Question: how can i count the total exon in the sequence structure?
0
gravatar for loly.pearl86
2.1 years ago by
loly.pearl8620
Australia
loly.pearl8620 wrote:

Hi,

Can someone help me to know how can i count the number of exon within the sequence of target genes? In general i would like to visualized the whole sequence structure.

I use SMART but its only show the functional domains within the sequences and i want to see the number of exons and UTRs regions also i tried to use enseble but my gene not belong to ensemble organism

rna-seq gene • 770 views
ADD COMMENTlink written 2.1 years ago by loly.pearl8620
1

Which species are you working with? You may or may not have gene structure information for your species of interest. If not, you may use a closely related species and assume a similar gene structure. In ensembl (not only vertebrates-ensembl but metazoa-ensembl, plant-ensembl...) there are lots of species available. You may also find the UCSC browser useful.

ADD REPLYlink written 2.1 years ago by abascalfederico1.1k

Its Sea anemone and i have the Gene and protein sequences and i want to analyse the genomic organisation incluing the total exon/intron, central regioun and functional protien domain

ADD REPLYlink written 2.1 years ago by loly.pearl8620
1

Do you have the gene structure information also (exons, introns...)? If you have a GTF with all this information you can write a script to extract the sequence corresponding to each exon and translate according to the correct reading frame.

If you are working with Nematostella, it is available in Ensembl which might be of great help: http://metazoa.ensembl.org/Nematostella_vectensis/Info/Index

ADD REPLYlink written 2.1 years ago by abascalfederico1.1k

Where can i write the script?

ADD REPLYlink written 2.1 years ago by loly.pearl8620
1

Try searching for "extracting CDS sequences from GTF" or something like. It must have been asked here A quick search found Extract Cds Fastas From A Gff Annotation + Reference Sequence but must be others

ADD REPLYlink written 2.1 years ago by abascalfederico1.1k
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