TOHO rSNP DB2

Index
 

CAR/RXRα-binding sites in the human genoeme. 

The human genomic library that was constructed by inserting approximately 300 bp fragments in reporter plasmids and treating with 5FOA to efficiently eliminate false-positive interactions in the yeast one-hybrid assay was described previously [J Recept Signal Transduct Res. 2010 Apr;30(2):88-105, Methods Mol Biol. 2013;977:125-36] .The CAR/RXRαexpression plasmids were transformed into the library were selected on synthetic complete media lacking leucine, tryptophan, and uracil but containing 25 µg/ml 6-azauracil. After 3 weeks, positive colonies were picked from the selection plates and colony-direct PCR was performed to recover human genomic fragments. The PCR fragments were directly sequenced and unique sequences were obtained. To examine the direct interaction of RXR homodimer with the DR-1 motif in the obtained fragments, we performed a semi-quantitative EMSA competition assay. In this method, it is possible to examine binding intensity using a 10- and 100-fold molar excess of unlabeled competitors.


# Position Length
(bp)
Neighboring Gene
(Distance to TSS)
CAR/RXRα-
bindnig sequence
Motif Competition (%) 
×10 ×100
1 Chr18 : 55201286-55201390 105 FECH (+52,631), ONECUT2 (+98,421) tggAGTTCAaAGGTCAcat DR1 14.6±1.6 95.2±0.4
2 Chr7 : 138292264-138292495 232 SVOPL (+71,410), TRIM24 (+147,301) cgcAGGTCAaAGGTCAggt DR1 10.7±2.2 78.7±2.9
3 Chr5 : 76841961-76842018 58 OTP (+92,532), PDE8B (+335,284) cagAGGTCGgAGGTCAagt DR1 17.9±0.5 43.5±2.1
4 Chr20 : 23387626-23387738 113 NAPB (+14,474), GZF1 (+42,682) caaAGTTCAaAGGTCActg DR1 52.0±1.3 115.8±0.9
5 Chr13 : 59071533-59071644 112 PCDH17 (+865,800) ttaAGTGCAgGGGTCAgga DR1 25.2±0.9 44.6±0.8
6 Chr17 : 1918186-1918361 176 RTN4RL1 (+9,904), RPA1 (+185,001) tggAGCTCAgAGTTCAaag DR1 41.4±1.8 90.3±1.1
7 Chr4 : 121700806-121701088 283 MAD2L1 (-712,934), PRDM5 (+143,066) ttgAGGTCAagAGTTCAagg DR2 30.2±2.6 101.9±1.4
8 ChrX : 40929970-40930061 92 MED14 (-335,212), USP9X (-14,872) tgtGGGTGAacAGGTCAatg DR2 71.5±3.0 102.7±0.3
9 Chr13 : 49397697-49397876 180 FNDC3A (-152,261), CYSLTR2 (+116,834) ggcGGATCAtgAGGTCAaga DR2 22.2±0.8 50.2±2.1
10 Chr17 : 8796437-8796604 168 PIK3R6 (-25,527), PIK3R5 (+19,313) tggAGGTCAgagAGGTCAagc DR3 35.3±1.1 110.3±9.6
11 Chr2 : 103266921-103267061 141 SLC9A2 (+30,825), MFSD9 (+86,346) tgaAGGTCAaagAGTTTAaca DR3 56.8±0.5 102.8±1.1
12 Chr5 : 142827845-142828030 186 NR3C1 (-43,893), YIPF5 (+722,340) cagAGGTCAcagAGGTCAtaa DR3 60.0±0.6 111.6±2.1
13 Chr7 : 33720609-33720751 143 BMPER (-223,843), BBS9 (+551,528) ccaAGTTCAcatAGTTCAtaa DR3 65.5±0.4 111.3±1.3
