RSAT - variation-scan

Scan sequences of polymorphic variants with a list of motifs to predict transcription factor binding sites (TFBS) affected by the variations.

Conceptionc, implementationi and testingt:
Jacques van Heldencit , Alejandra Medina-Riveracit , Walter Santanacit , Jeremy Delerceci


Matrix collections

A set conformed by different motifs representing binding profiles for several transcription factors will be used to scan the variants. Provide your own motifs collection or select one to be used.

Input personal collection of motifs        Format 
Input motifs as text


Upload motifs file


Or Dynamic selection of motifs from the available collections
(select the collection and a dropdown menu will appear to select motifs)

Input1 - Select a database in list:
2 - Select a collection in list:
3 - Select one or more matrix identifiers:

View matrix descriptions & download full collections

Fungi

cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02) - [local copy]
cisBP Saccharomyces_cerevisiae - [1288 motifs] (2019-06_v2.00) - [local copy]
JASPAR core nonredundant fungi - [178 motifs] (2024) - [local copy]

Multi-organisms

footprintDB all - [13838 motifs] (2024-01) - [local copy]

Non-vertebrate Metazoa

Aniseed (Ciona robusta motifs detected by SELEX) - [275 motifs] (2020-08) - [local copy]
Drosophila IDMMPMM - [39 motifs] (2010_11) - [local copy]
Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
cisBP Caenorhabditis_remanei - [3289 motifs] (2019-06_v2.00) - [local copy]
cisBP Solenopsis_invicta - [3658 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_briggsae - [3261 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_melanogaster - [4514 motifs] (2019-06_v2.00) - [local copy]
cisBP Pristionchus_pacificus - [2683 motifs] (2019-06_v2.00) - [local copy]
cisBP Daphnia_pulex - [678 motifs] (2019-06_v2.00) - [local copy]
cisBP c_elegans - [1499 motifs] (2015-05_v1.02) - [local copy]
cisBP Tetranychus_urticae - [3909 motifs] (2019-06_v2.00) - [local copy]
cisBP Tribolium_castaneum - [4101 motifs] (2019-06_v2.00) - [local copy]
cisBP Megaselia_scalaris - [2683 motifs] (2019-06_v2.00) - [local copy]
cisBP Atta_cephalotes - [3404 motifs] (2019-06_v2.00) - [local copy]
cisBP Crassostrea_gigas - [4030 motifs] (2019-06_v2.00) - [local copy]
cisBP Ciona_intestinalis - [3788 motifs] (2019-06_v2.00) - [local copy]
cisBP Dendroctonus_ponderosae - [3846 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_pseudoobscura - [4286 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_sechellia - [4352 motifs] (2019-06_v2.00) - [local copy]
cisBP Schistosoma_mansoni - [3181 motifs] (2019-06_v2.00) - [local copy]
cisBP Strigamia_maritima - [3791 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichoplax_adhaerens - [2901 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_erecta - [4347 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_willistoni - [4319 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_yakuba - [4326 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_japonica - [3107 motifs] (2019-06_v2.00) - [local copy]
cisBP Nasonia_vitripennis - [4064 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_simulans - [4023 motifs] (2019-06_v2.00) - [local copy]
cisBP Zootermopsis_nevadensis - [3945 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_persimilis - [4161 motifs] (2019-06_v2.00) - [local copy]
cisBP Lottia_gigantea - [3989 motifs] (2019-06_v2.00) - [local copy]
cisBP Loa_loa - [3085 motifs] (2019-06_v2.00) - [local copy]
cisBP Octopus_bimaculoides - [3795 motifs] (2019-06_v2.00) - [local copy]
cisBP Apis_mellifera - [4133 motifs] (2019-06_v2.00) - [local copy]
cisBP Culex_quinquefasciatus - [3982 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_ananassae - [4154 motifs] (2019-06_v2.00) - [local copy]
cisBP Melitaea_cinxia - [3363 motifs] (2019-06_v2.00) - [local copy]
cisBP Helobdella_robusta - [3660 motifs] (2019-06_v2.00) - [local copy]
cisBP Ixodes_scapularis - [3701 motifs] (2019-06_v2.00) - [local copy]
cisBP Onchocerca_volvulus - [2988 motifs] (2019-06_v2.00) - [local copy]
cisBP Danaus_plexippus - [3886 motifs] (2019-06_v2.00) - [local copy]
cisBP Strongylocentrotus_purpuratus - [3989 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_grimshawi - [4226 motifs] (2019-06_v2.00) - [local copy]
cisBP Nematostella_vectensis - [3571 motifs] (2019-06_v2.00) - [local copy]
cisBP Pediculus_humanus - [4057 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_virilis - [4276 motifs] (2019-06_v2.00) - [local copy]
cisBP Heliconius_melpomene - [3647 motifs] (2019-06_v2.00) - [local copy]
cisBP Amphimedon_queenslandica - [2325 motifs] (2019-06_v2.00) - [local copy]
cisBP Brugia_malayi - [3105 motifs] (2019-06_v2.00) - [local copy]
cisBP Lucilia_cuprina - [3942 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_gambiae - [4089 motifs] (2019-06_v2.00) - [local copy]
cisBP Aedes_aegypti - [3985 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_elegans - [3438 motifs] (2019-06_v2.00) - [local copy]
cisBP drosophila - [1427 motifs] (2014-10_v0.9) - [local copy]
cisBP Anopheles_darlingi - [3542 motifs] (2019-06_v2.00) - [local copy]
cisBP Bombyx_mori - [3662 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichinella_spiralis - [3131 motifs] (2019-06_v2.00) - [local copy]
cisBP Acyrthosiphon_pisum - [4022 motifs] (2019-06_v2.00) - [local copy]
cisBP Rhodnius_prolixus - [3380 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_mojavensis - [4293 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_brenneri - [3169 motifs] (2019-06_v2.00) - [local copy]
JASPAR core nonredundant urochordates - [94 motifs] (2024) - [local copy]
JASPAR core nonredundant nematodes - [103 motifs] (2024) - [local copy]
JASPAR core nonredundant insects - [286 motifs] (2024) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [8838 motifs] (2024-01) - [local copy]
DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
RSAT non-redundant insects - [350 motifs] (2017) - [local copy]
Database of Drosophila DNA-binding specificities (FlyFactorSurvey) - [652 motifs] (2016_06) - [local copy]

