Here is a brief tutorial on how to get those UTRs, pls let me know if you have additional questions/comments.

There are a number of databases that already have done the prediction on 3'UTR of all protein coding genes, so chances are high that you can search your gene to find potential miRNA targets.

Here are a few database:

MicroSosm at http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ It is my favrite one. To use it, click Search and then choose the organism of your interest and gene name.

Targetscan at http://www.targetscan.org/. TargetScan put much weight on seed conservation

There are additional databases listed here http://www.exiqon.com/microrna-target-prediction

Best of Luck

Hi Mohsen,

Go to the UCSC genome browser http://genome.ucsc.edu/

click on "genome browser"

enter your gene symbol in the "search term" box

in the ucsc gene track, click in the symbol of your gene

click in the genomic sequence, it will take you to a page where you can select to see CDS in upper case, UTR in lower case

click "submit" and you should be able to see the UTRs sequences in lower case

Please, let me know if you need additional help

Good luck!

Rolando

thank you for your helping Mr Rolando, I have tried but I got just some maps not sequence, I need UTR sequence,Could you please help me?

thank you Mr Ajit Maurya , I know about that database ,but those have given only binding site as complementary to the micro RNA not all the UTR sequence.

Here is a brief tutorial on how to get those UTRs, pls let me know if you have additional questions/comments.

thank you so much Mr Rolando, It's very use full for me , I did it.

Hi:

You can go to this page http://utrdb.ba.itb.cnr.it/

You can find the 5' and 3' untranslated regions of eukaryotic mRNAs. It is possible to download databases from several taxa.

Cheers,

Rodolfo.

The tutorials you all have referred to look like the only work for published genomes.  Does anyone know how to find 3'UTRs for non-model organisms? I have an unannotated genome.

I just confirmed something, you could go to NCBI nucleotide to look for your GOI. Then, click on CDS and it gives you complete information about coding DNA with UTRs. These UTRs exactly matched with one shown in UCSC. I just cross checked because it was not mentioned in NCBI, however was logical to think that!

I would appreciate it if you would help me to find the 5 UTR sequences on Gene Bank

درود بر شما محسن عزیز

سوال شمارو از دو دیدگاه میشه بررسی کرد اول از لحاظ آماری و بیوانفورماتیک هست، که بفهمیم کدام قسمت های از یک ژن UTR  هستند، مسلما برنامه های کامپیوتری زیادی دراین باره هستن که خودت بهتر از من میدونی، که به بهترین هایشان در سایت NCBI میتوانی دسترسی داشته باشی.

راه حل دوم از لحاظ تکنیکی هست که بنده به شما تکنیک RACE را پیشنهاد میکنم.

امیدوارم سربلند و پیروز باشی.

خالصانه

امین

Please have a look

Dear Mohsen.

Hello

Search for this http://www.nbnc.ir a persian website that teach Bioinformatics

or http://www.biodatacenter.ir

Both are very good.

Mohsen Honarpisheh

Dear Amir Reza,

The question was from a very long time ago. But I appreciate it and thanks a lot.