miRNA

miRNA name or miRNA id

miRNA target site on gene

miRNA target site position on gene: xxx-xxx (start from xxx to xxx)

miRNA target on transcript

ASTD database transcript id or GenBank database trasncript id

miRNA target site on transcript

miRNA target site position on transcript: xxx-xxx (start from xxx to xxx)

miRNA target site on which region of the transcript

If the trasncript can be translated to protein, the regions can be identified such as 5' untranslated region(5'UTR), protein coding region(CDS),
and 3'untranslated region(3'UTR)

miRNA target site on which exon type of the transcript

miRNA target site might be located in the exon region of the transcript. Because of the mechanism RNA alternative splicing it can be divided
into two types such as alternatively spliced exon(AS) and constitutively spliced exon(CS)

miRNA target region conservation
We used PhastCons conservation score, which measures the evolutionary conservation of sequence blocks across multiple vertebrates using a phylogenetic hidden Markov model (Siepel et al., Genome research, 15, (2005), 1034-1050.), to annotate the conservation of predicted target sites.
Target site accessibility
miRNAs hybridize to the target sites, which is within more accessible regions, are with more possibility to be real.
MFE
Minimum free energy (MFE) is caculated by miRanda.
Alignment score
The score is caculated by miRanda. Notably, the terminal miRNA nucleotides the first and last two nucleotides no longer contribute to the miRanda score, according to Wang et al. , who stated that these nucleotides are inaccessible to base-pairing (Wang et al. 2008b)
Alignment sequence
Seed type
Four seed types - 8mer, 7mer-m8, 7mer-A1 and 6mer - which were defined clearly by the Bartel group, are considered here (Bartel 2009).