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Links tagged with '3' untranslated regions'

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AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite [open in a new window]

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RNA > Databases

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
AREsite: a database for the comprehensive investigation of AU-rich elements201113
NAR Database Issue 2011
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external linksLink on Wikipedia
tags3' untranslated regions adenine animals base sequence conserved sequence genomics humans mice nucleic acid databases rna sequence analysis rna-binding proteins sequence alignment uracil

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
RNA > Functional RNAs

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

links directory index: 28
TitlePublication YearGoogle Scholar Citation Count
CRSD: a comprehensive web server for composite regulatory signature discovery200628
NAR Web Server Issue 2006
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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

ERANGETool Content

http://woldlab.caltech.edu/rnaseq/ [open in a new window]

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Expression > Gene Regulation

A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper "Mapping and quantifying mammalian transcriptomes by RNA-Seq" (Mortazavi, 2008). ERANGE is built on top of Cistematic.

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tags3' untranslated regions algorithms alternative splicing animals brain chromosome mapping exons gene expression profiling genetic promoter regions inbred c57bl mice liver messenger rna mice nucleic acid databases oligonucleotide array sequence analysis rna rna sequence analysis rna splicing sensitivity and specificity skeletal muscle software

miRGenDatabase Content

http://www.diana.pcbi.upenn.edu/miRGen [open in a new window]

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RNA > Databases

miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data. Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface.

links directory index: 30
TitlePublication YearGoogle Scholar Citation Count
miRGen 2.0: a database of microRNA genomic information and regulation201030
NAR Database Issue 2010
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tags3' untranslated regions algorithms animals computational biology genetic databases humans mice micrornas nucleic acid databases single nucleotide polymorphism transcription factors tumor cell line

miRvestigatorTool Content

http://mirvestigator.systemsbiology.net [open in a new window]

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Expression > Gene Regulation

miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the most likely miRNA regulating the genes. It searches for an over-represented sequence motif in the 3' UTRs of the genes using Weeder and compares the motif to all unique miRNA seed sequences in miRBase using our custom built miRvestigator hidden Markov model (HMM).

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links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling20111
NAR Web Server Issue 2011
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tags3' untranslated regions animals Co-expression Co-Regulation gene expression profiling gene expression regulation Gene Set humans mice micrornas miRNA rats rna sequence analysis

RepTarDatabase Content

http://reptar.ekmd.huji.ac.il [open in a new window]

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RNA > Databases

RepTar is a database of miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
RepTar: a database of predicted cellular targets of host and viral miRNAs20115
NAR Database Issue 2011
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tags3' untranslated regions algorithms animals binding sites gene expression regulation humans mice micrornas nucleic acid databases rna sequence analysis viral rna

RNAhybridTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/ [open in a new window]

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Expression > Gene Regulation
RNA > Functional RNAs

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.

links directory index: 748
TitlePublication YearGoogle Scholar Citation Count
RNAhybrid: microRNA target prediction easy, fast and flexible2006146
Fast and effective prediction of microRNA/target duplexes2004602
NAR Web Server Issue 2006
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tags3' untranslated regions algorithms animals binding sites body patterning caenorhabditis elegans caenorhabditis elegans proteins computational biology drosophila homeodomain proteins insect genes messenger rna micrornas nucleic acid conformation nucleic acid databases post-transcriptional rna processing rna interference thermodynamics

SatellogDatabase Content

http://satellog.bcgsc.ca/ [open in a new window]

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DNA > Structure and Sequence Feature Detection
Human Genome > Health and Disease

Satellog is a database for the identification and prioritization of satellite repeats in disease association studies.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies200518
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tags3' untranslated regions base sequence biomedical research cluster analysis computational biology dna sequence analysis genetic databases genetic polymorphism genetic predisposition to disease human genome humans huntington disease inborn genetic diseases microsatellite repeats nucleic acid databases schizophrenia sequence alignment trinucleotide repeat expansion trinucleotide repeats untranslated regions

UTRdb/UTRsiteDatabase Content

http://utrdb.ba.itb.cnr.it/ [open in a new window]

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DNA > Databases

UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs201035
NAR Database Issue 2010
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tags3' untranslated regions 5' untranslated regions algorithms animals computational biology genetic databases humans nucleic acid databases plant genome protein databases protein isoforms

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