14 ChrX : 45732008-45732304 297 CXorf36 (-672,010), ZNF673 (-574,468) ctgAGGCCAgggAGTTCAcca DR3 35.9±2.1 91.5±2.9
15 Chr17 : 54747517-54747691 175 NOG (+76,544), C17orf67 (+145,767) cacAGGTCAggcAGTTGAtgc DR3 13.1±0.9 46.9±1.9
16 Chr6 : 4942951-4943334 384 RPP40 (+61,128), CDYL (+166,463) cggAGGACAgtgGGGTCAggc DR3 34.4±5.8 89.6±2.6
17 Chr3 : 120575966-120576060 95 STXBP5L (-51,037), GTF2E1 (+114,455) taaAGGTCAaggaAGTTCAatt DR4 62.8±1.3 107.8±1.4
18 Chr12 : 14672183-14672322 140 PLBD1 (+48,538), ATF7IP (+153,642) ttaAGGTCAactgAGGTCAtat DR4 51.5±1.2 107.6±0.7
19 Chr1 : 220849174-220849356 183 C1orf115 (-14,363), MARK1 (+147,697) gcaAGGGCAggggAGGTCAata DR4 30.6±1.1 77.2±0.6
20 Chr10 : 30521090-30521250 161 SVIL (-597,269), MTPAP (+117,097) agtGGATCActtgAGGTCAgga DR4 20.6±0.8 69.0±1.1
21 Chr2 : 55562474-55562589 116 MTIF2 (-66,148), CCDC88A (+84,525) gtgAGGTCAttaaAGTTCAtgt DR4 70.8±0.8 112.6±0.4
22 Chr8 : 1165688-1165800 113 C8orf42 (-670,413), DLGAP2 (-283,825) atgGGTTCAtttgGGTGCAtca DR4 50.1±0.7 104.2±0.0
23 Chr13 : 91370194-91370452 259 GPC5 (-680,612) ctgGGGTCAtatgATTTCAtag DR4 41.2±1.2 93.4±0.8
24 Chr3 : 177287827-177287945 119 KCNMB2 (-966,338), TBL1XR1 (-372,838) ttaGGGTCAgctgAGTTCAtat DR4 61.5±1.9 100.8±1.3
25 Chr6 : 42700810-42701034 225 PRPH2 (-10,564), TBCC (+12,962) tcaAGGTTAcaagAGTTCAaga DR4 75.4±0.2 127.9±4.5
26 ChrX : 66743819-66744135 317 EDA2R (-908,105), AR (-19,897) gagAGGTCAatgaGGTTCAcag DR4 49.7±0.8 99.8±0.7
27 Chr9 : 13275072-13275351 280 MPDZ (-24,841) taaAGGTTAaatgAGGTCActa DR4 53.2±0.8 104.7±1.6
28 Chr19 : 5982545-5982685 141 RANBP3 (-4,295) tcaAGTTCAtgaaAGGTCAcac DR4 61.7±1.3 114.6±0.6
29 Chr5 : 168554759-168554923 165 PANK3 (-548,227), SLIT3 (+173,292) caaAGTTCActtaAGTTCAgag DR4 57.6±0.7 116.7±0.7
30 Chr8 : 4846264-4846562 299 CSMD1 (+5,915) caaAGGTCActtaAGGTCAttt DR4 71.4±1.5 125.1±1.1
31 Chr1 : 88626432-88626556 125 PKN2 (-523,428), LMO4 (+832,343) tttAGGTCAttgaAGTTCAagt DR4 55.4±0.7 106.2±3.5
32 Chr8 : 95584473-95584707 235 ESRP1 (-68,774), KIAA1429 (-18,844) aagAGGTCAgttgGGGTCAgat DR4 45.0±1.3 99.8±1.3
33 Chr7 : 15597442-15597713 272 DGKB (-716,503), AGMO (+4,062) caaAGGGCAccagAGTTAAcag DR4 23.9±1.6 67.6±0.8
34 Chr14 : 54345870-54346006 137 DDHD1 (-725,892), BMP4 (+75,332) ctgAGGTCAagtgAGTTCAcct DR4 70.2±0.9 118.5±1.4
35 Chr15 : 49543989-49544276 288 FGF7 (-171,242), GALK2 (+81,711) ggtGGATCActtgAGGTCAgga DR4 26.0±2.4 65.0±0.7
36 Chr13 : 55084028-55084114 87 NONE atgGGGTCAacaaAGTTTAaga DR4 83.3±4.9 119.2±5.2
37 Chr8 : 112300235-112300383 149 NONE aagAGGTTAcaagAGTTCAtat DR4 69.2±1.1 112.9±0.3
