Introduction

Exons display significant length variability, with those measuring less than 51 nucleotides (nt) categorized as microexons. This database specifically targets ultra-short microexons, characterized as those ranging from 1 to 15 nt.

Using large-scale RNA-seq datasets consisting of 990 samples from diverse tissues, developmental stages, and environmental conditions, we conducted a genome-wide identification of microexons in 10 representative plant species. This analysis discovered 2,398 high-confidence internal microexons.

Leveraging these data, we developed a microexon prediction tool and applied it to 132 plant genomes , identifying a total of 20,224 microexons . This database provides comprehensive information on these microexons to facilitate further research.

Cluster IDs

Species

A. thalianaC. reinhardtiiG. maxH. annuus
O. sativaP. somniferumP. patensS. moellendorffii
V. viniferaZ. maysB. napusH. vulgare
P. trichocarpaS. bicolorS. lycopersicumT. aestivum
Abrus_precatoriusActinidia_rufaAegilops_tauschii_subsp._tauschii
Amborella_trichopodaAnanas_comosusAquilegia_coerulea
Arabidopsis_lyrata_subsp._lyrataArachis_duranensisArachis_hypogaea
Arachis_ipaensisAsparagus_officinalisBenincasa_hispida
Beta_vulgaris_subsp._vulgarisBrachypodium_distachyonBrassica_oleracea_var._oleracea
Brassica_rapaCajanus_cajanCamelina_sativa
Camellia_sinensisCannabis_sativaCapsella_rubella
Capsicum_annuumCarica_papayaCeratophyllum_demersum
Chenopodium_quinoaCicer_arietinumCinnamomum_micranthum
Citrus_clementinaCitrus_sinensisCoffea_arabica
Coffea_canephoraCoffea_eugenioidesColocasia_esculenta
Cucumis_meloCucumis_sativusCucurbita_maxima
Cucurbita_moschataCucurbita_pepo_subsp._pepoCynara_cardunculus_var._scolymus
Daucus_carota_subsp._sativusDendrobium_catenatumDioscorea_cayenensis_subsp._rotundata
Durio_zibethinusElaeis_guineensisErythranthe_guttata
Eucalyptus_grandisEuryale_feroxEutrema_salsugineum
Fragaria_vesca_subsp._vescaGinkgo_bilobaGlycine_soja
Gnetum_montanumGossypium_arboreumGossypium_hirsutum
Gossypium_raimondiiHerrania_umbraticaHevea_brasiliensis
Hibiscus_syriacusIpomoea_nilIpomoea_triloba
Jatropha_curcasJuglans_regiaLactuca_sativa
Liriodendron_chinenseLupinus_angustifoliusMacleaya_cordata
Malus_domesticaManihot_esculentaMedicago_truncatula
Momordica_charantiaMorus_notabilisMusa_acuminata_subsp._malaccensis
Nelumbo_nuciferaNicotiana_attenuataNicotiana_sylvestris
Nicotiana_tabacumNicotiana_tomentosiformisNymphaea_colorata
Olea_europaea_var._sylvestrisOryza_brachyanthaPanicum_hallii
Persea_americanaPhalaenopsis_equestrisPhaseolus_vulgaris
Phoenix_dactyliferaPiper_nigrumPistacia_vera
Populus_albaPopulus_euphraticaProsopis_alba
Prunus_aviumPrunus_dulcisPrunus_mume
Prunus_persicaPunica_granatumPyrus_x_bretschneideri
Quercus_lobataQuercus_suberRaphanus_sativus
Rhodamnia_argenteaRhododendron_simsiiRicinus_communis
Rosa_chinensisSesamum_indicumSetaria_italica
Setaria_viridisSolanum_pennelliiSolanum_tuberosum
Spinacia_oleraceaSyzygium_oleosumTarenaya_hassleriana
Theobroma_cacaoTripterygium_wilfordiiTriticum_dicoccoides
Vigna_angularisVigna_radiata_var._radiataVigna_unguiculata
Vitis_ripariaZiziphus_jujuba

References

H. Yu, M. L, J. Sandhu, G. Sun, J.C. Schnable, W. Xie, B. Yu, J.P. Mower, Chi Zhang. Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nature Communications (2022); 13, 820. (featured in Editors' Highlights)