| Motif | RARA.H13RSNP.2.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO |  |
| LOGO (reverse complement) |  |
| Motif subtype | 2 |
| Quality | B |
| Motif | RARA.H13RSNP.2.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO | |
| LOGO (reverse complement) | |
| Motif subtype | 2 |
| Quality | B |
| Motif length | 16 |
| Consensus | vAGGTCAbnnhRhhYh |
| GC content | 54.57% |
| Information content (bits; total / per base) | 10.659 / 0.666 |
| Data sources | ChIP-Seq |
| Aligned words | 1001 |
| Previous names | RARA.H12RSNP.2.P.B |
| ChIP-Seq benchmarking | Num. of experiments (peaksets) | auROC, median | auROC, best | auPRC, median | auPRC, best | pseudo-auROC, median | pseudo-auROC, best | pseudo-log-auROC, median | pseudo-log-auROC, best | Centrality, median | Centrality, best |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Human | 5 (29) | 0.714 | 0.814 | 0.525 | 0.779 | 0.667 | 0.771 | 1.604 | 3.383 | 47.959 | 135.699 |
| Mouse | 10 (46) | 0.71 | 0.806 | 0.562 | 0.668 | 0.684 | 0.765 | 1.817 | 2.235 | 43.549 | 175.886 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.761 | 0.732 | 0.737 | 0.711 | 0.704 | 0.682 |
| best | 0.952 | 0.919 | 0.934 | 0.897 | 0.886 | 0.849 | |
| Methyl HT-SELEX, 1 experiments | median | 0.95 | 0.917 | 0.929 | 0.891 | 0.881 | 0.843 |
| best | 0.95 | 0.917 | 0.929 | 0.891 | 0.881 | 0.843 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.572 | 0.547 | 0.544 | 0.531 | 0.527 | 0.521 |
| best | 0.952 | 0.919 | 0.934 | 0.897 | 0.886 | 0.849 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 1.56 | 1.639 | 0.152 | 0.053 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.559 | 0.077 | 0.417 | 0.207 |
| TF superclass | Zinc-coordinating DNA-binding domains {2} (TFClass) |
| TF class | Nuclear receptors with C4 zinc fingers {2.1} (TFClass) |
| TF family | Thyroid hormone receptor-related {2.1.2} (TFClass) |
| TF subfamily | RAR (NR1B) {2.1.2.1} (TFClass) |
| TFClass ID | TFClass: 2.1.2.1.1 |
| HGNC | HGNC:9864 |
| MGI | MGI:97856 |
| EntrezGene (human) | GeneID:5914 (SSTAR profile) |
| EntrezGene (mouse) | GeneID:19401 (SSTAR profile) |
| UniProt ID (human) | RARA_HUMAN |
| UniProt ID (mouse) | RARA_MOUSE |
| UniProt AC (human) | P10276 (TFClass) |
| UniProt AC (mouse) | P11416 (TFClass) |
| GRECO-DB-TF | yes |
| ChIP-Seq | 5 human, 10 mouse |
| HT-SELEX | 3 |
| Methyl-HT-SELEX | 1 |
| Genomic HT-SELEX | 0 overall: 0 Lysate, 0 IVT, 0 GFPIVT |
| SMiLE-Seq | 0 |
| PBM | 0 |
| PCM | RARA.H13RSNP.2.P.B.pcm |
| PWM | RARA.H13RSNP.2.P.B.pwm |
| PFM | RARA.H13RSNP.2.P.B.pfm |
| Threshold to P-value map | RARA.H13RSNP.2.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H13RSNP.2.P.B_jaspar_format.txt |
| MEME format | RARA.H13RSNP.2.P.B_meme_format.meme |
| Transfac format | RARA.H13RSNP.2.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 346.0 | 367.0 | 194.0 | 94.0 |
| 02 | 803.0 | 7.0 | 181.0 | 10.0 |
| 03 | 68.0 | 2.0 | 802.0 | 129.0 |
| 04 | 20.0 | 18.0 | 934.0 | 29.0 |
| 05 | 22.25 | 51.25 | 130.25 | 797.25 |
| 06 | 26.25 | 932.25 | 28.25 | 14.25 |
| 07 | 968.25 | 9.25 | 13.25 | 10.25 |
| 08 | 153.25 | 336.25 | 341.25 | 170.25 |
| 09 | 281.25 | 318.25 | 266.25 | 135.25 |
| 10 | 218.25 | 284.25 | 353.25 | 145.25 |
| 11 | 213.25 | 127.25 | 93.25 | 567.25 |
| 12 | 178.25 | 130.25 | 623.25 | 69.25 |
| 13 | 486.25 | 227.25 | 120.25 | 167.25 |
| 14 | 157.25 | 590.25 | 83.25 | 170.25 |
| 15 | 130.25 | 654.25 | 64.25 | 152.25 |
| 16 | 142.25 | 339.25 | 118.25 | 401.25 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.346 | 0.367 | 0.194 | 0.094 |
| 02 | 0.802 | 0.007 | 0.181 | 0.01 |
| 03 | 0.068 | 0.002 | 0.801 | 0.129 |
| 04 | 0.02 | 0.018 | 0.933 | 0.029 |
| 05 | 0.022 | 0.051 | 0.13 | 0.796 |
| 06 | 0.026 | 0.931 | 0.028 | 0.014 |
| 07 | 0.967 | 0.009 | 0.013 | 0.01 |
| 08 | 0.153 | 0.336 | 0.341 | 0.17 |
| 09 | 0.281 | 0.318 | 0.266 | 0.135 |
| 10 | 0.218 | 0.284 | 0.353 | 0.145 |
| 11 | 0.213 | 0.127 | 0.093 | 0.567 |
| 12 | 0.178 | 0.13 | 0.623 | 0.069 |
| 13 | 0.486 | 0.227 | 0.12 | 0.167 |
| 14 | 0.157 | 0.59 | 0.083 | 0.17 |
| 15 | 0.13 | 0.654 | 0.064 | 0.152 |
| 16 | 0.142 | 0.339 | 0.118 | 0.401 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.322 | 0.381 | -0.253 | -0.968 |
| 02 | 1.161 | -3.363 | -0.321 | -3.067 |
| 03 | -1.285 | -4.214 | 1.16 | -0.656 |
| 04 | -2.451 | -2.547 | 1.312 | -2.104 |
| 05 | -2.352 | -1.559 | -0.647 | 1.154 |
| 06 | -2.198 | 1.31 | -2.129 | -2.758 |
| 07 | 1.348 | -3.134 | -2.823 | -3.046 |
| 08 | -0.486 | 0.294 | 0.308 | -0.382 |
| 09 | 0.116 | 0.239 | 0.062 | -0.61 |
| 10 | -0.136 | 0.127 | 0.343 | -0.539 |
| 11 | -0.159 | -0.67 | -0.976 | 0.815 |
| 12 | -0.337 | -0.647 | 0.908 | -1.267 |
| 13 | 0.661 | -0.096 | -0.726 | -0.4 |
| 14 | -0.461 | 0.854 | -1.087 | -0.382 |
| 15 | -0.647 | 0.957 | -1.34 | -0.493 |
| 16 | -0.56 | 0.302 | -0.742 | 0.47 |
| P-value | Threshold |
|---|---|
| 0.001 | 4.57906 |
| 0.0005 | 5.45011 |
| 0.0001 | 7.23271 |