAAGTCAGGA   chr7:16888093-16888109 chr7:16879991-16879992  
BCMP11 cassette exon Short   TGAGCATAAAAGAGACCTTCTTCATAAGT chr7:16879935-16879963  
BMP4 alternative 5' splice site Long GAGGGAAGGAGCGCGGAG   chr14:53493244-53493261  
BMP4 alternative 5' splice site Long   ATACTCAGCCGGAGCAGCAG chr14:53493163-53493182  
BTC cassette exon Long AAAGGGAGATGCCGCTTCGT   chr4:75900120-75900139  
BTC cassette exon Long   ACACCTTGCTCCAATGTAGCCT chr4:75894923-75894944  
BTC cassette exon Short TGCCCCAAGCAATACAAGCA   chr4:75900150-75900169  
BTC cassette exon Short   CGACGTTTCCGAAGAGGGAC chr4:75892366-75892383 chr4:75900093-75900094  
C11orf17 cassette exon Long GCGCCCCACCTAGAGAAACA   chr11:8889738-8889757  
C11orf17 cassette exon Long   TGAAGGAAGCACTAAGGGTTGGG chr11:8890590-8890612  
CASC4 cassette exon Long AAAGCAGGCTACCAAGGACAGA   chr15:42460417-42460438  
CASC4 cassette exon Long   TGCGGATCAACAGGGGATTCAT chr15:42482395-42482416  
CASC4 cassette exon Short ACAGTGAACCCAGAATTCAAACAGA   chr15:42460386-42460410  
CASC4 cassette exon Short   AGCTCTCGTTCTTCATCATTTTGCT chr15:42492826-42492844 chr15:42460461-42460466  
CCL4 cassette exon Long TCTCCTCATGCTAGTAGCTGCCT   chr17:31455438-31455460 rs9635771 rs62079739
CCL4 cassette exon Long   TGTAAGAAAAGCAGCAGGCGGT chr17:31456051-31456072  
CCL4 cassette exon Short TGCGTGACTGTCCTGTCTCT   chr17:31455421-31455440  
CCL4 cassette exon Short   TGCTTGCTTCTTTTGGTTTGGAATTT chr17:31456731-31456754 chr17:31455486-31455487 rs1130760
CCNE1 cassette exon Long TTACATGAAGTGCTACTGCCGC   chr19:35004821-35004842  
CCNE1 cassette exon Long   TCCAGGACACAGAGATCCAACA chr19:35004988-35005009  
CCNE1 cassette exon Short CACCATGGAATTAATGATTATGAAGCTGT   chr19:35004540-35004564 chr19:35004987-35004990 rs34609353
CCNE1 cassette exon Short   GCCGAAGCAGCAAGTATACCAT chr19:35005033-35005054  
CD40 alternative 3' splice site Long TCTCACCTCGCTATGGTTCGT   chr20:44180378-44180398 rs1883832
CD40 alternative 3' splice site Long   AAGTCATCCAGGACAGAGGCT chr20:44183775-44183795  
CD40 alternative 3' splice site Short TCGCTATGGTTCGTCTGCCT   chr20:44180385-44180404 rs1883832
CD40 alternative 3' splice site Short   TGGGTGGTTCTGGATGGACAG chr20:44183866-44183884 chr20:44180439-44180440  
DDR1 cassette exon Long CGCTCCCTGTGTCCCCAATG   chr6:30970402-30970421 rs1264319 rs55787895
DDR1 cassette exon Long   GGCGTAAGTGGCCAGAAGGA chr6:30971190-30971209  
DDR1 cassette exon Short AGAGCCACCCCCGTACCA   chr6:30970351-30970368  
DDR1 cassette exon Short   CCATATAGTCCCCACTGTAGGCA chr6:30972377-30972397 chr6:30970426-30970427  
DRF1 alternative 3' splice site Long AGCAGGAAGTTTCGTCCTTTCC   chr17:40171314-40171318 chr17:40174230-40174246  