38 Chr3 : 28008615-28008785 171 CMC1 (-274,424), EOMES (-244,915) gtgGGGTCAcatgAGGGCAcat DR4 51.9±1.8 105.3±1.0
39 Chr15 : 87420670-87420730 61 AGBL1 (+735,458) aagAGGTCAactgAGTTCAtcc DR4 69.2±0.6 114.4±0.3
40 Chr9 : 81575106-81575356 251 TLE4 (-611,647), PSAT1 (+663,172) aggAGGTGAtaaaGGTTAAatg DR4 21.0±1.5 64.6±0.5
41 Chr15 : 65168224-65168305 82 PIF1 (-50,427), ANKDD1A (-35,836) atgGTGTCAgaagAGTTCAtca DR4 64.7±0.6 107.5±0.2
42 Chr10 : 31605586-31605754 169 ZEB1 (-2,431) aaaAGGTGAacagAGTTCAttg DR4 73.5±1.4 113.6±1.0
43 Chr4 : 4003949-4004240 292 OTOP1 (+224,526), ADRA2C (+235,799) atgGGGTCAgctaGGTTTActt DR4 43.3±0.8 100.1±2.4
44 Chr5 : 154114732-154114879 148 LARP1 (+22,344), C5orf4 (+115,407) ggcAGGTCAcctgAGGTCAgga DR4 34.2±1.1 97.2±0.3
45 Chr15 : 69230539-69230630 92 NOX5 (-76,449), SPESP1 (+7,746) ggtGGGTCAactaAGGTCAgga DR4 50.2±3.9 100.7±0.9
46 Chr8 : 140124212-140124570 359 COL22A1 (-198,155), KCNK9 (+590,908) gccAGTGCAgaagAGGTCAcac DR4 27.7±2.0 78.3±0.9
47 Chr8 : 107263662-107263790 129 OXR1 (-196,426), ZFPM2 (+932,579) gtcGGGTCActtaAGGTCAgga DR4 40.7±0.4 95.7±0.9
48 Chr15 : 78475549-78475775 227 IDH3A (+33,943), ACSBG1 (+51,387) ggaGGGTCAtttgAGGTCAgga DR4 39.3±0.8 98.1±2.7
49 Chr14 : 65099982-65100056 75 PLEKHG3 (-94,292), HSPA2 (+92,833) attAGTTAAgatgAGGTCAtac DR4 19.3±5.4 62.2±5.6
50 Chr6 : 31790280-31790663 384 HSPA1B (-5,040), HSPA1A (+7,181) caaGGATCAaagaAGTTCAgtg DR4 57.1±1.0 88.6±0.2
51 Chr13 : 90222946-90223063 118 NONE gtaAGGTCAtaaaAGTTCAggt DR4 63.1±1.8 110.6±0.4
52 ChrX : 132353555-132353667 113 TFDP3 (-1,235) ttaAGGTTAaatgAGGTCAtaa DR4 55.1±0.2 97.8±0.4
53 Chr12 : 80739933-80740212 280 PTPRQ (-98,053), OTOGL (+136,840) caaGGTTGAttagAGTTCAgcc DR4 48.2±1.3 93.5±0.3
54 Chr6 : 133030154-133030300 147 TAAR1 (-63,085), VNN1 (+4,967) aaaAGGTCGtctgAGGGCAtca DR4 37.7±2.3 89.0±0.3
55 Chr20 : 38461220-38461351 132 MAFB (+856,590), DHX35 (+870,305) acaGGGTCAcaaaAGGCCAata DR4 34.3±0.2 88.9±1.6
56 Chr18 : 609485-609841 357 CLUL1 (-7,037), CETN1 (+29,294) ggtGGGTCAtttgAGGTCAgga DR4 41.9±1.1 96.9±0.6
57 Chr4 : 4081417-4081706 290 OTOP1 (+147,059), ADRA2C (+313,266) ggcGGATCActtgAGGTCAgga DR4 17.5±1.0 60.6±0.7
58 Chr4 : 27697777-27697856 80 STIM2 (+835,504) gggAGGTCActcaAGTTCActg DR4 66.1±1.5 114.3±1.4
59 Chr11 : 70447681-70447959 279 CTTN (+203,208), SHANK2 (+488,022) ggtGGATCAcctgAGGTCAgga DR4 17.5±0.9 55.7±2.6
60 Chr17 : 71023806-71024052 247 SLC39A11 (+64,924), SOX9 (+906,768) caaGGGTCAaatcAGGGCActg DR4 40.6±1.4 102.2±0.3
61 Chr7 : 87875231-87875351 121 SRI (-25,898), STEAP4 (+60,937) caaAGGTTAcaagAGTTCTctt DR4 60.4±1.4 96.3±1.8
