The genome coordinates for the underlined genomic sequences are indicated.
The genome coordinates for the miR-tags were obtained using miRanalyzer [20].
Genome coordinates for TE sequence within all sampled promoters are included in Table S5.
This database records 528 items of genome coordinates of human miRNAs.
We first mapped the genome coordinates of human miRNAs and protein-coding genes using Galaxy tool (http://g2.trac.bx.psu.edu/).
With the 90% confidence length set, 67% of the Unigene clusters were broken up into 2 to 5 subclusters based on their genome coordinates.
The V1R sequences obtained from other species were checked against their known mouse genome coordinates with the BLAT tool on the UCSC genome browser [56], [79], [80].
Our final result set contained 3476 candidate pre-miRNAs from mouse and 3441 from human (Table 2; detail genome coordinates are in Dataset S1 and Dataset S2).
The genome coordinates of the archaeal iPGM hits were distinct from those for the two bacterial iPGM queries in all cases.
The genome coordinates were used to discriminate whether one miRNA locates within the intron of a protein-coding gene or not.
In the TarBase's UCSCS track, absolute genome coordinates of the miRNA target sites were provided for the genome assembly version hg17.