DRF1 alternative 3' splice site Long   TCGGGGCCTCAAAGGGACTT chr17:40174299-40174318  
DRF1 alternative 3' splice site Short TCCTCAAAATCGAAGATGAAAGCAGAT   chr17:40171294-40171318 chr17:40174295-40174296 rs61660093
DRF1 alternative 3' splice site Short   TTCTCTGGTATGGTGCATGCTG chr17:40179977-40179980 chr17:40174329-40174346  
DSC3 cassette exon Long CTCGGTGAAGAATCCATTAGAGGAC   chr18:26830755-26830763 chr18:26828445-26828460  
DSC3 cassette exon Long   TGGCATGCGGTCTTCATTCTGA chr18:26828298-26828319  
DSC3 cassette exon Short ACCCCGTCTCGGTGAAAAATTG   chr18:26830755-26830770 chr18:26828331-26828336  
DSC3 cassette exon Short   GACATAATCTTGGGATGGCATGCGG chr18:26828283-26828307  
ECGF1 intron retention Short CCGCCTACTCCATCTACGGC   chr22:49316905-49316924  
ECGF1 intron retention Short   CGGGAAGTACCTGCCAGGT chr22:49316577-49316590 chr22:49316865-49316869  
FANCA cassette exon Long AGGCTGCGTGTACCATTCTTGT   chr16:88352513-88352534  
FANCA cassette exon Long   CGGCCACCAAAGACCAAATCA chr16:88346081-88346101  
FANCA cassette exon Short GATGCTCTTTCAGATACTGAACGCT   chr16:88355858-88355880 chr16:88346130-88346131  
FANCA cassette exon Short   ATTTCCTGTGCGGCCACCAA chr16:88346071-88346090  
FGFR2 cassette exon Long ACTCCGGCCTCTATGCTTGTA   chr10:123314996-123315016  
FGFR2 cassette exon Long   ATCATCTCCGGATGAGATGGCA chr10:123314061-123314082  
FGFR2 cassette exon Short TCACCATGGCAACCTTGTCCC   chr10:123343264-123343284  
FGFR2 cassette exon Short   CTCCGGATGAGATGGCATCTTC chr10:123314066-123314083 chr10:123343213-123343216  
FN1 alternative 3' splice site Long AACCCTTCCACACCCCAATCTT   chr2:215945303-215945324  
FN1 alternative 3' splice site Long   TGGGTGACGAAAGGGGTCTTTT chr2:215945244-215945265  
FN1 cassette exon Long GTCCCTATCTCTGATACCATCATCCC   chr2:215967498-215967523  
FN1 cassette exon Long TGGTTGCCTTGCACGATGAT   chr2:215953816-215953835  
FN1 cassette exon Long   TGAACTTCAGGTCAGTTGGTGC chr2:215952256-215952277  
FN1 cassette exon Long   AGGCCGATGCTTGAATCGGTTA chr2:215966114-215966135 rs61732520
FN1 intron retention Long AAGACCATACCCGCCGAATGT   chr2:215945079-215945099  
FN1 intron retention Long   ACCGTGTGGGTACAGGTGATA chr2:215945012-215945032  
FN1 alternative 3' splice site Short CCCTGATTGGAAGGAAAAAGACAGTT   chr2:215946290-215946313 chr2:215945267-215945268  
FN1 alternative 3' splice site Short   ACCAGAAGTGCCAGGAAGCTG chr2:215945195-215945215  
FN1 cassette exon Short CGGCCTGGAGTACAATGTCAGT   chr2:215967554-215967575  
FN1 cassette exon Short   GGGAGGAGGAACAGCTGGG chr2:215964769-215964782 chr2:215967496-215967500  
FN1 intron retention Short CATGGTTTTAGGCGGACCACA   chr2:215945135-215945155  
FN1 intron retention Short   TCTGAGAGAGAGCTTCTTGTCCTAC chr2:215944963-215944983 chr2:215945077-215945080  