Plants

Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
cisBP Arabidopsis_thaliana - [1653 motifs] (2019-09_v2.00) - [local copy]
cisBP Physcomitrella_patens - [1033 motifs] (2019-06_v2.00) - [local copy]
cisBP Aegilops_tauschii - [1177 motifs] (2019-06_v2.00) - [local copy]
cisBP Selaginella_moellendorffii - [1077 motifs] (2019-06_v2.00) - [local copy]
cisBP Leersia_perrieri - [1300 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glaberrima - [1281 motifs] (2019-06_v2.00) - [local copy]
cisBP Phaseolus_vulgaris - [12 motifs] (2019-06_v2.00) - [local copy]
cisBP Fragaria_vesca - [1363 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_rapa - [1532 motifs] (2019-06_v2.00) - [local copy]
cisBP a_thaliana - [309 motifs] (2015-06_v1.02) - [local copy]
cisBP Brassica_napus - [25 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_aestivum - [1293 motifs] (2019-06_v2.00) - [local copy]
cisBP Populus_trichocarpa - [1428 motifs] (2019-06_v2.00) - [local copy]
cisBP Zea_mays - [1334 motifs] (2019-06_v2.00) - [local copy]
cisBP Hordeum_vulgare - [1279 motifs] (2019-06_v2.00) - [local copy]
cisBP Gossypium_raimondii - [1448 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_nivara - [1297 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_brachyantha - [1264 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_barthii - [1296 motifs] (2019-06_v2.00) - [local copy]
cisBP Arabidopsis_lyrata - [1556 motifs] (2019-06_v2.00) - [local copy]
cisBP Ostreococcus_lucimarinus - [418 motifs] (2019-06_v2.00) - [local copy]
cisBP Helianthus_annuus - [4 motifs] (2019-06_v2.00) - [local copy]
cisBP Vitis_vinifera - [1418 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_urartu - [1124 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlamydomonas_reinhardtii - [340 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_persica - [1406 motifs] (2019-06_v2.00) - [local copy]
cisBP Amborella_trichopoda - [1291 motifs] (2019-06_v2.00) - [local copy]
cisBP Cucumis_sativus - [1398 motifs] (2019-06_v2.00) - [local copy]
cisBP Setaria_italica - [1305 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_oleracea - [1539 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_sativa - [1321 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_meridionalis - [1289 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glumaepatula - [1311 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_rufipogon - [1302 motifs] (2019-06_v2.00) - [local copy]
cisBP Brachypodium_distachyon - [1295 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_lycopersicum - [1399 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_tuberosum - [1361 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_punctata - [1341 motifs] (2019-06_v2.00) - [local copy]
cisBP Glycine_max - [1491 motifs] (2019-06_v2.00) - [local copy]
cisBP Sorghum_bicolor - [1306 motifs] (2019-06_v2.00) - [local copy]
cisBP Medicago_truncatula - [1422 motifs] (2019-06_v2.00) - [local copy]
cisBP Manihot_esculenta - [1425 motifs] (2019-06_v2.00) - [local copy]
cisBP Musa_acuminata - [1391 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_mume - [1386 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_longistaminata - [1151 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_indica - [1310 motifs] (2019-06_v2.00) - [local copy]
JASPAR core nonredundant plants - [805 motifs] (2024) - [local copy]
footprintDB-plants [only plant DNA motifs] - [2940 motifs] (2024-01) - [local copy]

