UCNEbase 2013, Ultra-Conserved Sequence Elements.

Vertebrate ultraconserved sequence elements (UCNEs) from UCNEbase. The collection is offered: (i) as an oriented "regions" SGA file where positions on the + and - strand indicate the beginning and end of a UCNE, respectively, and (ii) as an unoriented SGA file where the positions indicate the center of a UNCE.

• Source data was downloaded from: https://epd.expasy.org/ftp/UCNEbase/ucnes/hg19_UCNE_coord.bed
• Input file format: BED (4 fields)
• Download date: 26-5-2017

From H. sapiens (Feb 2009 GRCh37/hg19).

Sequence-derived:

	Filename	Description	Feature	GEO-ID
1	ucne_hg19.sga	UCNEs from UCNEbase	UCNE	-
2	ucne_hg19_c.sga	UCNEs from UCNEBase	UCNE	-

Notes on samples:

The sixth field of the SGA files contains the name of the UCNE.

The input BED file was converted into SGA and FPS format using custom Perl scripts available from the MGA ftp sitei (https://epd.expasy.org/ftp/mga/). Chromosome name conversion and generation of the FPS files was done with chr_replace_sga.pl and sga2fps from ChIP-Seq v. 1.5.3.

• Dimitrieva S, Bucher P
  UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res. 2013 Jan;41(Database issue):D101-9. doi: 10.1093/nar/gks1092. Epub 2012 Nov 27. 23193254