TOHO rSNP DB

Index
 

RXR homodimer-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 RXR homodimer expression 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.


# Chr. position
(GRCh38/hg38)		 length
(bp)		 Gene
Symbol		 Gene
ID		 OMIM
ID		 Distance DR-1 Motif EMSA competition (%)
x12.5 x100
1 14 90095975 283 KCNK13 56659 607367 on the gene tgaAGGTCAaAGGGGAagc 13.9±0.6 24.7±1.5
2 3 53843442 225 CHDH 55349 not found on the gene agcAGAGCAaAGGTCAggg 14.0±1.5 36.5±1.1
3 19 9985881 94 COL5A3 50509 120216 on the gene tatGGGACAaAGGTCAgaa 3.1±1.8 9.0±2.2
4 1 195715329 263 KCNT2 343450 610044 500,000 gtgACTTCAgAGGTCCagc ND ND
5 8 94589349 244 KIAA1429 25962 not found 35,000 tctGGGTGAcAGAGCAaga ND ND
6 3 186523494 268 CRYGS 1427 123730 14,500 aggAAGGCAaAGTCCAcaa ND ND
7 1 242108507 112 PLD5 200150 not found on the gene cccACATCAtAAGCCAagt ND ND
8 22 49364796 128 C22orf34 348645 not found 500,000 tcgAGGTCAgAGGTCAgcc 50±1.2 73.1±1.2
9 4 143283947 205 GAB1 2549 604439 50,000 ctgAGGTCAgAGTTCAaga 32.2±2.9 52.1±1.6
10 17 49922375 128 DLX4 1748 601911 50,000 tagAGGGCAgAGGTCAggg 7.1±1.2 26.7±0.9
11 1 120351254 215 PFN1P2 767846 not found 17,000 acaAGATCAcAGCTCAgta ND 2.3±1.1
12 6 68741281 256 BAI3 577 602684 on the gene taaAGGTCAaAGGTCAcat 91.6±0.8 98.8±0.1
13 10 117481910 206 EMX2OS 196047 607637 3,000 taaAGGTCAaAGGTCAaat 100±0.2 108.0±1.0
14 10 118550187 262 PRLHR 2834 600895 43,000 ccaAGGTCAaAGGTCTagc 12.8±1.1 34.2±2.1
15 2 48085891 230 FOXN2 3344 not found 90,000 gcaAGTTCAaAGGTCAaat 77.8±1.1 95.6±7.5
16 2 236797467 329 COPS8 10920 616011 210,000 atgGGGTCAaAGGTCGagg 86.4±0.3 97.3±0.5
17 6 140784416 121 LOC10057477 not found not found 7,000,000 gagAGGTCAaAGGTTAatt 81.3±0.5 92.9±0.8
18 5 64098978 256 RNF180 285671 616015 70,000 gtcAGGTCAaAGTTCAact 58.7±2.4 72.9±0.9
19 6 761274 114 TP53TG3D 729264 not found 180,000 ttgAGGTCAaAGGTGAgaa 43.6±0.5 68±1.0
6 573074 114 BC041879 390705 not found 350,000
6 299915 114 BC041879 390705 not found 60,000
20 5 181051964 232 BTNL9 153579 not found on the gene ggaGGGTCAcAGGTCAgag 13.8±2.3 30.7±1.5
21 19 38458296 161 RYR1 6261 180901 on the gene ctgGGGTCAaTGGTCAggg 8.1±0.2 27.2±1.5
22 7 38207555 148 STARD3NL 83930 611759 on the gene aagAGGTCAaAGGTGAcaa 62.1±0.7 78.2±0.2
23 19 633005 257 POLRMT 5442 601778 on the gene agcAGGTCAaAGGTTAaga 67.0±2.4 74.6±0.2
