dbrip.brocku.ca
dbRIPA Database of Retrotransposon Insertion Polymorphisms in Humans (dbRIP)
http://dbrip.brocku.ca/
A Database of Retrotransposon Insertion Polymorphisms in Humans (dbRIP)
http://dbrip.brocku.ca/
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dbRIP | dbrip.brocku.ca Reviews
https://dbrip.brocku.ca
A Database of Retrotransposon Insertion Polymorphisms in Humans (dbRIP)
dbrip.brocku.ca
dbRIP
http://dbrip.brocku.ca/others.html
Release notes and Stats. Other databases that may adopt dbRIP data or collect RIPs. Database of Genomic Variants (DGV). NCBI database of structural variation (dbVAR). Journals focus on mutations and mobile DNA. Evidence for evolution: Alu elements. Last modified:Wednesday, 04-Jan-2012 15:50:20 EST .
dbRIP
http://dbrip.brocku.ca/introduction.html
Release notes and Stats. Constitute over 40% of the human genome and consist of several millions of family members. They play important roles in shaping the structure and evolution of the genome and in participating in gene functioning and regulation. Since L1, Alu. Is a database of human Retrotransposon Insertion Polymorphisms (RIPs). In which RIPs are highly integrated into the human genome annotation data provided by UCSC Genome Browser. DbRIP contains all currently known Alu.
dbRIP
http://dbrip.brocku.ca/citations.html
Release notes and Stats. Wang J, Song L, Grover D, Azrak S, Batzer MA, Liang P. dbRIP: a highly integrated database of retrotransposon insertion polymorphisms in humans. Hum Mutat. 27(4):323-329, 2006; PMID: 16511833. A more update list is available at Google Scholar. Wang J, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: a fruitful approach for ascertaining Alu insertion polymorphisms. Gene. Chen J, Ferec C, Cooper DN. Mechanism ...
dbRIP
http://dbrip.brocku.ca/example.html
Release notes and Stats. Querying Retrotransposon Insertion Polymorphisms (RIPs). You may query RIPs by RIP IDs, RIP subfamily, gene context, ethnic group name, allele frequency, disease association, etc. Using Genome Gateway. You may query RIPs by genetic IDs (gene IDs, accessions, STS, etc), and chromosome locations; Using BLAT. You may search RIP by DNA or protein sequences. Identifying RIPs associated with particular genes. Genome-wide browsing of RIPs. Downloading the entire set of RIP data.
Search dbRIP
http://dbrip.brocku.ca/cgi-bin/link2dbripByID.cgi?dbripid=1000002&genome=hg18
Your search of dbRIP by dbRIP ID "1000002" and genome id "hg18" produced the following result:. 1000002; Original ID(s). AluyMICB; RIP Alu chr6 031 01.
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Gypsy Database 2.0
http://www.gydb.org/index.php/GINGER1
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Gypsy-Integrase-Related Type 1 ( GINGER1. Is a recently described pool of exon-intron transposons ( Bao et al. Which encode for a transposase (TR) showing the occurrence of a GPY/F module ( Malik and Eickbush 1999. Thought to mediate multimerization ( Ebina et al. At its C-terminus. GINGER1. Cysteine protease domain, or an Ulp1. Element...
Gypsy Database 2.0
http://www.gydb.org/index.php/Retroviridae
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Evolutionary history and viral taxonomy:. Vertebrate retroviruses ( Retroviridae. Originally received attention when infectious representatives were characterized in humans. However, it is now known that any LTR retrotransposon capable of recruiting a third ORF envelope gene ( env. Is potentially capable of becoming a retrovirus ( env.
Gypsy Database 2.0
http://www.gydb.org/index.php/GINA
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Is a recently described pool of exon-intron transposons ( Marin 2010. Which encode for a transposase (TR) showing the occurrence of a GPY/F module ( Malik and Eickbush 1999. Thought to mediate multimerization ( Ebina et al. At its C-terminus. GINA. Cysteine protease domain, or an Ulp1. Protease catalytic domain ( Marin 2010. Elements ar...
Gypsy Database 2.0
http://www.gydb.org/index.php/GINNY
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Is a recently described pool of exon-intron transposons ( Marin 2010. Which encode for a transposase (TR) showing the occurrence of a GPY/F module ( Malik and Eickbush 1999. Thought to mediate multimerization ( Ebina et al. At its C-terminus. GINNY. Cysteine protease domain, or an Ulp1. Protease catalytic domain ( Marin 2010. Elements a...
Gypsy Database 2.0
http://www.gydb.org/index.php/Bel/Pao
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Evolutionary history and in-progress taxonomy:. LTR retroelements ( Malik et al. Constitute a family of LTR retrotransposons and retroviruses described to date only in metazoan genomes ( Copeland et al. This family was originally characterized with the discovery of element sequences such as Pao. Davis and Judd 1995. And the various Cer.
Gypsy Database 2.0
http://www.gydb.org/index.php/Retroelements
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Tyrosine recombinase (YR) retroelements. Retroelements (retrotransposons and retroviruses) can currently be divided into four systems or groups commonly known as the long terminal repeat (LTR) retroelements. Eickbush and Jamburuthugoda 2008. Genes, and env. Families (for more details, see LTR retroelements. On the basis of their molecul...
Gypsy Database 2.0
http://www.gydb.org/index.php/Ty3/Gypsy
GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Evolutionary history and in-progress taxonomy:. Branch 2 (non-chromodomain retroviruses and LTR retrotransposons). Of particular interest is the common evolutionarily history between several Ty3/Gypsy. Retroviruses (see, Eickbush and Malik 2002. Upon this, it is now known that env. Like genes are not exclusive of Retroviridae. Species t...
Gypsy Database 2.0
http://gydb.uv.es/index.php/LTR_retroelements
BLAST and HMM servers are currently under maintenance. GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. And other non-autonomous retroelements evolved from LTR retroelements. We additionally consider caulimoviruses of plants within the system of autonomous LTR retroelements because of their common evolutionary relationship with them based on the gag-pol region. The internal region con...
Gypsy Database 2.0
http://gydb.uv.es/index.php/Intro
BLAST and HMM servers are currently under maintenance. GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. LTR retroelements, and clan AA of Aspartic Peptidases. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia. LTR retroelements and the Caulimoviridae. Since the existence of mobile DNA was first suggested by McClintock ( McClintock 1948. That mediate the...
Gypsy Database 2.0
http://gydb.uv.es/index.php/Caulimoviridae
BLAST and HMM servers are currently under maintenance. GIN/GINGER TRs and INTs. Clan AA Ref. DB. Cores Seq. DB. Genome Seq. DB. LTRs and TIRs Seq. DB. Mobile Group II introns DB. Tree of Life Project. From The Gypsy Database. Biological distribution and host symptomatology. Evolutionary history and viral taxonomy. Are DNA pararetroviruses that replicate in plants via a RNA intermediate evolved from LTR retroelements (for more details, see Bousalem et al. To define animal ( Hepadnaviridae. The caulimovira...
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dbRIP
Release notes and Stats. 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 "http:/ dbrip.org/cgi-bin/link2dbripByID.cgi? 10/5/2010] dbRIP obtained its new and permernent URL: dbRIP.org.
dbRIP
Release notes and Stats. 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 "http:/ dbrip.org/cgi-bin/link2dbripByID.cgi? 10/5/2010] dbRIP obtained its new and permernent URL: dbRIP.org.
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