ABOUT THIS RECORDspecies: Populus trichocarpa
miRNA family: MIR156
source: miRBase, original name: ptc-MIR156e (MI0002188)
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 TGACAGAAGAGAGTGAGCAC miRNA* GCTCATTTCTCTTTCTGTCACT mismatches: 0 bulges: 2 |
pre-miRNA
CATTAGAAATTGACAGAAGAGAGTGAGCACACAGAGGCATATTTGTATAAAATTATACCATTGCTTTTGCGTGCTCATTTCTCTTTCTGTCACTTCCAGA
dot-bracket secondary structure
.....(((..((((((((((((((((((((.((((((((.....(((((....)))))...)))))))).))))))).))))).)))))))).)))....
SIMILARITIES
MORE
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)"
[2] 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"
CATTAGAAATTGACAGAAGAGAGTGAGCACACAGAGGCATATTTGTATAAAATTATACCATTGCTTTTGCGTGCTCATTTCTCTTTCTGTCACTTCCAGA
dot-bracket secondary structure
.....(((..((((((((((((((((((((.((((((((.....(((((....)))))...)))))))).))))))).))))).)))))))).)))....
SIMILARITIES| miRBase ptc-MIR156c: 3e-35 PMRD ptc-miR156e: 5e-52 microPC miR156: 0.000000001 | UniProt no hits RFAM mir-156: 2e-24 |
Identical with: ptc-miR156e from PMRD (MNEST051595) |
MOREmiRNEST target predictions
non-miRNEST targets
HuntMi prediction: true miRNA
additional data
download this record
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)"
[2] 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"