24 9 37568694 341 FBXO10 26267 609092 on the gene ctaAGGTCAgAGTTCAtgt 28.2±1.7 52.1±0.6
25 10 80499223 275 TSPAN14 81619 not found on the gene ctaAGGTGAaAGGTCAata 40.5±0.4 56.6±0.9
26 5 132539609 277 IL5 3567 147850 1000 tgtATGTCAgGGGTCAgag 2.4±0.5 19.4±1.5
27 12 70711954 318 PTPRR 5801 602853 on the gene ccaAGGTGAaAGGCCAgtg 0.5±1.1 8.3±1.7
28 2 121992901 140 TSN 7247 600575 225,000 aagAGGTCAaAGGTGAgca 48.0±3.2 70.3±5.9
29 17 10931719 256 PIRT not found not found 100,000 gagAGGTCAaAGGTGAtgt 39.7±2.4 56.9±1.6
30 22 24945324 304 TMEM211 255349 not found 5,000 tgaAGGGCAaAGGTCAagc 30.1±1.8 60.6±1.0
31 1 12134367 248 TNFRSF8 943 153243 on the gene gaaAGGTGAgAGGGCAtcc ND 12.3±2.3
32 5 24496287 500 CDH10 1008 604555 on the gene aaaAGGTGAaGGGTCAagc 20.1±3.1 52.5±3.2
33 Y 18890414 244 TTTY14 83869 not found on the gene caaAGGTCAgAGTTCAggg 21.6±1.7 43.6±1.5
34 2 99354948 264 EIF5B 9669 606086 on the gene ttgAGGTCAgAGTTCAaga 28.0±1.5 47.7±1.5
35 17 50723347 308 LUC7L3 51747 609434 on the gene ccgAGTTCAaAGGTCAgct 87.8±0.8 94.6±1.3
36 3 66229469 229 SLC25A26 115286 611037 on the gene cagAGGGCAaAGGTGAagc 12.0±0.8 26.3±1.6
37 5 132815462 216 SOWAHA 134548 not found on the gene ccaGGGTCAaAGGTTAagg 73.2±1.5 78.2±0.6
38 10 99910506 242 DNMBP 23268 611282 on the gene gatAGGTCAaAGGGCAcag 20.6±2.1 46.0±1.1
39 7 124778 222 C7orf50 84310 not found 37,000 ttgAGGTCCaAGGTCAaag ND 13.7±1.6
40 5 167875891 235 TENM2 57451 610119 on the gene gagGGGTCAaAGGTCAgca 97.0±1.6 102.4±0.7
41 2 78427334 310 BC024248 not found not found on the gene ttcAGGTCAaAGGTCAtaa 69.7±2.2 82.9±1.5
42 21 25387028 73 LINC00158 54072 not found on the gene actGGGTCAaAGGTTAtaa 36.2±3.3 57.8±0.2
43 1 182721614 254 RGS8 85397 607189 50,000 gaaAGGTCAgAGTTCAtat 34.1±2.7 51.0±0.9
44 3 152446636 233 MBLN1 4154 not found on the gene aaaAGGTGAaAGGTCAtag 46.4±3.9 70.1±1.5
45 16 48603767 266 N4BP1 9683 not found on the gene acaGGGTCAaAGGTCTtgt 13.3±2.3 34.3±0.9
46 4 23983034 86 PPARGC1A 10891 604517 on the gene tatAGGTCAaAGGTCAgtt 63.7±0.5 77.0±0.7
47 19 46324352 270 HIF3A 64344 609976 on the gene ctgAGGTCAaAGGTCAgac 101.7±0.3 109.5±1.3
48 8 25623445 259 PPP2R2A 5520 604941 on the gene ggtAGGTCAaAGGTCAtca 86.7±0.1 99.2±1.3
49 8 111380681 146 LOC101927487 101927487 not found 150 gggAGGTCAaAGGTCAtca 98.8±1.0 108.1±0.8
