miRNEST 2.0, an integrative microRNA resource

miRNEST 2.0, an integrative microRNA resource :: Browse

Species belonging to selected taxon:

Persea americana, Actinidia chinensis, Actinidia deliciosa, Actinidia eriantha, Adiantum capillus-veneris, Agrostis stolonifera, Allium cepa, Amborella trichopoda, Antirrhinum majus, Aquilegia formosa x Aquilegia pubescens, Arachis duranensis, Oryza sativa, Arachis hypogaea, Arachis ipaensis, Aristolochia fimbriata, Avena barbata, Avena sativa, Barnadesia spinosa, Beta vulgaris, Botryococcus braunii, Brassica napus, Brassica oleracea var. alboglabra, Brassica rapa, Cichorium intybus, Citrus aurantium, Citrus reticulata, Citrus sinensis, Citrus unshiu, Coccomyxa sp. C-169, Coffea canephora, Cryptomeria japonica, Cucumis melo subsp. melo, Curcuma longa, Cycas rumphii, Cynodon dactylon, Dioscorea alata, Elaeis guineensis, Eragrostis curvula, Eschscholzia californica, Eucalyptus globulus, Eucalyptus gunnii, Euonymus alatus, Euphorbia esula, Fagus sylvatica, Festuca arundinacea, Festuca pratensis, Fragaria vesca, Fragaria x ananassa, Fraxinus excelsior, Gerbera hybrid cultivar, Glycine soja, Glycyrrhiza uralensis, Gnetum gnemon, Gossypium arboreum, Gossypium hirsutum, Gossypium raimondii, Guizotia abyssinica, Helianthus argophyllus, Helianthus ciliaris, Helianthus exilis, Helianthus paradoxus, Helianthus petiolaris, Helianthus tuberosus, Hevea brasiliensis, Hordeum vulgare, Hordeum vulgare subsp. spontaneum, Humulus lupulus, Ipomoea batatas, Jatropha curcas, Juglans hindsii x Juglans regia, Lactuca perennis, Lactuca saligna, Lactuca sativa, Lactuca serriola, Lactuca virosa, Leymus cinereus x Leymus triticoides, Limnanthes alba, Linum usitatissimum, Liriodendron tulipifera, Lolium perenne, Lotus japonicus, Manihot esculenta, Medicago sativa, Mesembryanthemum crystallinum, Mesostigma viride, Mimulus guttatus, Mimulus guttatus var. nasutus, Mimulus lewisii, Musa ABB Group, Nicotiana benthamiana, Nicotiana langsdorffii x Nicotiana sanderae, Nicotiana tabacum, Nuphar advena, Ocimum basilicum, Panax ginseng, Panicum virgatum, Papaver somniferum, Parthenium argentatum, Paullinia cupana var. sorbilis, Petunia axillaris subsp. axillaris, Phaseolus acutifolius, Phaseolus coccineus, Picea abies, Bicyclus anynana, Picea engelmannii x Picea glauca, Picea glauca, Picea sitchensis, Pinus banksiana, Pinus contorta, Pinus pinaster, Pinus taeda, Pisum sativum, Populus deltoides, Populus euphratica, Populus nigra, Populus tremula, Populus tremula x Populus alba, Populus tremula x Populus tremuloides, Populus tremuloides, Populus trichocarpa x Populus nigra, Populus x canadensis, Prunus armeniaca, Prunus persica, Pseudoroegneria spicata, Pseudotsuga menziesii var. menziesii, Quercus petraea, Quercus robur, Raphanus raphanistrum, Raphanus raphanistrum subsp. landra, Raphanus raphanistrum subsp. maritimus, Raphanus sativus, Raphanus sativus var. oleiformis, Saccharum hybrid cultivar CoS 767, Saccharum hybrid cultivar SP70-1143, Saccharum officinarum, Salvia miltiorrhiza, Saruma henryi, Solanum habrochaites, Solanum lycopersicum, Solanum melongena, Solanum pennellii, Solanum torvum, Sorghum propinquum, Striga hermonthica, Tamarix hispida, Taraxacum kok-saghyz, Taraxacum officinale, Thellungiella halophila, Theobroma cacao, Trifolium pratense, Triphysaria pusilla, Triphysaria versicolor, Triticum monococcum, Triticum turgidum subsp. durum, Tropaeolum majus, Vitis shuttleworthii, Volvox carteri, Welwitschia mirabilis, Zamia vazquezii, Zingiber officinale, Zinnia violacea, Bruguiera gymnorhiza, Cajanus cajan, Carica papaya, Capsicum annuum, Carthamus tinctorius, Catharanthus roseus, Cenchrus ciliaris, Centaurea maculosa, Centaurea solstitialis, Cicer arietinum, Cichorium endivia, Artemisia annua, Brachypodium distachyon, Citrus clementina, Helianthus annuus, Glycine max, Arabidopsis thaliana, Acropora millepora, Zea mays, Mus musculus, Sus scrofa, Bos taurus, Danio rerio, Ciona intestinalis, Rattus norvegicus, Triticum aestivum, Drosophila melanogaster, Xenopus laevis, Oryzias latipes, Gallus gallus, Salmo salar, Caenorhabditis elegans, Canis lupus familiaris, Physcomitrella patens, Ictalurus punctatus, Ovis aries, Branchiostoma floridae, Bombyx mori, Aedes aegypti, Oncorhynchus mykiss, Gasterosteus aculeatus, Pimephales promelas, Aplysia