Hello,
I am trying to figure out the protein product of a chromosomal translocation. I have the chromosome and location (base number) of the breakpoint. I would like to know if the breakpoint is located within an exon, and if so, which one so I can determine the MW of the protein that would be produced from that fragment.
Thanks!
Becky
Using information via NCBI on your gene of interest...using the complete mRNA and gene sequence includin information about exon and introns.
Dear Becky, please use "NCBI gene" (https://www.ncbi.nlm.nih.gov/gene/?term=ACTB). Plase the query about your target gene in search window. Click your gene and below the general information on the top you can find big interactive window with exon/intronic structure and chromosome sequence with numbers. It is very easy to find any sequence even by your eyes. But you can also use integrated module for sequence finding.
Next one. If you have any software for working with sequences, you can easyli find all locuses of mRNAs (all transcripts XM and NM) and place them on DNA sequence of the target gene to vizualise. Or use only locuses (with numbers only) sequences by your choice.
I hope it helps you.
Thank you for the responses! The gene that I am looking at has many isoforms
https://www.ncbi.nlm.nih.gov/gene/4781
so I am a bit confused in that case. I have a DNA sequence about 80-100nt long, and I would like to know where that sequence is. But it looks like the sequence is not in all of the isoforms. Is there a nucleotide search tool? I tried to just BLAST the sequence but it just says "NFIB" and does not include isoform information. Thanks again for the help!
determined by the sequence the promoter because location of promoter in initial of exon
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