50 1 4175914 273 DFFB 1677 601883 15,000 cggAGGTCAgAGGGCAcca 19.7±4.7 33.4±0.5
51 20 47780453 212 SULF2 55959 610013 on the gene tctAGGTCAcAGTTCAaag 7.9±3.3 20.9±1.4
52 13 97214927 258 MBNL2 10150 607327 on the gene gtcAGGTCAaAGGTTAcag 10.4±1.2 23.0±2.4
53 1 30452183 205 MATN1 4146 115437 5,000 tgtAGGTCAtAGGTGActt 33.1±1.0 58.7±1.8
54 5 95800243 280 RHOBTB3 22836 607353 4,000 tagAGGTCAaAAGTCAcgc 71.9±0.4 90.3±0.7
55 13 97214927 258 MBNL2 10150 607327 on the gene gaaAGGTGAaAGGTCAaag 54.4±1.3 76.2±1.3
56 1 213728971 154 PROX1 5629 601546 250, 000 cagAGGGCAaAGGTCAgca 16.1±1.7 40.6±1.4
57 3 77602871 270 ROBO2 6092 602431 on the gene taaAGGGCAgAGGTCAtag 10.2±0.5 31.0±4.6
58 8 23390872 237 LOXL2 4017 606663 on the gene ggaAGGTGAaAGGTGAaag ND 6.5±1.0
59 7 47098235 178 TNS3 64759 606825 200 atgAGGTGAgAGGTGAggg ND 11.2±0.3
60 3 42462430 366 VIPR1 7433 192321 4,000 ccaAGGTCTaAGTTCAaag ND 16.5±3.3
61 20 63035066 170 LOC63930 63930 not found on the gene gctGGGTCAcGGGTCAgcc ND 12.0±4.2
62 3 123702886 283 MYLK 4638 600922 on the gene ataGGGTCAcAGGTCCcaa 62.2±1.0 84.7±1.8
63 8 57844525 315 FAM110B 90362 611394 125 taaAGGTTAaAGGTTAaag 79.5±1.1 99.6±1.2
64 15 91501090 247 SV2B 9899 185861 20,000 cagGGGTCAaGGGTCAtgg 52.6±1.4 73.3±0.7
65 8 28244632 281 ELP3 55140 612722 50,000 gaaAGGTCAgGGGTCAaag 54.3±1.2 79.7±1.8
66 17 27748155 305 NOS2 4843 163730 5,000 cagAGGTCAaAGGGCAtcc 36.3±3.0 63.1±2.3
67 2 20511193 258 RHOB 388 165370 60,000 cagAGGTGAgAGGTCAgaa ND 25.2±2.1
68 4 69832539 208 SULT1E1 6783 600043 9,000 gttAGTTCAaAGTTCAaag 23.6±2.5 49.8±0.9
69 22 49364796 135 C22orf34 348645 not found 700,000 actCGGTCAaAGGTGAttt 11.2±1.7 25.2±1.2
70 19 44813981 74 BCAM 4059 612773 on the gene ggcGGGTCAaAGGTTAcgg 67.8±0.4 99.3±1.3
71 6 31947504 153 CFB 629 138470 on the gene tacAGGTCAaAGGTCAcct 91.8±1.5 103.5±0.9
72 13 97214927 258 MBNL2 10150 607327 8,000 caaAGGTTAcAGGACAtgc ND 11.3±5.0
73 12 22942875 267 AK094733 not found not found 30,000 ctcAGGTCCaACGTCAgtg ND ND
74 19 50791020 228 ACPT 93650 606362 on the gene ttgGGGTCAaATGTCAgag 15.3±2.0 45.2±2.5
75 12 120978464 41 HNF1A 6927 142410 300 tgaAGTTCAaAGTTCAgtc 29.4±2.0 49.4±1.1
76 9 37568694 341 FBXO10 26267 609092 on the gene ctaAGGTCGgAGTTCAtgt 6.3±1.4 21.2±1.2

 Index
 

 Kazuyuki Yanai

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