ABOUT THIS RECORDspecies: Populus trichocarpa
miRNA family: MIR160
source: PMRD, original name: ptc-miR160b
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 TGCCTGGCTCCCTGTATGCCA miRNA* GCGTATGAGGAGCCATGCATA mismatches: 3 bulges: 0 |
pre-miRNA
AATATTATATGTGCCTGGCTCCCTGTATGCCATTTGCAGAGCCCAACGGATCCTCGATGGCCTCCGTGGATGGCGTATGAGGAGCCATGCATATTCGCA
dot-bracket secondary structure
).......((((((.(((((((..((((((((((..(.(((.(((.(((....))).))).))).)..))))))))))..))))))).)))))).....
SIMILARITIES
MORE
miRNEST target predictions
non-miRNEST targets
HuntMi prediction: true miRNA
additional data
download this record
references
[1] Dezulian T, Palatnik JF, Huson DH, Weigel D, http://genomebiology.com/2005/6/11/p13 (2005)., "Conservation and divergence of microRNA families in plants"
[2] 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)"
[3] Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL, Plant Cell. 17:2186-2203(2005)., "Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis"
AATATTATATGTGCCTGGCTCCCTGTATGCCATTTGCAGAGCCCAACGGATCCTCGATGGCCTCCGTGGATGGCGTATGAGGAGCCATGCATATTCGCA
dot-bracket secondary structure
).......((((((.(((((((..((((((((((..(.(((.(((.(((....))).))).))).)..))))))))))..))))))).)))))).....
SIMILARITIES| miRBase ptc-MIR160b: 8.0E-51 PMRD ptc-miR160c: 7.0E-42 microPC miR160: 7.0E-33 | UniProt no hits RFAM 0mir-160: 2.0E-42 |
Identical with: ptc-MIR160b from miRBase (MNEST041306) |
MOREmiRNEST target predictions
non-miRNEST targets
HuntMi prediction: true miRNA
additional data
download this record
references
[1] Dezulian T, Palatnik JF, Huson DH, Weigel D, http://genomebiology.com/2005/6/11/p13 (2005)., "Conservation and divergence of microRNA families in plants"
[2] 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)"
[3] Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL, Plant Cell. 17:2186-2203(2005)., "Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis"