62 Chr2 : 89376298-89376461 164 RPIA (+385,204) caaAGGTTAccttAGGTCAtat DR4 36.9±1.5 92.5±1.1
63 Chr2 : 95707549-95707691 143 MAL (+16,141), MRPS5 (+80,134) gggGGGTTAgcagAGTTGAgct DR4 33.8±3.4 76.2±5.0
64 Chr4 : 88898879-88898955 77 PKD2 (-29,882), SPP1 (+2,115) cagAGTTCAattccAGTTGAaca DR5 17.6±2.2 73.4±0.3
65 Chr1 : 177083927-177084138 212 ASTN1 (+49,991), PAPPA2 (+651,726) gctGGGTCAggaaaAGTTCAtgg DR5 69.6±9.1 98.0±0.2
66 Chr6 : 133330363-133330649 287 EYA4 (-231,989), RPS12 (+194,798) agtGGTTCAatcacAGTTCActg DR5 49.6±0.2 89.9±1.0
67 Chr14 : 35253086-35253208 123 CFL2 (-69,118), BAZ1A (+91,706) aaaAGTTCAaacacAGTTCAttt DR5 71.6±1.9 109.9±0.9
68 Chr1 : 84080031-84080193 163 TTLL7 (+384,721) aagAGGTCAagtcaGGTACAaac DR5 37.2±0.7 86.4±1.0
69 Chr5 : 89560627-89560695 69 CETN3 (+144,942) aggAGGTCAggaggAGTTCActg DR5 67.0±2.5 102.2±0.8
70 ChrX : 36376152-36376213 62 PRRG1 (-832,345), CXorf59 (+311,130) aggAGGTCAatatgAGGTCAcag DR5 39.2±0.3 95.8±1.2
71 Chr1 : 48570878-48571087 210 SLC5A9 (-117,374), LOC388630 (-108,421) gaaAGGTCActcagAGTTCAttt DR5 68.6±9.7 120.4±0.4
72 Chr10 : 16445680-16445852 173 FAM188A (-543,247), PTER (-33,201) taaAGTTCAtggtaaAGTTCAtgg DR6 74.0±1.2 119.3±0.6
73 Chr4 : 80819846-80819929 84 GK2 (-490,516), ANTXR2 (+174,589) gaaAGTTCAtattgtAGGTCAttc DR6 64.7±1.0 112.9±1.4
74 Chr2 : 33407228-33407375 148 RASGRP3 (-331,640), LTBP1 (+234,933) ctaAGTTCAtgatagAGTTCAaag DR6 65.3±1.3 112.5±1.2
75 Chr6 : 23048624-23048748 125 PRL (-745,604) ttgAGCTCAattcctAGTTCAcca DR6 27.2±0.8 74.3±0.8
76 Chr2 : 135675135-135675350 216 CCNT2 (-1,149) ttgAGGTCAggagttcgAGGGCAagg DR8 11.7±1.0 54.8±2.6
77 Chr20 : 36825053-36825172 120 BPI (-107,439), TGM2 (-31,413) ctgGGGTCAcagggccagAGGTCActg DR9 18.8±3.0 70.2±3.6
78 Chr21 : 34190796-34190941 146 C21orf62 (-4,816) tagGGGTCAcctcggtagGGGTCAggg DR9 17.9±0.6 58.7±0.7
79 Chr1 : 154209880-154209999 120 HAX1 (-35,099), UBAP2L (+16,615) tcaGGGTCAaacaatgctgAGTTCAaat DR10 34.4±1.2 90.0±0.6
80 Chr14 : 98635538-98635762 225 NONE gacTGAACTcTGGTCAttt ER1 13.0±5.0 58.3±3.2
81 Chr12 : 34343448-34343791 344 ALG10 (+168,404) tggTGCCCTcctAGGTCAtgg ER3 37.6±0.8 41.6±4.5
82 Chr12 : 10876774-10876871 98 CSDA (-870) attTGGCCCctagGGTTCAgac ER4 19.6±0.2 42.6±0.6
83 Chr9 : 130011528-130011906 379 ANGPTL2 (-126,673), GARNL3 (-15,039) tctTGAACTcctgGGCTCAagt ER4 4.4±2.5 55.2±0.9
84 Chr10 : 58646226-58646342 117 ZWINT (-525,250) ctgTGACCTcttgAGAACTtaa ER4 19.7±0.5 81.6±1.7
85 Chr20 : 7438451-7438525 75 HAO1 (+482,605), BMP2 (+689,743) acaTGAACTtttggAGGTCAtat ER5 78.2±0.5 115.0±0.4
