Table 2.
List of primers used in validation of intron usage for different genes in CLL-B and normal B cells
| Gene symbol | HGNC approved Name/Gene symbol of the molecule (genomic region tested) | HGNC ID | HPRD ID | Refseq ID | Coordinates on UCSC genome browser | Primers | Primer sequence [5′ sequence 3′] | Tm (oC) | PCR product (bp) |
|---|---|---|---|---|---|---|---|---|---|
| ADTRP | Androgen-dependent TFPI regulating protein (chr6:11716510-11716630) | 21214 | 12836 | GenBank: NM_032744 | chr6:11716510-11716529 | FP | AATGGGTCTCTGTGGTGCTC | 59 | 121 |
| chr6:11716611-11716630 | RP | ACTAAGACCCGCTTGCCATT | |||||||
| RPL39L | Ribosomal protein L39-like (chr3:186,847,868-186,848039) | 17094 | 09610 | GenBank: NM_052969 | chr3:186,847,868-186,847,887 | FP | TCCTTCAAGACAGCCCTTGC | 56 | 172 |
| chr3:186,848,019–186,848,039 | RP | TGCTTTGAAGGTGACATCGTG | |||||||
| HS3ST1 | Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 (chr4:11,424,163-11,424,329) | 5194 | 04455 | GenBank: NM_005114 | chr4:11,424,163-11,424,182 | FP | GACAGGCAGAGACTCGGTT | 57 | 167 |
| chr4:11,424,310-11,424,329 | RP | TTGTGCCCTTGGAGACTCTG | |||||||
| CTLA4 | Cytotoxic T-lymphocyte-associated antigen 4 (chr2:203871925-203872008) | 2505 | 00474 | GenBank: NM_005214 | chr2:203871925-203871944 | FP | TGGTGCCTTCCTTGTCGAAG | 53 | 84 |
| chr2:203871989-203872008 | RP | AAGGCAAAACGTCCCAGTCA | |||||||
| FMOD | Fibromodulin (chr1:203343741-203343920) | 3774 | 02591 | GenBank: NR_103757 | chr1:203343741-203343760 | FP | TAGGTGTGACCATGAGGGCT | 56 | 180 |
| chr1:203343896-203343920 | RP | GCTGCAACCTCACCTCATCT | |||||||
| GUCY2C | Guanylate Cyclase 2C (chr12:14625022-14625136) | 4688 | 07529 | GenBank: NM_004963 | chr12:14625022-14625041 | FP | GTTCCCTACTGTTCCCAGGC | 55 | 115 |
| chr12:14625117-14625136 | RP | GGATCACAGCTTGGGGGAAA | |||||||
| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase (chr12:6536514-6536754) | 4141 | 00713 | GenBank: NM_002046 | chr12:6536514-6536531 | FP | 5′ TGGTCACCAGGGCTGCTT 3′ | 57 | 151 |
| chr12:6536735-6536754 | RP | 5′ AGCTTCCCGTTCTCAGCCTT 3′ |
FP, Forward Primer; RP, Reverse Primer.