Conserved RNA Structures (CRSs) in the vertebrate genome

Supplemental Data of

The identification and functional annotation of RNA structures conserved in vertebrates

Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J Genome Res. 2017 Aug;27(8):1371-1383. Epub 2017 May 9
[ PubMed | Paper | Dataresource | Supplement ]

Supplemental_Data_1.csv.gz  List of all CRSs
Supplemental_Data_2.csv.gz  List of all CRS alignments
Supplemental_Data_3.csv.gz  Gene annotation of CRSs (based on Gencode v25)
Supplemental_Data_4.csv.gz  List of expressed (P<0.1) CRS regions found by CaptureSeq

patch_2020-07-28_fix_hg38_coordinates:
fixes the genomic coordinates in hg38 for 33,449 CRSs (272 CRSs were removed); aligned to webserver version 2.1

Supplemental_Data_1__patch_2020-07-28_fix_hg38_coordinates.csv.gz  List of all CRSs
Supplemental_Data_2__patch_2020-07-28_fix_hg38_coordinates.csv.gz  List of all CRS alignments

Software

The screen used CMfinder version 0.2.1 and 0.3 for pscore calculation of the vertebrate tree.
Both have been integrated in version 0.2.2: cmfinder-0.2.2.tgz
Latest version of CMfinder: https://sourceforge.net/projects/weinberg-cmfinder/