86 Chr1 : 242533417-242533615 199 MAP1LC3C (-371,131), PLD5 (+154,482) caaGGAACTaaataAGTTCAttt ER5 30.9±1.1 75.6±0.9
87 Chr1 : 219789689-219789818 130 SLC30A10 (+312,239), LYPLAL1 (+442,562) atgTGAACTcttctaAGTTCAtgg ER6 79.0±0.7 111.1±0.7
88 Chr9 : 46385533-46385719 187 NONE gtgTGACCTttttaaAGTTAAatt ER6 26.9±2.5 87.2±1.4
89 Chr3 : 74240550-74240667 118 PDZRN3 (-566,537), CNTN3 (+329,734) aacTGACCCattttcaGGTTCActg ER7 30.0±4.9 53.0±2.5
90 Chr8 : 41543991-41544261 271 NKX6-3 (-39,251), ANK1 (+210,154) tgcTGACCTtgctgagAGTTCAtgt ER7 66.1±0.2 101.5±0.5
91 Chr6 : 108964946-108965090 145 ARMC2 (-204,601), FOXO3 (+82,949) agcTGAACTctgcactaAGGTCAgat ER8 65.3±1.6 103±0.3
92 Chr14 : 91348266-91348370 105 TTC7B (-65,557), RPS6KA5 (+178,675) gatTAAACTctaatcaaAGGTCAaag ER8 76.5±1.2 106.7±3.1
93 Chr20 : 1565505-1565776 272 SIRPD (-27,298), SIRPB1 (+35,048) tctTGACCCttttgtcaaAGGTCAatt ER9 58.9±1.5 101.4±0.6
94 Chr18 : 66213526-66213902 377 TMX3 (+168,639) tttTGAACTctgtctgaaAGGTCActt ER9 72.2±1.5 105.3±0.5
95 Chr1 : 42946546-42946764 219 PPIH (-177,393), PPCS (+24,482) ggaTGACCTgaggccaggAGTTCAaga ER9 54.4±0.4 96.9±1.5
96 Chr5 : 88641418-88641561 144 MEF2C (-441,568) accTTAACTctgtctggaAGGTCAaga ER9 21.9±1.0 79.5±1.9
97 Chr5 : 54048617-54048892 276 ESM1 (+232,659), SNX18 (+235,162) agaTGACCTctgcccgctaAGTTCAagt ER10 53.4±1.5 111.2±0.8
98 Chr17 : 22251179-22251327 149 MTRNR2L1 (+228,816) accTGAACTttcaaaggaaGGTTCAatt ER10 31.8±1.0 101.7±1.7
99 Chr21 : 42948507-42948610 104 TMPRSS2 (-68,567), RIPK4 (+238,690) tggAGTTCATGACCTtgt IR0 50.8±2.9 126.6±2.0
100 Chr22 : 51188718-51188943 226 ACR (+12,179), RABL2B (+33,256) caaAGGACATGAACTctt IR0 6.4±1.0 52.9±1.1
101 Chr5 : 113265138-113265327 190 KCNN2 (-432,783), YTHDC2 (+415,842) atgAGTTCATGTCCTttg IR0 19.2±2.8 72.2±3.0
102 Chr19 : 27990058-27990456 399 NONE caaAGGACATGAACTcat IR0 20.4±2.7 65.6±0.7
103 Chr3 : 135695587-135695826 240 PPP2R3A (+11,192), MSL2 (+218,981) ttaAGTTCAtcTGAAATtta IR2 15.9±2.3 46.0±1.5
104 Chr16 : 27714860-27714998 139 GTF3C1 (-153,678), GSG1L (+359,901) cttAGTTCAgcTGACCTctg IR2 48.7±2.4 116.6±1
105 Chr14 : 58472137-58472540 404 SLC35F4 (-139,747), C14orf37 (+146,508) aggAGGTCAaagTGTCCTctg IR3 8.8±6.8 54.4±6.9
106 Chr7 : 152388241-152388469 229 ACTR3B (-68,496), XRCC2 (-15,105) tggAGTTCAttggcaTGACCTcgg IR6 12.4±3.7 85.6±1.3
107 Chr5 : 162859214-162859417 204 CCNG1 (-5,261) taaAGGTCAttgcctTAACCTagg IR6 16.1±1.2 70.0±1.1
108 Chr18 : 30395764-30395944 181 ASXL3 (-762,687), KLHL14 (-42,880) aaaAGTTCAacctcccTTAACTatg IR7 32.9±1.4 95.7±0.8


 Index

 

 Kazuyuki Yanai

Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan