Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays

Srinivasan, Subhashini; Patil, Arun H; Verma, Mohit; Bingham, Jonathan L; Srivatsan, Raghunathan

doi:10.1186/2043-9113-2-21

Journal of Clinical Bioinformatics

Table 5 PCR primers for events for which a transcript sequence was available in the public databases

From: Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays

Sl. no	SpliceJunctionID_GeneName	Amplicon	Forward primer	Reverse primer
1	JHS32215053_TARP	119	TCCCGGAACAAAGCTTATCA	AAGACCAGGGTTCCAGTCCT
2	JHS31939933_SH3RF1	113	AGTTCCCATCGCTCCACCT	GAGGAGGATAGGAAACCACCA
3	JHS31912679_PPP3CA	106	GTGTGTGCATGGTGGTTTGT	CAGGATATCACACATAGGTCCA
4	JHS31958799_march6	108	GGGAAAGAATGCTAGGACTTGA	GGTAAGGGCAAAATGCAAAA
5	JHS31704238_ARFGAP3	121	GGGCAAGCATAACCTATGGA	TGAAACCATGACCAGTTGGA
6	JHS30608278_TAOK3	132	AAAGCATGTCATGGAACTTCG	TCCAACTGGTGATTCTTGAGTG
7	JHS30807650_EIF2AK4	103	TGAAATTCTGGCTGTGGATCT	CAGCTGCTTCACAGTTGTGTT
8	JHS30813189_TMEM87A	114	TGGCATTTCATCCTCAAAGG	AAGGGATAGTCTTCAAGTGTGAGG
9	JHS31115850_TOM1L1	117	CAGAAGCAGAGGCTGAAACA	CAGTCGAGTTCTTTGGAGCA
10	JHS32114870_RPL7L1	148	CGGAGCAAGAGCAAAGAAAA	CGCTTAAACCTGAGCCCTTT
11	JHS31615632_TTC3	110	GCTGAACGGTTTAGATCCTCA	CAGGCTGTCCTATTCCAAGG
12	JHS31498135_SF3B1	116	AGCATAGGCGGACCATGATA	TTGTTCTCGCATTACATCCA
13	JHS31332823_KLK3	146	ACAGCTGAGCCACTCTGAGG	CAGGGGTCGGGGAGATATAG
14	JHS30347840_CTBP2	106	TCCCTTAAAAAGACGGACAGC	AGGGGAACTTGCAGGAGTCT
15	JHS31820386_SR140	100	GCCAGAGTTTTCAGGAGCAA	TCTTTCTTGTCTCTTTCTCGTTCTC
16	JHS30945721_GTF3C1	123	GGTGCTTCAGAACCTGATCC	AAGGCCTTCACAAGAACGTG
17	JHS30838314_C15orf44	131	GCCTGCAGACAGATGTACAGA	TTTCAGCAGGTCCAGGAAAC
18	JHS31803136_CCDC14	125	TCTCAGGCAACTCCTCATTCT	GCAAACTGACTGTTGCCATC
19	JHS32473823_KIAA0368	107	GGAGAGACAGTGGTATTTCAAGG	GGCTGGCTAAGATCACTTGC
20	JHS30556221_"COPZ1,MIR148B"	107	GACGACACCTACCCCAGTGT	ACTGTCAGGCCTTCCAAGAG
21	JHS31292790_"ECH1,HNRNPL"	104	AGAATGGAGTTCAGGCGATG	CAGAGTGCAACAGCCAGAATA
22	JHS32163374_BCLAF1	107	CCAAGTACCCTGAGGAAGCA	CGAAGGTCAGCAGAGTCACA
23	JHS31612151_SON	126	GGGAACTTCTCTGCTGCAAT	ATCAGGGCCACTATCATGGA
24	JHS30594323_HSP90B1	118	GTCAAGGGTGTGGTGGACTC	TCATGTCCAGCGTTTTACGA
25	JHS31048200_TTC19	103	ATTTTGCATGACGCTCTTCG	GCTGACCCCGTATAAATGCT
26	JHS30077792_TSPAN1	103	CAAGTGTGGAACACCACCAT	GGGGAAAGGCACTGTTCTCT
27	JHS30255522_NET1	101	CCCGAGGTGAACAGGATTTA	TGTGAGTTCCTCTTCTGACATGA
28	JHS31707588_ATXN10	130	ATTGTTTGGGTGCATGCTTT	CCTCCAGTTCTTTCATTCTTTCA
29	JHS31151584_CANT1	116	TGCTGTGGAAAGACTTCACG	ATCCGGAGGGAGTGCATAG
30	JHS30592849_CCDC53	112	TGAGGAGAAACTGGCAGACC	TTCAACTGTGACATCATCTAGGC
31	JHS31375495_HADHA	115	TGGACATGATGCTGACTGGT	GTCCGTTCCTCTGGAGGTTT
32	JHS30830235_SLTM	113	TCTGCAGAAGAAAACAAGAGAGC	TCATCTTCACCTTCTTGAGCTTC
33	JHS31129340_DDX5	124	GCCCGAAGCCAGTTCTAAAT	CTTAGAGCAACTGGCCATCC
34	JHS30485155_HSPA8	109	AGTAGCAATGAACCCCACCA	CACCATAAAGGGCCAATGTT
35	JHS30035592_PINK1	123	CGGAAACGGCTGTCTGAT	AGCCCGAAGATTTCATAGGC
36	JHS31111518_ITGA3	117	CTGCACACAAGGGACCTTCA	GCTAAGCGAGGTCTGGAGTG
37	JHS32407856_HEATR7A	112	GTCAGCATTGGGAAACGACT	TCTCGCAGGAACATCAACAG
38	JHS30295263_AIFM2	123	AAGATCAACAGCTCCGCCTA	ACAGTCACCAATGGCGTAGA
39	JHS32488635_DPM2	134	TACTACACCGCCTGGGTGAT	AGTCCCACAAACAGGAGCAG
40	JHS31214980_CNN2	116	AGATGGGCACGAACAAGTG	CAGGGACATGGAGGAGTTGT
41	JHS31314031_"EML2,MIR330"	118	GAATGGGCCACAGCTACTTG	AAGCCAGCAACTTCCCATC
42	JHS31324130_RUVBL2	119	CCTGATCATGGCCACCAA	TGTAGGGGGTGGTGGAGAC
43	JHS32401588_LYNX1	128	CTGATCCTGGTGGTCCTCAT	GTGGTCATGCAGTAGGCAAC
44	JHS32407984_HEATR7A	136	TCAAGAGCAGCTGGGAGAAC	TCCTTCAGCAGGATCTGGAG
45	JHS31597126_LAMA5	125	GGGAGTTCTCCACGTCAGTG	CACGGTGTGGTTGCTCTG
46	JHS30447530_"ARAP1,STARD10"	104	TCAACCTCTGTGTTGTTATCTGC	CCACACCTTCCTGTCCATCT
47	JHS30554360_MAP3K12	107	AGCACCCCAACATCATCACT	AGCCCGCAGTACCTCATACA
48	JHS31372783_KLHL29	100	GTAGTGAGTGCAGGGGACAAC	TCCAGTTATCAAGCAGGGACA
49	JHS30600491_ATP2A2	106	TGTCACTCCACTTCCTGATCC	GGCAAGGAGATTTTCAGCAC
50	JHS32096926_"ATF6B,TNXB"	121	CTGGGCGCAAGTACAAGATG	GTCATGGTAGGCACTGCTTG
51	JHS31749149_ALS2CL	111	ACCTTCACCAGGGACCTGAC	CTGTGTGTGCAGTCCTCTCC

Back to article page