Stem-loop sequence ptc-MIR396d

Accession

MI0002328 (change log)

Description

Populus trichocarpa miR396d stem-loop

Gene family

MIPF0000047; MIR396

Literature search

6 open access papers mention ptc-MIR396d
(14 sentences)

Stem-loop

             ----      c        a          a    cu  cca    uaa  u  -gu         gauc       a 
5' gaaaguccug    gucaug uuuuccac gcuuucuuga cuuc  ug   ugcu   cu gu   guguguaua    acuauau u
   ||||||||||    |||||| |||||||| |||||||||| ||||  ||   ||||   || ||   |||||||||    |||||||  
3' uuuuuaggac    cgguac agagggug cgaaagaacu gaag  ac   acga   ga cg   uacacauau    ugauaug c
             ucaa      a        c          c    uu  --c    -uc  u  auu         ----       u 

Confidence

Annotation confidence: not enough data

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Genome context

• Coordinates (Poptr2_0; GCA_000002775.2): CM000342.2: 4642885-4643050 [-]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from ptc-MIR396d

• ptc-MIR396d: CM000342.2: 4642885-4643050 [-]
• ptc-MIR396a: CM000342.2: 4636167-4636289 [+]

Database links

• RNAcentral:URS00007A1E55_3694
• miRBase Tracker:MI0002328

Mature sequence ptc-miR396d

• Accession: MIMAT0002034
• Sequence: 20 - uuccacagcuuucuugaacuu - 40
• Evidence: by similarity; MI0001014

References

1. "Conservation and divergence of microRNA families in plants" Dezulian T, Palatnik JF, Huson DH, Weigel D http://genomebiology.com/2005/6/11/p13 (2005).
2. PMID: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. 313:1596-1604(2006).