How to look EXON/INTRON sequence?

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Firoz Ahmad
Firoz Ahmad's picture
How to look EXON/INTRON sequence?

Hi everyone!
Can anyone help me to give me idea how to identify Introns and exonic sequences in the genomic DNA sequence for a particular gene, say FLT3 gene which i am working on.

Marina Fomin
Marina Fomin's picture
One way to do it is to blast

One way to do it is to blast mRNA sequence with genome sequence for this gene. But you can do it easy on ensemble website. For example I did it for you for human flt3 (you didn't specify the species): http://www.ensembl.org/Homo_sapiens/exonview?db=core;transcript=ENST00000204637
So, if you go to http://www.ensembl.org, choose animal, put name of gene, then go to trtanscript, and then to exons.

Jon Moulton
Jon Moulton's picture
At Gene Tools, we regularly

At Gene Tools, we regularly target Morpholino oligos to exon/intron and intron/exon boundaries in order to modify splicing. The easiest resource we have worked with is the Ensembl website, as Marina suggested.

However, mRNA is often subject to alternative splicing. If you need to know the specific splicoform in your specific organism/tissue/developmental stage, you might need to isolate the mRNA and do a Northern blot for your messenger of interest; if the mass information from the Northern is not enough to determine the splicoform, you can go on to RT-PCR and/or sequencing. The surest way to determine splice sites is to compare the messenger's sequence with the genomic sequence -- but if you can accept some uncertainty, using a resource like Ensembl can save lots of time!

Best regards,

- Jon

Jon D. Moulton, Ph.D.
Gene Tools, LLC

ryan_m
ryan_m's picture
Another method that will work

Another method that will work for un-annotated genes (maybe you have a novel mRNA in your hands) is to use BLAT (available on the UCSC website). BLAT will align a spliced sequence to the genome, so you can visually see where the introns and exons lie. The BLAT output also gives you the exact alignment boundaries.

Try it out:

http://genome.ucsc.edu/cgi-bin/hgBlat

Margaret Pearl
Margaret Pearl's picture
Try this mybioinfo.info

Try this mybioinfo.info search engine. You might like its output format.

http://www.mybioinfo.info/exon_display.php?search_type=GENE&search_sp=9606&search_key=MAP1A&B3=Search

NM_002373.5_chr15 NT_010194.17_on_+strand

1
UTR(93bp)
14600363~14600455

2
Intron(2940bp)
14600456~14603395

3
UTR(83bp)
14603396~14603478

4
Intron(248bp)
14603479~14603726

5
UTR(141bp)
14603727~14603867

6
Intron(211bp)
14603868~14604078

7
UTR(150bp)
14604079~14604228

8
CDS(8035bp)
14604229~14612263

9
Intron(141bp)
14612264~14612404

10
CDS(221bp)
14612405~14612625

11
Intron(198bp)
14612626~14612823

12
CDS(156bp)
14612824~14612979

13
UTR(1396bp)
14612980~14614375

bhupinder uppal
bhupinder uppal's picture
 how i can get exon and

 how i can get exon and intron sequences from any database...?????

Jon Moulton
Jon Moulton's picture
See the second post of this

See the second post of this thread. In Ensembl exon view, you'll get exon sequence and about 25 bases of intron sequence at each splice junction.  Click on the intron name and zoom as needed to see sequence in the intron.

veronicafbb
veronicafbb's picture
 Hi, 

 Hi, 
excuse me ..... My name's Veronica and I am having the same problem: I red your reply but I need to find exons on genes of filamentous fungi , where could I find them? Because every database you reported is focussed on human and animals .... please help me :( Thanks a lot: Veronica