Stem-loop sequence ptc-MIR395c

Accession

MI0002317

Description

Populus trichocarpa miR395c stem-loop

Gene family

MIPF0000016; MIR395

Community annotation

This text is a summary paragraph taken from the Wikipedia entry entitled mir-395_microRNA_precursor_family. miRBase and Rfam are facilitating community annotation of microRNA families and entries in Wikipedia.

mir-395 is a non-coding RNA called a microRNA that was identified in both Arabidopsis thaliana and Oryza sativa computationally and was later experimentally verified. mir-395 is thought to target mRNAs coding for ATP sulphurylases. The mature sequence is excised from the 3' arm of the hairpin. miR-395 is upregulated in Arabidopsis during sulphate-limited conditions, when the mature miRNA then regulates sulphur transporters and ATP sulphurylases.

Stem-loop

g  u c  ua         ug         u      ucuucgauuaaau 
 ug c cc  gaguuccuc  agcacuuca ugggaa             g
 || | ||  |||||||||  ||||||||| ||||||              
 ac g gg  cucaagggg  uugugaagu auccuu             a
-  u u  uc         gu         c      acuauuaugagaa 

Genome context

• Coordinates (JGI_Poptr2.0): scaffold_6: 8406701-8406801 [+]
• Overlapping transcripts:

  intergenic

Clustered miRNAs

< 10kb from ptc-MIR395c

• ptc-MIR395c: scaffold_6: 8406701-8406801 [+]
• ptc-MIR395d: scaffold_6: 8410822-8410922 [+]

Mature sequence ptc-miR395c

• Accession: MIMAT0002023
• Sequence: 72 - cugaaguguuugggggaacuc - 92
• Evidence: by similarity; MI0001010

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).