Stem-loop sequence ptc-MIR169u

Accession

MI0002271 (change log)

Description

Populus trichocarpa miR169u stem-loop

Gene family

MIPF0000012; MIR169_1

Literature search

9 open access papers mention ptc-MIR169u
(12 sentences)

Stem-loop

   gag       -       -   c    u      --u    -   ug   uc     ---a  aau 
5'    gguuggg uagccaa gga gacu gccuau   uccu cca  ggg  cugaa    ag   g
      ||||||| ||||||| ||| |||| ||||||   |||| |||  |||  |||||    ||   a
3'    ucaaucc aucgguu ccu cuga cggaua   ggga ggu  cuc  gacuu    uc   a
   ---       u       u   -    -      cuu    u   ua   ga     gcug  aua 

Confidence

Annotation confidence: not enough data

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Genome context

• Coordinates (Poptr2_0; GCA_000002775.2): CM000351.2: 12074209-12074330 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from ptc-MIR169u

• ptc-MIR169u: CM000351.2: 12074209-12074330 [+]
• ptc-MIR169r: CM000351.2: 12082579-12082697 [+]

Database links

• RNAcentral:URS00007B801E_3694
• miRBase Tracker:MI0002271

Mature sequence ptc-miR169u-5p

• Accession: MIMAT0001977
• Previous IDs: ptc-miR169u
• Sequence: 11 - uagccaaggacgacuugccua - 31
• Evidence: experimental; miRNAseq [2]

Mature sequence ptc-miR169u-3p

• Accession: MIMAT0022900
• Sequence: 97 - ggcagucuccuuuggcuaucc - 117
• Evidence: experimental; miRNAseq [2]

References

1. 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).
2. PMID:22442676 "Deep annotation of Populus trichocarpa microRNAs from diverse tissue sets" Puzey JR, Karger A, Axtell M, Kramer EM PLoS One. 7:e33034(2012).