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Protocols

U12DB specifications

Information


Unique identifier OMICS_18085
Name U12DB
Alternative name U12 Intron Database
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Version 1.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/U12_intron_database

Maintainer


  • person_outline Tyler Alioto

Publication for U12 Intron Database

U12DB citations

 (5)
library_books

IntEREst: intron exon retention estimator

2018
BMC Bioinformatics
PMCID: 5896110
PMID: 29642843
DOI: 10.1186/s12859-018-2122-5

[…] To carry out the analysis, we used RefSeq as a reference and identified and annotated 510 U12-type introns using the annotateU12() function that uses Position Weigh Matrices (PWM) extracted from the U12DB database []. Next we performed the differential IR analysis using the DESeq2-based function of IntEREst (comparing the ZRSR2mut samples vs ZRSR2wt and HEALTHY). The DESeq2 test was run by consid […]

library_books

The RNA binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

2016
RNA Biol
PMCID: 5270529
PMID: 27763814
DOI: 10.1080/15476286.2016.1247148

[…] U12-introns were bound by RBM10, we used the ‘full’ list of RBM10 binding sites. We only analyzed introns of expressed genes (using the RNA-seq data – see below). U12 introns were retrieved from the U12DB database. The comparison between the proportion of U2- and U12-introns bound by RBM10 was done using a z-test. To analyze the distance between RBM10 binding site and the branch point, we predict […]

library_books

Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA

2013
eLife
PMCID: 3728624
PMID: 23908766
DOI: 10.7554/eLife.00780.017

[…] pectively (). Cufflinks () was used to assemble transcripts, estimate their abundance, and score differential expression.Focusing first on predicted minor introns (∼700) in the minor intron database (U12DB) (), we detected 429 that passed the threshold for expressed genes of fragments per kilobase per million mapped reads (FPKM) > 1 in control AMO. Interestingly, 206 (48%) of these were expressed […]

call_split

The importance of identifying alternative splicing in vertebrate genome annotation

2012
PMCID: 3308168
PMID: 22434846
DOI: 10.1093/database/bas014
call_split See protocol

[…] formed by, and checked against, computational predictions of alternatively spliced transcripts by PASA () and Ensembl (, ), supported introns (Mark Diekhans, personal communication), U12 introns from U12DB (), coding exons by CONGO () and pseudogenes by PseudoPipe (, ), Retrofinder () and Pseudofinder (). Computational gene predictions are visible in the annotation interface to provide hints to an […]

library_books

Evolutionary dynamics of U12 type spliceosomal introns

2010
BMC Evol Biol
PMCID: 2831892
PMID: 20163699
DOI: 10.1186/1471-2148-10-47

[…] nalis, Apis mellifera, Drosophila melanogaster, Anopheles gambiae, Caenorhabditis elegans, and Arabidopsis thaliana. We utilized orthologous U12-type intron clusters and related data available in the U12DB []. Members of an orthologous intron cluster are introns in orthologous genes that are flanked by alignable exonic sequences. The status of each intron in each species was designated in the U12D […]

Citations

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U12DB institution(s)
Genome Bioinformatics Laboratory, Center for Genomic Regulation, Barcelona, Spain
U12DB funding source(s)
Supported by the Biosapiens Network of Excellence project.

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