Stem-loop ptc-MIR408

Accession

MI0002352

Description

Populus trichocarpa ptc-MIR408 precursor miRNA

Literature search

13 open access papers mention ptc-MIR408
(246 sentences)

Sequence

14881 reads, 230.0 reads per million, 9 experiments

agagacagaugaagACGGGGAACAGGCAGAGCAUGgauggagcuacuaacagaaguacuuguuuuggcucuacccaUGCACUGCCUCUUCCCUGGCUUGuggcuc
.(((.(.....(((.(((((((.((((((.((((((.((((((((..(((((......))))).)))))))).)))))).)))))).))))))).)))...))))

Structure

a   a agaug   A       C      A      a        cu     aa 
 gag c     aag CGGGGAA AGGCAG GCAUGg uggagcua  aacag  g
 ||| |     ||| ||||||| |||||| |||||| ||||||||  |||||   
 cuc g     UUC GUCCCUU UCCGUC CGUacc aucucggu  uuguu  u
-   - --guG   G       C      A      c        -u     ca 

Annotation confidence High

Genome context

CM000338.2: 14802196-14802300 [+]

Mature ptc-miR408-5p

• Accession: MIMAT0022913
• Description: Populus trichocarpa ptc-miR408-5p mature miRNA
• Sequence: 15 - ACGGGGAACAGGCAGAGCAUG - 35
• Evidence: experimental ; miRNAseq [5]

Mature ptc-miR408-3p

• Accession: MIMAT0002058
• Description: Populus trichocarpa ptc-miR408-3p mature miRNA
• Sequence: 77 - UGCACUGCCUCUUCCCUGGCUUG - 99
• Evidence: experimental ; cloned [1], miRNAseq [5]

References

1. PubMed ID: 15916721
   Identification and characterization of new plant microRNAs using EST analysis
   "Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA"
   "Cell Res (2005) 15:336-360


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


3. 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


4. PubMed ID: 15994906
   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis
   "Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL"
   "Plant Cell (2005) 17:2186-2203


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