ABOUT THIS RECORDspecies: Populus trichocarpa
miRNA family: MIR162
source: PMRD, original name: ptc-miR162a
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 TCGATAAACCTCTGCATCCAG miRNA* GGAGGCAGCGGTTCATCGATC mismatches: 3 bulges: 0 |
pre-miRNA
TGGGAAGACACTGGAGGCAGCGGTTCATCGATCTCTTCCTGGCCAATTTTTTGTTTAGCACGAAAAACATGAACCGATCGATAAACCTCTGCATCCAGCG
CTTCCTT
dot-bracket secondary structure
.((((((.(.(((((.((((.((((.(((((((..(((.((.....((((((((.....)))))))))).)))..))))))).)))).)))).))))).)
)))))).
SIMILARITIES
MORE
miRNEST target predictions: none
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"
TGGGAAGACACTGGAGGCAGCGGTTCATCGATCTCTTCCTGGCCAATTTTTTGTTTAGCACGAAAAACATGAACCGATCGATAAACCTCTGCATCCAGCG
CTTCCTT
dot-bracket secondary structure
.((((((.(.(((((.((((.((((.(((((((..(((.((.....((((((((.....)))))))))).)))..))))))).)))).)))).))))).)
)))))).
SIMILARITIES| miRBase ptc-MIR162a: 4e-56 PMRD ptc-miRf10578-akr: 9e-54 microPC miR162: 1e-43 | UniProt no hits RFAM MIR162_2: 2e-45 |
Identical with: ptc-miRf10577-akr from PMRD (MNEST052399) |
MOREmiRNEST target predictions: none
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"
