Hello. We are currently studying a protein that is transcribed in both cardiac fibroblasts and cardiac myocytes but only translated in fibroblasts. As a first step to trying to figure out may be driving cell type-specific translation, I would like to examine any control elements in the 5'UTR. Are there any bioinformatic tools available that we could use to screen the sequence and identify possible control elements?
Hello, Bruce Allen,
I have very good experience with this user-friendly web-based tool:
http://regrna2.mbc.nctu.edu.tw/detection.html
Hope this help
Martin
Hi Dr. Allen,
I have used a few prediction algorithms are available for identifying putative response elements in a given gene region. My personal favorite is PROMO (http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3), although TRANSFAC (http://gene-regulation.com/pub/databases.html) is also fine.
To use PROMO, simply input the DNA sequence of interest (in FASTA format, so pull it from UCSC genome browser or equivalent), select your species, and it will give you a ranked list of response elements which MAY exist within the given region.
Alternatively, you can pull from ChIP-sequencing databases (ENCODE, ChEA, etc...) and find empirical binding sites for various tissue/cell types.
I hope this helps!
Dear Bruce
I think this paper is good for you:
Huang HY, Chien CH, Jen KH, Huang HD. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic acids research. 2006 Jul 1;34(suppl_2):W429-34.
Best
Martin, Mark, Zahra
Thank you for your suggestions. I'll give them a shot and see how it goes.
regards
Bruce
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics