Supplementary Table 1. Primer sequences and design for cloned ncECRs.
| HIndIII: CCC AAGCTT | |||||||
|---|---|---|---|---|---|---|---|
| ECRs in
SNCA locus on chromosome 4
Human Genome assembly NCBI36/hg18 (March 2006) |
XhoI: CCGCTCGAG | ||||||
| KpnI: CGG GGTACC | |||||||
| BglII: GGA AGATCT | |||||||
| ECR | Length | Identity | Location | Primers | PCR
product length |
Ann.
Temp |
Restriction
sites within PCR product |
| D1 | 146bp | 78.10% | chr4:90833665-
90833810 |
CGG GGTACCCACGAAATCGTGCCAAAAAT | 601bp | no RE | |
| GGA AGATCTaagtcacaaggtcgaggcttt | 60C | ||||||
| D2 | 239bp | 74.50% | chr4:90844830+
90845413 |
CGG GGTACCtgcgaaattccacacaacat | 584bp | no RE | |
| GGA AGATCTTCAGCAGATGGCATGGAATA | 60C | ||||||
| D3-1/2 | 143bp | 72% | chr4:90848813-
90848955 |
CGG GGTACCAAGGGCTGACATTGGAATTG | no RE | ||
| 99bp | 75.80% | chr4:90849405-
90849503 |
GGA AGATCTCCGCCTCTGAAAATAAGCAA | 989bp | 60C | ||
| D4 | 110bp | 73.60% | chr4:90850858-
90850967 |
CGG GGTACCGATGCAGCCATCAACTCTGA | no RE | ||
| GGA AGATCTtgttggtagGCAGGAGAAATG | 944bp | 60C | |||||
| D5-1 | 241bp | 75.90% | chr4:90853634-
90853874 |
CGGGGTACCACTTCCTTGGGTAGGCGAAT | BglII at 1143 | ||
| D5-2 | 114bp | 75.40% | chr4:90854429-
90854542 |
CCGCTCGAGGCTGAGATCACGCCACTGTA | 1258bp | 60C | use XhoI site |
| D6-1/2 | 234bp | 83.30% | chr4:90855871-
90856104 |
GGA AGATCTCCATTCCCTCACCTCAAATG | 582bp | 60C | |
| 190bp | 75.30% | chr4:90856150-
90856339 |
CGGGGTACCTCTGCATGAATGTGCAAACA | ||||
| D7 | 167bp | 72.50% | chr4:90859690-
90859856 |
GGAAGATCTggggctgtagtgtggaaatc | no RE | ||
| CGGGGTACCGGGCAGTGCATACTTGTCCT | 856bp | 60C | |||||
| D8-1/2 | 100bp | 75% | chr4:90860722-
90860821 |
GGAAGATCTAGCTTCTGCCTTGTGTCTCC | no RE | ||
| 216bp | 75.90% | chr4:90861289-
90861504 |
CGGGGTACCTTGAAGAACCCAAAATGCAA | 1061bp | 59C | ||
| I1 | 192 bps | 81.80% | chr4:90871989-
90872180 |
CCGCTCGAGaggataggctccaaccacct | 840bp | 60C | BglII at 571 |
| CGGGGTACCCAAATTCGGATCACGTAGGG | use XhoI site | ||||||
| I2 | 154bp | 74% | chr4:90878220-
90878373 |
GGA AGATCTcaggaattGGTGCAAAATCA | 393bp | 60C | |
| CGG GGTACCaggggctgaccttcaagatt | |||||||
| I3-1/2 | 276 bps, | 77.50% | chr4:90887100-
90887375 |
GGAAGATCTtgaatgtgatggttcagcaaa | 986bp | 60C | no RE |
| 153 bps | 76.50% | chr4:90887445-
90887597 |
CGGGGTACCgggaaggcaccctctaggta | ||||
| I4-1/2 | 194 bps | 75.80% | chr4:90891860-
90892053 |
GGAAGATCTCCACCCCTCCACTTGACATA | 899bp | 60C | no RE |
| 100 bps | 75.00% | chr4:90892381-
90892480 |
CGGGGTACCGCAATGGAACTGTGGTGATG | ||||
| I5-1/2 | 109 bps | 76.10% | chr4:90893684-
90893792 |
GGAAGATCTCAGGCATGATTCCTCCCTTA | 705bp | 60C | no RE |
| 155 bps | 73.50% | chr4:90893990-
90894144 |
CGGGGTACCCCATCAACATCCCAAGAACA | ||||
