Click here for old announcements
- [04/26/2018] Pre-release announcement: dbRIP version 3 is expected
to be released in May and it will provide full sequence
characterization and allele frequency data for 28 populations
(26 from the 1000 Genome Project) for a total of 4,500 polymorphic mobile elements (MEs). The current version of the data for hg19 is now also available on UCSC Genome Browser's Track Hubs (dbRIP).
- [04/10/2018] Human-specific ME (HS-ME) data has been updated to be based
on the analysis of hg38 in comparison with the latest version of 9 other non-human
primates. Our manuscript reporting the work ( W. Tang; S. Mun; A. Joshi; K. Han, P. Liang. "Mobile elements
contribute to the uniqueness of human genome with 15,000
human-specific insertions and 14 Mbp sequence increase".) is currently
under review with DNA Research. The full list of HS-MEs
is available at the Download
page.The data are also expected to be available soon via the UCSC Genme
Browser's Track Hub for hg19 and for hg38.
- [06/01/2013] We started to use study IDs to facilitate search of
MEIs in dbRIP that are associated with specific studies. The data for
an individial study are also available as one downloadable file. The full list of
study IDs is avaibable at here.
- [1/12/2012] As a heads-up, we are working on depositing a subset
of RIPs reported by the 1000 genome project and adding a track for
human-specific retrotransposon insertions, and will try to make them
available at dbRIP in the near future.
- [1/12/2012] A utility has been added to allow other sites to link
directly to dbRIP based on dbRIP and genome ID using a format like
in which the "1000002" and "hg18" are to be replaced by the actual
dbRIP ID and genome ID, respectively. Currently, this service is only
available for hg18 and hg19, while the entries
containing incomplete sequence (e.g. 1000001i) available only for hg19.
- [4/2/2011] A dataset representing 483 Alu insertions with
incomplete insertion sequences identified using ME-SCAN as described in Witherspoon et al,
BMC Genomics 11:410, 2010 has been deposited. These entries are denoted by
a letter "i" at the end of the dbRIP accession#, e.g.: "1000002i" for differentiating from the regular RIP entries. They may be upgraded to
the regular entries later once complete sequence information becomes
available. The data is available by setting the "sequence integrity level" to "incomplete" in SearchdbRIP. Please
note that the data is only available in hg19.
- [3/30/2011] dbRIP v2h released: added new L1 RIP data based on Kidd
et al. Cell 143:837-1847, 2010 from Fosmid-end sequencing. Total entries retrieved and
curated: 191 (135 novel, 56 overlapping with existing RIPs in
dbRIP). The data can be checked using author name,
e.g. "Kidd" or "Eichler" in SearchdbRIP
- [10/5/2010] A new and stable dbRIP ID system is
implemented in this test version. This system uses 7-digit
numerical IDs, with the first digit used to indicate the major
type of retrotransposons (1xxxxxx, 2xxxxxx, 3xxxxxx, 4xxxxxxx
for Alu, L1, SVA and HERV, respectively). For example, dbRIP
1000001 is an Alu RIP, while 2000100 is a L1. The remaining
5 digits (5-9) are saved for new types of RIPs and for accommodating
existing types that exceed 1 million in number.
- [10/5/2010] dbRIP obtained its new and permernent URL:
- [9/1/2010] HERV RIP data is added. For HERV RIPs with the
presence of both full length LTR and solo-LTR, we provide both
versions of the sequences and genotype data whenever available.
- [5/1/2010] The PositionMapping utility is added. This is
useful for users with a need of comparing a list of newly
identified candidate RIPs with data in dbRIP.
- [2/1/2010] dbRIP data to hg19 is provided.
- [12/15/2009] A test version of dbRIP with updated data
(data from venter diploid genome) for both hg17 and hg18 is now
available. Starting from hg18, the dbRIP ID is changed to a new
system, in which a serial ID is used (e.g. "dbRIP_Alu_00001") to
replace the old chr_Mbp_ID system. The new ID system provides
stability not affected by the genome migration.
- [12/01/2008] dbRIP was relocated to http://dbRIP.brocku.ca from falcon.roswellpark.org:8080/ as of January 1, 2009.
Last modified:Friday, 04-May-2018 14:16:44 EDT .