californica, Lottia gigantea, Solanum tuberosum, Gadus morhua, Alvinella pompejana, Schistosoma mansoni, Ixodes scapularis, Vigna unguiculata, Hydra vulgaris, Macaca fascicularis, Litopenaeus vannamei, Anolis carolinensis, Trichosurus vulpecula, Papio anubis, Paracentrotus lividus, Ictalurus furcatus, Lepeophtheirus salmonis, Homo sapiens, Vitis vinifera, Medicago truncatula, Acyrthosiphon pisum, Sorghum bicolor, Culex quinquefasciatus, Chlamydomonas reinhardtii, Saccoglossus kowalevskii, Nematostella vectensis, Anopheles gambiae, Dendroctonus ponderosae, Daphnia pulex, Nasonia vitripennis, Strongylocentrotus purpuratus, Brassica oleracea, Petromyzon marinus, Drosophila simulans, Oreochromis niloticus, Molgula tectiformis, Schistosoma japonicum, Helobdella robusta, Petrolisthes cinctipes, Taeniopygia guttata, Populus trichocarpa, Aphis gossypii, Clytia hemisphaerica, Ciona savignyi, Phaseolus vulgaris, Ricinus communis, Ipomoea nil, Ancylostoma caninum, Tetranychus urticae, Glossina morsitans morsitans, Peromyscus maniculatus bairdii, Fundulus heteroclitus, Choristoneura fumiferana, Sparus aurata, Spodoptera frugiperda, Amphimedon queenslandica, Halocynthia roretzi, Heliothis virescens, Crassostrea gigas, Patiria pectinifera, Ascaris suum, Dicentrarchus labrax, Biomphalaria glabrata, Heterorhabditis bacteriophora, Rhipicephalus microplus, Brachionus plicatilis, Pongo abelii, Locusta migratoria, Acropora palmata, Phlebotomus papatasi, Mytilus californianus, Anemonia viridis, Penaeus monodon, Ursus americanus, Drosophila sechellia, Drosophila auraria, Artemia franciscana, Pristionchus pacificus, Nilaparvata lugens, Equus caballus, Dissostichus mawsoni, Osmerus mordax, Euprymna scolopes, Pleurobrachia pileus, Antheraea assama, Drosophila pseudoobscura, Oryctolagus cuniculus, Macaca nemestrina, Anoplopoma fimbria, Cyprinus carpio, Teleopsis dalmanni, Montastraea faveolata, Lutzomyia longipalpis, Caenorhabditis japonica, Esox lucius, Squalus acanthias, Caligus rogercresseyi, Leucoraja erinacea, Taenia solium, Nasonia giraulti, Homarus americanus, Caenorhabditis brenneri, Bombus terrestris, Metridium senile, Rana catesbeiana, Myzus persicae, Strongyloides ratti, Drosophila willistoni, Brugia malayi, Takifugu rubripes, Cynops pyrrhogaster, Trichinella spiralis, Meloidogyne hapla, Heterodera glycines, Eptatretus burgeri, Sebastes caurinus, Drosophila ananassae, Solenopsis invicta, Drosophila virilis, Drosophila erecta, Misgurnus anguillicaudatus, Perca flavescens, Paralabidochromis chilotes, Drosophila grimshawi, Ceratitis capitata, Hippoglossus hippoglossus, Spodoptera littoralis, Peregrinus maidis, Ambystoma tigrinum tigrinum, Meloidogyne incognita, Caenorhabditis remanei, Samia cynthia ricini, Lumbricus rubellus, Cavia porcellus, Drosophila mojavensis, Danaus plexippus, Bos indicus, Rhipicephalus appendiculatus, Cochliomyia hominivorax, Rutilus rutilus, Anopheles stephensi, Diabrotica virgifera virgifera, Meleagris gallopavo, Trichinella pseudospiralis, Tubifex tubifex, Haematobia irritans irritans, Eriocheir sinensis, Papilio xuthus, Onychiurus arcticus, Lonchura striata domestica, Poecilia reticulata, Mnemiopsis leidyi, Rhodnius prolixus, Carcinus maenas, Bos sp., Polypedilum vanderplanki, Onchocerca volvulus, Ostrinia nubilalis, Lernaeocera branchialis, Macropus eugenii, Caligus clemensi, Peromyscus polionotus subgriseus, Nippostrongylus brasiliensis, Laupala kohalensis, Oncorhynchus tshawytscha, Frankliniella occidentalis, Capra hircus, Daphnia magna, Suberites domuncula, Paralichthys olivaceus, Psetta maxima, Gammarus pulex, Trichoplusia ni, Meloidogyne chitwoodi, Pan troglodytes verus, Spadella cephaloptera, Globodera rostochiensis, Lymnaea stagnalis, Lates calcarifer, Porites astreoides, Calanus finmarchicus, Strongyloides stercoralis, Oncorhynchus nerka, Gryllus bimaculatus, Sebastes rastrelliger, Oscarella carmela, Drosophila yakuba, Thymallus thymallus, Ancylostoma ceylanicum, Solea senegalensis, Epiphyas postvittana, Callinectes sapidus, Peripatopsis sedgwicki, Fenneropenaeus chinensis, Coregonus clupeaformis, Aiptasia pallida, Torpedo californica, Thunnus thynnus, Cynoglossus semilaevis, Salvelinus fontinalis, Schmidtea mediterranea, Apis mellifera, Tribolium castaneum, Macaca mulatta, Populus trichocarpa x Populus deltoides

