- Where can I get a list of non-coding cDNAs?
- Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/noncoding/
- Where can I get the transcribed genome regions
defined by 5' and 3' ends?
- Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/boundary_set/
- Where can I get the GIS and GSC sequences?
- Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/GIS/
- Where can I get the 5,154 new protein
- Please find here, https://fantom.gsc.riken.jp/3/download/FANTOM3/coding/
- Different rearray IDs are derived for the same cDNA
clone from ftp site (https://fantom.gsc.riken.jp/3/download/fantomdb/3.0/)
and RIKEN cDNA annotation viewer https://fantom.gsc.riken.jp/3/db/.
- We have two types of rearray IDs for cDNA clones: for our sequencing,
and for distribution of our cDNA clones on your request ( https://www.dnaform.jp/en/products/clone/fantom/
). Rearray IDs in the clone distribution are accessible from the cDNA
annotation viewer, while fantomdb 3.0 at the ftp site provides rearray
IDs used in our cDNA sequencing. If you are interested in only cDNA
clone sequences and/or functions, please use clone IDs, not rearray
IDs. For the purpose of bulk downloading the 'clone
distribution' rearray IDs, https://fantom.gsc.riken.jp/3/ofc/Archive/FANTOM3setInfo.txt
is also available.
- How many bps would be transcribed when we approved
- Please find here. https://fantom.gsc.riken.jp/3/download/FANTOM3/opt/forrest_aggressive/
- Where can I find promoters determined by CAGE?
- We classified CAGE tags and other 5'-end sequences into tag clusters
(TC) to define promoters. You can look up tag cluster (TC) by CAGE
analysis database (mouse
- Where can I download tag clusters (TCs) and their
- All data in the CAGE basic and analysis databases are avaliable.
Tag clusters and their attributes are written in these files,
and tss_*.bz2, at the download directories of the CAGE Analysis
and human). Additional
data used in our paper in Nature
Genetics is available here,
which contains classifications of tag clusters (TCs) based on the CAGE
tag distirbution, and associations of tag clusters (TCs) with some
- Where can I download genomic coordinates used in
- Please take a look at here,
before e-mailing to us. Esepcially, genomic coordinates of transcripts
are included in 'alltrans.gff.bz2' or 'alltrans_symbolSynonym.gff.bz2'
of the Genomic Elements Databases.
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