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Links tagged with '3' untranslated regions'

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AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite

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.

NAR Database Issue 2011
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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

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).

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

miRGenDatabase Content

http://www.diana.pcbi.upenn.edu/miRGen

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.

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

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).

This content is being maintained by cplaisier.

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

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.

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/

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.

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/

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.

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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/

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.

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