GATA3 cassette exon Long AAAATGAACGGACAGAACCGGC   chr10:8146060-8146081  
GATA3 cassette exon Long   TGGTGGTCTGACAGTTCGCA chr10:8151471-8151490  
GATA3 cassette exon Short CCCGGTCCAGCACAGTCT   chr10:8140796-8140810 chr10:8151442-8151444  
GATA3 cassette exon Short   TCCCCATTGGCATTCCTCCT chr10:8151505-8151524  
GNB3 intron retention Long ATGGAGCAACTGCGTCAGGA   chr12:6820722-6820741  
GNB3 intron retention Long   TCATGTCCCCAGCTGTTTTCTG chr12:6820799-6820820  
GNB3 intron retention Short AGCTCAAGAAGCAGATTGCAGAT   chr12:6820750-6820769 chr12:6821011-6821013  
GNB3 intron retention Short   TCTAGGCCAGACACCAGCTCT chr12:6822395-6822411 chr12:6821046-6821049  
INSR cassette exon Long CGTCCCCAGAAAAACCTCTTCA   chr19:7103737-7103745 chr19:7101531-7101543  
INSR cassette exon Long   ATTCCCAACATCGCCAAGGGA chr19:7094062-7094082  
INSR cassette exon Short GGTTTTCGTCCCCAGGCCAT   chr19:7103737-7103751 chr19:7094097-7094101  
INSR cassette exon Short   AAGTGTTGGGGAAAGCTGCC chr19:7094019-7094038  
KITLG cassette exon Long TGTTGCAGCCAGCTCCCTTA   chr12:87433466-87433485  
KITLG cassette exon Long   AGTCTCCAGGGGGATTTTTGGC chr12:87425019-87425040 rs41283112
KITLG cassette exon Short GCCTTCAAGGACTTTGTAGTGGC   chr12:87434292-87434314  
KITLG cassette exon Short   GGGGGATTTTTGGCCTTCCCT chr12:87425027-87425045 chr12:87434242-87434243  
LIG3 alternative 3' splice site Long TGTAATGAGCAAGTTCCGAGGC   chr17:30331703-30331724 rs9910720
LIG3 alternative 3' splice site Long   ACGGAGGGTTTGTGGAAAGAAG chr17:30334158-30334179  
LIG3 alternative 3' splice site Short GCGGCCTGTAATGAGCAAGTT   chr17:30331697-30331717 rs12945428 rs9910720
LIG3 alternative 3' splice site Short   GTCCCACATGCAACCCTGC chr17:30334364-30334378 chr17:30331751-30331754  
LIG4 cassette exon Long TAGCGGCTGAGCTTCAGGCTT   chr13:107665841-107665861  
LIG4 cassette exon Long   GCAAGCTCCGTTACCTCTGTGA chr13:107664897-107664918  
LIG4 cassette exon Short GCTTCAGGCTTGACGTCAGTT   chr13:107665833-107665851 chr13:107661644-107661645  
LIG4 cassette exon Short   TGTGAAGTTTGTGAGGCAGCCA chr13:107661595-107661616 rs1805389
MCL1 cassette exon Long AAGGACAAAACGGGACTGGCT   chr1:148817363-148817383  
MCL1 cassette exon Long   CACATTCCTGATGCCACCTTCT chr1:148816535-148816556 rs12036617
NRG1 cassette exon Long TGGTGATCGCTGCCAAAACT   chr8:32719753-32719772  
NRG1 cassette exon Long   CTCCGCCTCCATAAATTCAATCCC chr8:32731432-32731439 chr8:32726629-32726644  
NRG1 cassette exon Short GCCCAAATGAGTTTACTGGTGATCG   chr8:32719737-32719761  
NRG1 cassette exon Short   GGTACAGCTCCTCCGCCTTG chr8:32731432-32731449 chr8:32719792-32719793  
PAXIP1 alternative 5' splice site Long AACGGGCACACGTTTCTCCA   chr7:154370555-154370574  