ABOUT THIS RECORD

ID: MNEST051746
species: Populus trichocarpa
miRNA family: MIR398
source: PMRD, original name: ptc-miR398c

Taxonomy by NCBI:
Populus trichocarpa Populus Saliceae Salicaceae Malpighiales fabids rosids core eudicotyledons eudicotyledons Magnoliophyta Spermatophyta Euphyllophyta Tracheophyta Embryophyta Streptophytina Streptophyta Viridiplantae Eukaryota cellular organisms

SEQUENCE & STRUCTURE

miRNA
TGTGTTCTCAGGTCGCCCCTG

miRNA*
GGAGCGACCTGAAATCACATG

mismatches: 4
bulges: 0

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pre-miRNA
AGGATTCCTACAGGAGCGACCTGAAATCACATGTGGGCTGCACCCTCCTGGGTTATCTTGAGCAACATGTGTTCTCAGGTCGCCCCTGCCGGGCTTT

dot-bracket secondary structure
.....(((..((((.(((((((((...(((((((..(((.(((((....))))......)))).)))))))...))))))))).))))..)))....

UniProt no hits

RFAM MIR398: 1e-16

Identical with: ptc-MIR398c from miRBase (MNEST041447)

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miRNEST target predictions
non-miRNEST targets
HuntMi prediction: true miRNA
additional data
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references
[1] Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapm, Science. 313:1596-1604(2006)., "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)"