Motif | VSX1.H13RSNP.0.SM.B |
Gene (human) | VSX1 (GeneCards) |
Gene synonyms (human) | RINX |
Gene (mouse) | Vsx1 |
Gene synonyms (mouse) | Rinx |
LOGO | ![]() |
LOGO (reverse complement) | ![]() |
Motif subtype | 0 |
Quality | B |
Motif | VSX1.H13RSNP.0.SM.B |
Gene (human) | VSX1 (GeneCards) |
Gene synonyms (human) | RINX |
Gene (mouse) | Vsx1 |
Gene synonyms (mouse) | Rinx |
LOGO | ![]() |
LOGO (reverse complement) | ![]() |
Motif subtype | 0 |
Quality | B |
Motif length | 11 |
Consensus | nbYAATTARSn |
GC content | 35.17% |
Information content (bits; total / per base) | 11.269 / 1.024 |
Data sources | HT-SELEX + Methyl-HT-SELEX |
Aligned words | 8514 |
Previous names | VSX1.H12RSNP.0.SM.B |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 10 experiments | median | 0.995 | 0.992 | 0.987 | 0.981 | 0.967 | 0.953 |
best | 0.998 | 0.996 | 0.995 | 0.992 | 0.984 | 0.979 | |
Methyl HT-SELEX, 2 experiments | median | 0.986 | 0.976 | 0.978 | 0.965 | 0.962 | 0.945 |
best | 0.998 | 0.996 | 0.995 | 0.992 | 0.984 | 0.979 | |
Non-Methyl HT-SELEX, 8 experiments | median | 0.995 | 0.992 | 0.987 | 0.981 | 0.967 | 0.953 |
best | 0.997 | 0.995 | 0.993 | 0.99 | 0.979 | 0.972 |
rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
---|---|---|---|---|
batch 1 | 0.947 | 0.214 | 0.903 | 0.483 |
batch 2 | 0.867 | 0.705 | 0.807 | 0.609 |
TF superclass | Helix-turn-helix domains {3} (TFClass) |
TF class | Homeo domain factors {3.1} (TFClass) |
TF family | Paired-related HD {3.1.3} (TFClass) |
TF subfamily | VSX {3.1.3.28} (TFClass) |
TFClass ID | TFClass: 3.1.3.28.1 |
HGNC | HGNC:12723 |
MGI | MGI:1890816 |
EntrezGene (human) | GeneID:30813 (SSTAR profile) |
EntrezGene (mouse) | GeneID:114889 (SSTAR profile) |
UniProt ID (human) | VSX1_HUMAN |
UniProt ID (mouse) | VSX1_MOUSE |
UniProt AC (human) | Q9NZR4 (TFClass) |
UniProt AC (mouse) | Q91V10 (TFClass) |
GRECO-DB-TF | yes |
ChIP-Seq | 0 human, 0 mouse |
HT-SELEX | 8 |
Methyl-HT-SELEX | 2 |
Genomic HT-SELEX | 0 overall: 0 Lysate, 0 IVT, 0 GFPIVT |
SMiLE-Seq | 0 |
PBM | 0 |
PCM | VSX1.H13RSNP.0.SM.B.pcm |
PWM | VSX1.H13RSNP.0.SM.B.pwm |
PFM | VSX1.H13RSNP.0.SM.B.pfm |
Threshold to P-value map | VSX1.H13RSNP.0.SM.B.thr |
Motif in other formats | |
JASPAR format | VSX1.H13RSNP.0.SM.B_jaspar_format.txt |
MEME format | VSX1.H13RSNP.0.SM.B_meme_format.meme |
Transfac format | VSX1.H13RSNP.0.SM.B_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 1953.0 | 2584.0 | 2422.0 | 1555.0 |
02 | 1142.0 | 3459.0 | 2632.0 | 1281.0 |
03 | 216.0 | 3146.0 | 189.0 | 4963.0 |
04 | 7477.0 | 558.0 | 465.0 | 14.0 |
05 | 8514.0 | 0.0 | 0.0 | 0.0 |
06 | 0.0 | 0.0 | 0.0 | 8514.0 |
07 | 0.0 | 0.0 | 0.0 | 8514.0 |
08 | 8514.0 | 0.0 | 0.0 | 0.0 |
09 | 2386.0 | 965.0 | 4889.0 | 274.0 |
10 | 259.75 | 4760.75 | 1876.75 | 1616.75 |
11 | 1433.75 | 1997.75 | 2994.75 | 2087.75 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.229 | 0.304 | 0.284 | 0.183 |
02 | 0.134 | 0.406 | 0.309 | 0.15 |
03 | 0.025 | 0.37 | 0.022 | 0.583 |
04 | 0.878 | 0.066 | 0.055 | 0.002 |
05 | 1.0 | 0.0 | 0.0 | 0.0 |
06 | 0.0 | 0.0 | 0.0 | 1.0 |
07 | 0.0 | 0.0 | 0.0 | 1.0 |
08 | 1.0 | 0.0 | 0.0 | 0.0 |
09 | 0.28 | 0.113 | 0.574 | 0.032 |
10 | 0.031 | 0.559 | 0.22 | 0.19 |
11 | 0.168 | 0.235 | 0.352 | 0.245 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.086 | 0.194 | 0.129 | -0.314 |
02 | -0.622 | 0.485 | 0.212 | -0.507 |
03 | -2.279 | 0.39 | -2.411 | 0.846 |
04 | 1.256 | -1.336 | -1.517 | -4.875 |
05 | 1.385 | -6.848 | -6.848 | -6.848 |
06 | -6.848 | -6.848 | -6.848 | 1.385 |
07 | -6.848 | -6.848 | -6.848 | 1.385 |
08 | 1.385 | -6.848 | -6.848 | -6.848 |
09 | 0.114 | -0.79 | 0.831 | -2.043 |
10 | -2.096 | 0.804 | -0.126 | -0.275 |
11 | -0.395 | -0.063 | 0.341 | -0.019 |
P-value | Threshold |
---|---|
0.001 | 4.21213 |
0.0005 | 5.55672 |
0.0001 | 7.815795 |