PAXIP1 alternative 5' splice site Long   AGCAGGTCCGTGTGTTATGCTT chr7:154370490-154370511  
PAXIP1 alternative 5' splice site Short ACGTTTCTCCACTCTTTAAGGCAA   chr7:154370546-154370565 chr7:154369453-154369456  
PAXIP1 alternative 5' splice site Short   TTTCCTCCTGCACACTCTACGA chr7:154369377-154369398  
PCSK6 cassette exon Long CCCTGACCTGGCCCCAAATTA   chr15:99789049-99789069  
PCSK6 cassette exon Long   TGCTGGCATCATATCGTGGAGA chr15:99787725-99787746  
PCSK6 cassette exon Short CCAACATGTGGTACCTGGATTCC   chr15:99789718-99789734 chr15:99787786-99787791  
PCSK6 cassette exon Short   TGCTGGCATCATATCGTGGAGA chr15:99787725-99787746  
PLD1 cassette exon Long TGAGTCTGAGCAAGGACTCACT   chr3:172887182-172887203 rs61246471
PLD1 cassette exon Long   TGGTTTCCCCATGCAGCTCT chr3:172878122-172878141  
PLD1 cassette exon Short AGCATTGACAGCACCTCCAATAC   chr3:172887855-172887873 chr3:172878175-172878178  
PLD1 cassette exon Short   TTTCCCCATGCAGCTCTCCC chr3:172878125-172878144  
POLB cassette exon Short AATCACCGACATGCTCACAGAAA   chr8:42315341-42315360 chr8:42321628-42321630  
POLB cassette exon Short   CAGGCAATTTCTTAGCTTCAGCTCC chr8:42325691-42325694 chr8:42321674-42321694  
PTPN13 cassette exon Long ATCCATTGAAGACCCTGGGCA   chr4:87891267-87891287  
PTPN13 cassette exon Long   GGGTACTTGGGATGAAGAGTTTCC chr4:87893206-87893229 rs61757792
PTPN13 cassette exon Short CCCTGGGCAAGCATATGTTCTAGAT   chr4:87891279-87891301 chr4:87898437-87898438  
PTPN13 cassette exon Short   GGTGATCTCCCTTTCTGGTGAAGA chr4:87898466-87898489  
PTPRB cassette exon Long ACAAGTGGTTGTGGAGGGAAGA   chr12:69261087-69261108  
PTPRB cassette exon Long   TACGACCGGAATTGTTCACCGT chr12:69256648-69256669  
RSN cassette exon Long GTGATCTTGAGCAAAAGAGCCAGA   chr12:121403226-121403236 chr12:121401631-121401643  
RSN cassette exon Long   TTCAAGCTCCTTAATGCGGGC chr12:121397938-121397958  
RSN cassette exon Short GAATCAATTACCAAAGGTGATCTTGAGAC   chr12:121403226-121403252 chr12:121397978-121397979  
RSN cassette exon Short   TTCAAGCTCCTTAATGCGGGC chr12:121397938-121397958  
RUNX2 cassette exon Long TGCCATCACCGATGTGCCTA   chr6:45588091-45588110  
RUNX2 cassette exon Long   TGCCTGGCTCTTCTTACTGAGAGT chr6:45620973-45620996  
RUNX2 cassette exon Short ACTCTACCACCCCGCTGTCTT   chr6:45588048-45588068  
RUNX2 cassette exon Short   GCCCAGTTCTGAAGCACCTGA chr6:45622542-45622558 chr6:45588119-45588122  
SHC1 cassette exon Long ATGCCAATCACTCTCACCGTCT   chr1:153207636-153207657  
SHC1 cassette exon Long   TTGCATGTGGTGGTTGGCGAT chr1:153207334-153207354  
SHC1 cassette exon Short CCGCAGACTGCAAACAGGA   chr1:153207595-153207611 chr1:153207130-153207131  
