Markup | Genome Research

Table 2.

Alu Ya5a2 PCR Primers, Chromosomal Locations, and PCR Product Sizes

Name		5′ Primer sequence (5′–3′)		3′ Primer sequence (5′A–3′)		A.T.[i]	Chromosome[ii]	Product size[iii]
Name		5′ Primer sequence (5′–3′)		3′ Primer sequence (5′A–3′)		A.T.[i]	Chromosome[ii]	filled	empty
Ya5NBC206	TCCTTAGCTATCTCACAAGCTACAT	ACACATTTCCTTCAAGAGGTCAAAG	60°C	4	734	424
Ya5NBC207	CAGTTTTATACACTGGCCTGTTTTC	TTGTAGGAGAAAGAGGGGAAATACT	50°C	6	443	122
Ya5NBC208	AATACCTTGTACATCTTCACCCCTA	TCTCTCTGCTGCACAGTTTGTT	50°C	14	441	115
Ya5NBC240	CAGGAGATAAATATGTTCGGAGAGT	TAACTGGGACAGTGAGTTTTACCTG	55°C	9	505	202
Ya5NBC241	GGTTCCAATAGAGAGCAACAGAA	ACCTTAAGCTTTCCCCCAGA	55°C	15	392	66
Ya5NBC242	AACAAAATTCCCTTTCCTCCA	GGCAATCTGACCTTGGGTAA	55°C	7	503	192
Ya5NBC7	TGATGGATATTTGGGTTGGTTC	GGACTGTAAACTAGTTCAACCATTGTG	60°C	7	522	216
Ya5NBC205	ACATGAAGGGCCGACTGTAT	TGCTGCTGCATTATCAACTG	50°C	21	435	81
Ya5NBC209	GTCTATGGGAAGATGAAGAATAGGA	GATGGAGTCACTCATGTGAAAAGTA	55°C	14	447	116
Ya5NBC239	CAGCTGAGAACTGTCACAAATAGAA	ATCAATGACTGACTTGTGCTGAGT	55°C	9	531	198
Ya5NBC243	CCATGATTCGTCATTCACCA	AGGAGACCTGCCAATGAATG	60°C	21	406	86
Ya5NBC220	AAATCAAGCTGCCATACCTCA	GAAACCATCCTTCACAGTGG	60°C	1	463	141
Ya5NBC235	CCCAAGGCACTTGCTGTTA	CCCTTCGAGAAAGAGGAAGG	50°C	2	391	76
Ya5NBC244	CCTATGGCTGAAACTTCTGAAACT	ATATCTTGGTCCACTAGACAAGCAC	60°C	18	453	130
Ya5NBC237[iv]	CCCATGGAGGGTCTTTCCTA	CTGGAAACCATCCTTCACAGT	60°C	1	410	88

[i] Amplification of each locus required 2.5 min at 94°C initial denaturing, and 32 cycles for 1 min 94°C, 1-min annealing temperature (A.T.) and 1-min elongation at 72°C. A final extension time of 10 min at 72°C was also used.

[ii] Chromosomal location determined from accession information or by PCR analysis of NIGMS monochromosomal hybrid cell line DNA samples.

[iii] Empty product sizes calculated by removing the Alu element and one direct repeat from the filled sites that were identified.

[iv] Alu Ya5a2 element of the FGFR2 gene.