Stem-loop ptc-MIR396d

Accession

MI0002328

Description

Populus trichocarpa ptc-MIR396d precursor miRNA

Literature search

7 open access papers mention ptc-MIR396d
(16 sentences)

Sequence

22395585 reads, 358792.0 reads per million, 9 experiments

gaaaguccuggucaugcuuUUCCACAGCUUUCUUGAACUUccuugccaugcuuaacuuguguguguguauagaucacuauauaucuguauaguuauacacauuuagcuagcuagcaccauugaagCUCAAGAAAGCCGUGGGAGAacauggcaacucaggauuuuu
((((((((((((((((.((((((((.((((((((((.((((..((...((((...((.((..(((((((((....(((((((....))))))))))))))))...)).))..)))).))..)))).)))))))))).)))))))).))))))....))))))))))

Structure

          ----      c        A          A    cu  cca    uaa  u  -gu         gauc       a 
gaaaguccug    gucaug uuUUCCAC GCUUUCUUGA CUUc  ug   ugcu   cu gu   guguguaua    acuauau u
||||||||||    |||||| |||||||| |||||||||| ||||  ||   ||||   || ||   |||||||||    |||||||  
uuuuuaggac    cgguac AGAGGGUG CGAAAGAACU gaag  ac   acga   ga cg   uacacauau    ugauaug c
          ucaa      a        C          C    uu  --c    -uc  u  auu         ----       u 

Annotation confidence High

Genome context

CM000342.2: 4642885-4643050 [-]

Clustered miRNAs

1 other miRNA is < 10 kb from ptc-MIR396d

Mature ptc-miR396d-5p

• Accession: MIMAT0002034
• Description: Populus trichocarpa ptc-miR396d-5p mature miRNA
• Sequence: 20 - UUCCACAGCUUUCUUGAACUU - 40
• Evidence: not_experimental

Mature ptc-miR396d-3p

• Accession: MIMAT0055639
• Description: Populus trichocarpa ptc-miR396d-3p mature miRNA
• Sequence: 126 - CUCAAGAAAGCCGUGGGAGA - 145
• Evidence: experimental ; unknown

References

1. Conservation and divergence of microRNA families in plants
   "Dezulian T, Palatnik JF, Huson DH, Weigel D"
   Genome Biol. (2005) 6:P13


2. PubMed ID: 16973872
   The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
   "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 (2006) 313:1596-1604