SHC1 cassette exon Short   GGCTCTCTGATTCACAGGGTCTTT chr1:153206896-153206897 chr1:153207080-153207101  
SHMT1 cassette exon Long ACCACTCACAAGACCCTGCG   chr17:18184117-18184136  
SHMT1 cassette exon Long   GCCAGTCTTGGGATCCACACTT chr17:18179686-18179707  
STIM1 cassette exon Long ATGACTGACGACGTGGATGACA   chr11:4061247-4061268  
STIM1 cassette exon Long   ACTGAACCTACGCCCCATCA chr11:4062491-4062510  
STIM1 cassette exon Short ATGACTGACGACGTGGATGACA   chr11:4061247-4061268  
STIM1 cassette exon Short   GCTCTGCAGGCTAGGGGAC chr11:4064283-4064299 chr11:4061303-4061304  
SYK cassette exon Long CCAAAGCCTGGCCACAGAAA   chr9:92669282-92669301  
SYK cassette exon Long   TGCAAGTTCTGGCTCATACGGA chr9:92676354-92676375  
SYK cassette exon Short CCAGGTTCCCATCCTGCGT   chr9:92667183-92667200 chr9:92676307-92676307  
SYK cassette exon Short   TGCAAGTTCTGGCTCATACGGA chr9:92676354-92676375  
SYNE2 cassette exon Long CTCTCACGAAGAGGACGAGGA   chr14:63750895-63750915  
SYNE2 cassette exon Long   TGCCTCAGGATTTTCAGGGATTTC chr14:63751762-63751785  
TLK1 cassette exon Long CACAGTTTTGGAAGCTTGGGATCTT   chr2:171647557-171647581  
TLK1 cassette exon Long   CGTCACTTGCACAGTCCTTTCA chr2:171646425-171646446  
TLK1 cassette exon Short CGAAAGCTCTAATCACAGTTTTGGAAGC   chr2:171647567-171647594  
TLK1 cassette exon Short   GATTGTTTCTTCTCCGGTGTCTCT chr2:171625893-171625912 chr2:171647537-171647540  
TOPBP1 alternative 3' splice site Long CCAGAAGCAAAGACTATGCCCA   chr3:134854918-134854939  
TOPBP1 alternative 3' splice site Long   TGCTGACATCTGAAAGAGTACGAC chr3:134854140-134854163 rs55633281
TOPBP1 alternative 3' splice site Short CAGCCAGATCAACACAATTGATAATGT   chr3:134854879-134854901 chr3:134854145-134854148  
TOPBP1 alternative 3' splice site Short   TGATTCACTTACGCAACTTGCATTT chr3:134854102-134854126  
TSSC4 intron retention Long AGCAGCCAAGAGAGGTGTGG   chr11:2380243-2380256 chr11:2380417-2380422  
TSSC4 intron retention Long   ATACTCCGTCCCGTGTTCGC chr11:2380483-2380502 rs2234278
TSSC4 intron retention Short TCCAGTGTCAACCACTGGCAC   chr11:2380220-2380240  
TSSC4 intron retention Short   GCTGGGAGGAGGCCTGTT chr11:2380651-2380663 chr11:2380454-2380458  
UTRN cassette exon Long TCATCAGTATGTGGCCAGAGCA   chr6:145190188-145190209  
UTRN cassette exon Long   GCCAGTCGTGTGGCATATTGTT chr6:145191619-145191624 chr6:145190490-145190505  
VLDLR cassette exon Long GGAAAATGGCCGAGACTGTCA   chr9:2640494-2640514  
VLDLR cassette exon Long   GTCCACTAGTTGCTGAAATTTCTGTTG chr9:2641460-2641486 rs34563292
VLDLR cassette exon Short CTCCAAAATATACCTGTTCCTGTCCC   chr9:2640451-2640476  
VLDLR cassette exon Short   TGCTGTGGTCACATTGATCCTTTG chr9:2641874-2641893 chr9:2640513-2640516

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