+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

miRTCat: a comprehensive map of human and mouse microRNA target sites including non-canonical nucleation bulges



miRTCat: a comprehensive map of human and mouse microRNA target sites including non-canonical nucleation bulges



Bioinformatics 29(15): 1898-1899



MicroRNAs (miRNAs) regulate various biological functions by binding hundreds of transcripts to impart post-transcriptional repression. Recently, by applying a transcriptome-wide experimental method for identifying miRNA target sites (Ago HITS-CLIP), a novel non-canonical target site, named 'nucleation bulge', was discovered as widespread, functional and evolutionally conserved. Although such non-canonical nucleation bulges have been proven to be predictive by using 'pivot pairing rule' and sequence conservation, this approach has not been applied yet. To facilitate the functional studies of non-canonical miRNA targets, we implement miRTCat: a comprehensive searchable map of miRNA target sites, including non-canonical nucleation bulges, not only mapped in experimentally verified miRNA-bound regions but also predicted in all 3'-untranslated regions (3'-UTRs) derived from human and mouse (∼15.6% as expected false-positive results). http://ion.skku.edu/mirtcat. swchi@skku.edu Supplementary data are available at Bioinformatics online.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 036908380

Download citation: RISBibTeXText

PMID: 23709495

DOI: 10.1093/bioinformatics/btt296


Related references

Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues. Plos One 7(3): E33720, 2012

Detection of canonical A-to-G editing events at 3' UTRs and microRNA target sites in human lungs using next-generation sequencing. Oncotarget 6(34): 35726-35736, 2016

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biology 11(8): R90, 2011

MicroRNA-602 and microRNA-608 regulate sonic hedgehog expression via target sites in the coding region in human chondrocytes. Arthritis and Rheumatology 67(2): 423-434, 2015

A comprehensive survey of non-canonical splice sites in the human transcriptome. Nucleic Acids Research 42(16): 10564-10578, 2015

Comprehensive analysis of human microRNA target networks. Biodata Mining 4: 17, 2011

Human polymorphism at microRNAs and microRNA target sites. Proceedings of the National Academy of Sciences of the United States of America 104(9): 3300-3305, 2007

A non-canonical plant microRNA target site. Nucleic Acids Research 42(8): 5270-5279, 2014

miRTar Hunter: a prediction system for identifying human microRNA target sites. Molecules and Cells 35(3): 195-201, 2013

microPIR: an integrated database of microRNA target sites within human promoter sequences. Plos One 7(3): E33888, 2012

PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse. Plos Computational Biology 12(10): E1005170, 2016

Polymorphisms in microRNA target sites modulate risk of lymphoblastic and myeloid leukemias and affect microRNA binding. Journal of Hematology and Oncology 7: 43, 2014

MicroRNA Target Recognition: Insights from Transcriptome-Wide Non-Canonical Interactions. Molecules and Cells 39(5): 375-381, 2017

Progress of polymorphism in microRNA and microRNA target sites. Yi Chuan 32(11): 1091-1096, 2011

miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes. Bmc Genomics 13: 44, 2012