Prokaryotes

RegulonDB prokaryotes - [0 motifs] (2015_08) - [local copy]
DBTBS (Bacillus Subtilis) - [88 motifs] (2015-11) - [local copy]

RNA binding

CISBP-RNA - [11897 motifs] (2017) - [local copy]
ATtRACT - [1322 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [local copy]

Vertebrates

Homer (Human TF motifs) - [332 motifs] (2016-07) - [local copy]
ENCODE (Human TFs) - [2065 motifs] (2018-03) - [local copy]
FactorBook SELEX human motifs - [0 motifs] (2022-04) - [local copy]
FactorBook ChIP-seq human motifs - [0 motifs] (2022-04) - [local copy]
hPDI (Human TFs identified by protein microarray assays) - [0 motifs] (2016-06) - [local copy]
Jolma_2013 (Human TFs) - [818 motifs] (2015-11) - [local copy]
cisBP Echinops_telfairi - [4813 motifs] (2019-06_v2.00) - [local copy]
cisBP Ailuropoda_melanoleuca - [5863 motifs] (2019-06_v2.00) - [local copy]
cisBP Danio_rerio - [5320 motifs] (2019-06_v2.00) - [local copy]
cisBP Oreochromis_niloticus - [5296 motifs] (2019-06_v2.00) - [local copy]
cisBP Xenopus_tropicalis - [5393 motifs] (2019-06_v2.00) - [local copy]
cisBP Cavia_porcellus - [5683 motifs] (2019-06_v2.00) - [local copy]
cisBP Erinaceus_europaeus - [4783 motifs] (2019-06_v2.00) - [local copy]
cisBP Dipodomys_ordii - [4810 motifs] (2019-06_v2.00) - [local copy]
cisBP Anas_platyrhynchos - [5038 motifs] (2019-06_v2.00) - [local copy]
cisBP Homo_sapiens - [6607 motifs] (2019-06_v2.00) - [local copy]
cisBP Choloepus_hoffmanni - [4069 motifs] (2019-06_v2.00) - [local copy]
cisBP mouse - [1715 motifs] (2014-10_v0.9) - [local copy]
cisBP Callithrix_jacchus - [6089 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlorocebus_sabaeus - [6176 motifs] (2019-06_v2.00) - [local copy]
cisBP Gallus_gallus - [5272 motifs] (2019-06_v2.00) - [local copy]
cisBP human - [1832 motifs] (2014-10_v0.9) - [local copy]
cisBP Rattus_norvegicus - [5946 motifs] (2019-06_v2.00) - [local copy]
cisBP Astyanax_mexicanus - [5191 motifs] (2019-06_v2.00) - [local copy]
cisBP Mus_musculus - [6014 motifs] (2019-06_v2.00) - [local copy]
cisBP Dasypus_novemcinctus - [5871 motifs] (2019-06_v2.00) - [local copy]
cisBP Bos_taurus - [5895 motifs] (2019-06_v2.00) - [local copy]
cisBP Equus_caballus - [5765 motifs] (2019-06_v2.00) - [local copy]
Hocomoco (Human and mouse TFs) - [1443 motifs] (2023-09) - [local copy]
JASPAR core nonredundant vertebrates - [879 motifs] (2024) - [local copy]
RSAT non-redundant vertebrates - [2233 motifs] (2017) - [local copy]
Epigram (Human Histone marks related motifs) - [589 motifs] (2016-06) - [local copy]

Select one motif collection

Input1 - Select a database in list:
2 - Select a collection in list:

Background

Background model estimation method

Scanning Parameters Length of sequence around the variant 
Thresholds
Field Lower
Threshold
Upper
Threshold
Weight of predicted sites
Weight difference between variants
P-value of predicted sites
P-value ratio between variants

Output  



AMR and WS are supported by a PAPIIT-UNAM (IA206517) grant.