| Motif | RARA.H12RSNP.1.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO |  |
| LOGO (reverse complement) |  |
| Motif subtype | 1 |
| Quality | B |
| Motif | RARA.H12RSNP.1.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO | |
| LOGO (reverse complement) | |
| Motif subtype | 1 |
| Quality | B |
| Motif length | 19 |
| Consensus | vRRGKTSAnnbdvRRKdSW |
| GC content | 53.46% |
| Information content (bits; total / per base) | 10.468 / 0.551 |
| Data sources | ChIP-Seq |
| Aligned words | 974 |
| 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) | 0.737 | 0.83 | 0.605 | 0.773 | 0.732 | 0.82 | 2.343 | 3.631 | 38.357 | 112.921 |
| Mouse | 10 (46) | 0.765 | 0.83 | 0.67 | 0.777 | 0.738 | 0.81 | 2.743 | 3.637 | 73.479 | 164.108 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.768 | 0.755 | 0.729 | 0.714 | 0.679 | 0.667 |
| best | 0.975 | 0.964 | 0.938 | 0.917 | 0.868 | 0.844 | |
| Methyl HT-SELEX, 1 experiments | median | 0.975 | 0.964 | 0.938 | 0.917 | 0.868 | 0.844 |
| best | 0.975 | 0.964 | 0.938 | 0.917 | 0.868 | 0.844 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.57 | 0.557 | 0.54 | 0.534 | 0.524 | 0.522 |
| best | 0.966 | 0.952 | 0.918 | 0.893 | 0.834 | 0.812 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 2.128 | 3.997 | 0.162 | 0.094 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.549 | 0.061 | 0.511 | 0.297 |
| 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 |
| PCM | RARA.H12RSNP.1.P.B.pcm |
| PWM | RARA.H12RSNP.1.P.B.pwm |
| PFM | RARA.H12RSNP.1.P.B.pfm |
| Alignment | RARA.H12RSNP.1.P.B.words.tsv |
| Threshold to P-value map | RARA.H12RSNP.1.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H12RSNP.1.P.B_jaspar_format.txt |
| MEME format | RARA.H12RSNP.1.P.B_meme_format.meme |
| Transfac format | RARA.H12RSNP.1.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 412.0 | 205.0 | 193.0 | 164.0 |
| 02 | 374.0 | 99.0 | 460.0 | 41.0 |
| 03 | 531.0 | 11.0 | 421.0 | 11.0 |
| 04 | 74.0 | 5.0 | 843.0 | 52.0 |
| 05 | 38.0 | 39.0 | 727.0 | 170.0 |
| 06 | 42.0 | 37.0 | 93.0 | 802.0 |
| 07 | 21.0 | 769.0 | 128.0 | 56.0 |
| 08 | 843.0 | 64.0 | 39.0 | 28.0 |
| 09 | 245.0 | 244.0 | 308.0 | 177.0 |
| 10 | 359.0 | 217.0 | 225.0 | 173.0 |
| 11 | 134.0 | 269.0 | 388.0 | 183.0 |
| 12 | 352.0 | 123.0 | 275.0 | 224.0 |
| 13 | 281.0 | 140.0 | 434.0 | 119.0 |
| 14 | 525.0 | 60.0 | 292.0 | 97.0 |
| 15 | 139.0 | 31.0 | 747.0 | 57.0 |
| 16 | 87.0 | 35.0 | 630.0 | 222.0 |
| 17 | 157.0 | 111.0 | 281.0 | 425.0 |
| 18 | 117.0 | 620.0 | 126.0 | 111.0 |
| 19 | 650.0 | 101.0 | 104.0 | 119.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.423 | 0.21 | 0.198 | 0.168 |
| 02 | 0.384 | 0.102 | 0.472 | 0.042 |
| 03 | 0.545 | 0.011 | 0.432 | 0.011 |
| 04 | 0.076 | 0.005 | 0.866 | 0.053 |
| 05 | 0.039 | 0.04 | 0.746 | 0.175 |
| 06 | 0.043 | 0.038 | 0.095 | 0.823 |
| 07 | 0.022 | 0.79 | 0.131 | 0.057 |
| 08 | 0.866 | 0.066 | 0.04 | 0.029 |
| 09 | 0.252 | 0.251 | 0.316 | 0.182 |
| 10 | 0.369 | 0.223 | 0.231 | 0.178 |
| 11 | 0.138 | 0.276 | 0.398 | 0.188 |
| 12 | 0.361 | 0.126 | 0.282 | 0.23 |
| 13 | 0.289 | 0.144 | 0.446 | 0.122 |
| 14 | 0.539 | 0.062 | 0.3 | 0.1 |
| 15 | 0.143 | 0.032 | 0.767 | 0.059 |
| 16 | 0.089 | 0.036 | 0.647 | 0.228 |
| 17 | 0.161 | 0.114 | 0.289 | 0.436 |
| 18 | 0.12 | 0.637 | 0.129 | 0.114 |
| 19 | 0.667 | 0.104 | 0.107 | 0.122 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.523 | -0.171 | -0.231 | -0.392 |
| 02 | 0.427 | -0.89 | 0.633 | -1.747 |
| 03 | 0.776 | -2.959 | 0.545 | -2.959 |
| 04 | -1.175 | -3.597 | 1.237 | -1.518 |
| 05 | -1.82 | -1.795 | 1.089 | -0.356 |
| 06 | -1.724 | -1.846 | -0.951 | 1.187 |
| 07 | -2.379 | 1.145 | -0.637 | -1.447 |
| 08 | 1.237 | -1.317 | -1.795 | -2.11 |
| 09 | 0.006 | 0.002 | 0.234 | -0.316 |
| 10 | 0.386 | -0.114 | -0.078 | -0.339 |
| 11 | -0.592 | 0.099 | 0.463 | -0.283 |
| 12 | 0.366 | -0.676 | 0.121 | -0.083 |
| 13 | 0.142 | -0.548 | 0.575 | -0.709 |
| 14 | 0.765 | -1.38 | 0.18 | -0.91 |
| 15 | -0.555 | -2.014 | 1.116 | -1.429 |
| 16 | -1.017 | -1.899 | 0.946 | -0.092 |
| 17 | -0.435 | -0.777 | 0.142 | 0.554 |
| 18 | -0.725 | 0.93 | -0.652 | -0.777 |
| 19 | 0.977 | -0.87 | -0.841 | -0.709 |
| P-value | Threshold |
|---|---|
| 0.001 | 4.59561 |
| 0.0005 | 5.40981 |
| 0.0001 | 7.11701 |