| I6 | 130 bps | 74.60% | chr4:90894785-
90894914 |
GGAAGATCTccttgtgggtattcctgaacat | 355bp | 60C | no RE |
| CGGGGTACCGAAGTTGCCTGAGCTCCAAT | |||||||
| I7 | 187 bps | 75.90% | chr4:90897558-
90897744 |
GGAAGATCTAGATGATGAGCAGGCAGTCC | 432bp | 60C | no RE |
| CGGGGTACCcgaaccatagtggaaatcagg | |||||||
| I8 | 112 bps | 76.80% | chr4:90901290-
90901401 |
CCGCTCGAGaaggcttgattggacattgc | 474bp | 60C | BglII at 34 |
| CGGGGTACCctggaaagaattggccacaa | use XhoI site | ||||||
| I9 | 199 bps, | 75.40% | chr4:90906237-
90906435 |
GGAAGATCTTGCAATGAAAACCACAATGG | 561bp | 60C | no RE |
| CGGGGTACCtgtttatgttctgtattccaccaa | |||||||
| I10 | 269 bps | 74.30% | chr4:90926832-
90927100 |
GGAAGATCTtgggatgggtgggtaaatAG | 899bp | 60C | no RE |
| CGGGGTACCtgtgtcaaggatGGGAAAAAG | |||||||
| I11 | 108 bps | 74.10% | chr4:90929480-
90929587 |
GGAAGATCTtcaaagcaaagatttttctcca | 429bp | 60C | no RE |
| CGGGGTACCtggttccttttagcccaattt | |||||||
| I12 | 255 bps | 77.30% | chr4:90940532-
90940786 |
GGAAGATCTagggaagaggaaaagcttgg | 669bp | 60C | no RE |
| CGGGGTACCAAGGTTGAAAAACCGTGGTG | |||||||
| I13 | 127 bps, | 75.60% | chr4:90945579-
90945705 |
CCGCTCGAGaggctctgggaccacaatta | 578bp | 60C | BglII at 328 |
| CGGGGTACCCCTCTTAACTTCTGGGCAACC | use XhoI site | ||||||
| I14 | 100 bps | 75.00% | chr4:90958054-
90958153 |
GGAAGATCTtcccacctagaaccttacagga | 701bp | 60C | no RE |
| CGGGGTACCACACTTGAGTGTTATGGACCCTCT | |||||||
| I15 | 329 bps | 76.30% | chr4:90961895-
90962223 |
GGAAGATCTttcaacgttgttgacacctca | 490bp | 60C | no RE |
| CGGGGTACCccaGATAAATGCCATGCAAA | |||||||
| I16 | 106 bps | 75.50% | chr4:90976615-
90976720 |
GGAAGATCTCCCGTTACCACCTGTTGACT | 651bp | 60C | no RE |
| CGGGGTACCgccattcgacgacaggttag | |||||||
| U1 | 261 bps, | 81.60% | chr4:90977921-
90978181 |
GGAAGATCTCCGTCCTCCTCCTCCTAGTC | 883bp | 60C | no RE |
| CGGGGTACCATCACGCTGGATTTGTCTCC | |||||||
| U2-1 | 105 bps, | 76.20% | chr4:90980743-
90980847 |
GGAAGATCTTTCATGTTTTGTTTTCTCTTTGCT | 860bp | 59.5C | no RE |
| U2-2 | 100 bps, | 75.00% | chr4:90981402-
90981501 |
CGGGGTACCcaccagagttgcagagttgc | |||
| U3 | 329 bps, | 73.90% | chr4:91004670-
91004998 |
CCGCTCGAGccatgcagttttccCCAATA | 751bp | 60C | BglII at 487 |
| CGGGGTACCTCTCTCTCATTTTTGGTTTTGACA | use XhoI site | ||||||
| U4-1 | chr4:91,008,097-
91,008,809 |
GGAAGATCTCTGAAGTAGGGGGCTCTTCC | 535bp | 60C | no RE | ||
| CGGGGTACCGAGTTCTTTGGCAGGAGTGC | |||||||
| U4-2 | 131 bps, | 74.00% | chr4:91009155-
91009285 |
GGAAGATCTtggagaattcagttgctattgg | 837bp | 60C | no RE |
| CGGGGTACCTGTGTTGCCATAGTCACATGTTT | |||||||
| U4-3 | chr4:91,010,061-
91,010,758 |
GGAAGATCTAAGAAGAAGCAAGCCACACC | 698bp | 58C | no RE | ||
| CGGGGTACCtttctgtagggtttatagtgtcca | |||||||