Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

Snezhkina, Anastasiya Vladimirovna; Krasnov, George Sergeevich; Zaretsky, Andrew Rostislavovich; Zhavoronkov, Alex; Nyushko, Kirill Mikhailovich; Moskalev, Alexey Alexandrovich; Karpova, Irina Yurievna; Afremova, Anastasiya Isaevna; Lipatova, Anastasiya Valerievna; Kochetkov, Dmitriy Vladimitovich; Fedorova, Maria Sergeena; Volchenko, Nadezhda Nikolaevna; Sadritdinova, Asiya Fayazovna; Melnikova, Nataliya Vladimirovna; Sidorov, Dmitry Vladimirovich; Popov, Anatoly Yurievich; Kalinin, Dmitry Valerievich; Kaprin, Andrey Dmitrievich; Alekseev, Boris Yakovlevich; Dmitriev, Alexey Alexandrovich; Kudryavtseva, Anna Viktorovna

doi:10.1186/s12864-016-3351-5

BMC Genomics

Table 2 Primer and probe sets for qPCR analysis

From: Differential expression of alternatively spliced transcripts related to energy metabolism in colorectal cancer

Gene	Transcripts (UCSC database)	Direction	Primer sequence, 5’ → 3’	Amplicon size, bp
COL6A3	universal	Forward Reverse Probe	TCCAAGCCAAGAACGCAGA TGACGCCCTCAGAGCCAT ACGGAGCACCAGCACCAGTTTCAGG	204
COL6A3	uc002vwo / NM_057167 uc002vwq / NM_057165 (not expressed according to RNA-Seq data)	Forward Reverse Probe	ACACACGCCTTCAGGTTTGC GACTGCGAAATTGACACTTCCG CAGCAGCAGCAAGCAGCACAAGACTC	218
ICAM1	universal	Forward Reverse Probe	CACCCCAGAGGACAACGG TGGCACATTGGAGTCTGCTG CCGGCCAGCTTATACACAAGAACCAGA	180
ICAM1	uc010xle / AK301412	Forward Reverse Probe	CGCTATGGCTCCCAGCAG TGGCAGCGTAGGGTAAGGTTC TCTGTTCCCAGGGACTCCAGAACGG	147
OGDH	universal	Forward Reverse Probe	AAGTCTAGTGAGAATGGCGTGGACT CAAGGTAATGTTCCTGTCGGTGAC TTCAGCCGCCCTCTGTGTGGCAT	219
OGDH	uc011kby / AK296400	Forward Reverse Probe	GATGTACTGTGCTTGGCTGGAAA GATGATCTCCCGCAGAGGAAGT CAGGCCATAGAACCCTTATGTACACTTTTGGG	147
PHPT1	universal	Forward Reverse Probe	AAGTACCCCGACTACGAGGTCA GGCTCTGAAGTGGCTGCTG CTAACGACGGCTACTGAGCACTCCCA	92
PHPT1	uc004cjq / NM_014172	Forward Reverse Probe	AAGGCTGCGACTGTGAGTGTCT CTCAGTTGAAATGGCGTGCTG CGGCTATTCCATGGCCTATGGTCCTG	122
PPP2R5D	universal	Forward Reverse Probe	CGGGACTTCCTCAAGACCATT ATGATGCTGCCCAGGATCTC CACATCTTCTACAGGTTCATCTACGAGACGGA	161
PPP2R5D	uc010jyd / NM_180977	Forward Reverse Probe	GGCCGAGATGCCCTATAAACT TTGAGTCCTGCCCGCTTC CTTCTGGATAAACAGCTCCTTCTCCTTTTTCAG	138
SLC29A1	universal	Forward Reverse Probe	CATTTTGACCATCATCTGTTACCTG GGTCCAACTTGGTCTCCTGCT CCCCGCCTGGAATTCTACCGCTACTA	107
SLC29A1	uc003owz / NM_001078177	Forward Reverse Probe	GAGCCTGAGGACCCTGCG CGATGGGGATCACCCGTC CAACGTGACCGCAGCCTGTTTTAGGC	127
TRIB3	universal	Forward Reverse Probe	GCGTGATCTCAAGCTGTGTCG GCCTTGCCCGAGTATGAGG CAGCTTCTTCCTCTCACGGTCAGCGAAG	183
	uc002wdm / NM_021158	Forward Reverse Probe	ACCTGCTGGTGCCCTGGAG CGTTTCTGGACGGGACGCT ACGGGGCGAGATGCGAGCCACC	168
	uc002wdn / AK297546	Forward Reverse Probe	GTCATCCCAGCCTCGAACCT TCCAACTCCAACCGCTTCTTC TACCTGGCAACAGATGCGAGCCACC	191

Only UCSC hg19 target transcripts are listed

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ISSN: 1471-2164

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