I have chromosome position (chr14:23851239) and also know the gene. But I want to know that in which intron or exon that particular variation. Is there any software or online database which can help in this regard?
Please help.
http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr14%3A23850651-23880223&hgsid=198356835_KQgEgMD1bqGWf8ufl6qGMdr7Td8O
http://www.ncbi.nlm.nih.gov/nuccore/289803014?report=graph
http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000197616;r=14:23381990-23408277;t=ENST00000405093
Hi Amitabh,
Here is a link for the position of the different exons on MYH6 cDNA.
http://www.ncbi.nlm.nih.gov/nuccore/NM_002471.3
So you can copy FASTA sequence on a word file and color the different exons using different colors.
Then you pick the entire MYH6 qDNA sequence and seek for the different exon. Then you will have exon and intron on your MYH6 sequence and by similarities you will be able to identify your variation.
It's not the easy I know but it works.
Good luck,
Sami
You can get the entire gene sequence or the mRNA sequence from NCBI. NCBI also has exon and intron information but may be a little confusing. You can paste the mRNA sequence in the program called BLAT (https://genome.ucsc.edu/cgi-bin/hgBlat?command=start ) on UCSC genome browser. you will get a 100% match on chr14 which corresponds to your region of interest. UCSC BLAT results are displayed as intronic and exonic sequences. here is the BLAT results for the mRNA of MYH6. regions in blue are exonic regions.
https://genome.ucsc.edu/cgi-bin/hgc?o=23851198&g=htcUserAli&i=../trash/hgSs/hgSs_genome_48d1_4ea1c0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_48d1_4ea1c0.fa+YourSeq&c=chr14&l=23851198&r=23876449&db=hg19&hgsid=384813791_x7oDhunqKcrYDeI2har0Ym1jAf2M
Thanks for the answers and help.
I can find manually exon and intron number of the gene through ensembl or ncbi or ucsc but my concern for this question is that if any software available where i can just enter the two information which i have is chr number and position and get the information of that locus like, which exon/intron etc??
thanks
Go for NCBI's 1000 genome. Identify the location. Moreover you can go to ensemble.org and search the name of the gene you are searching. Go the sequence and you will get the entire sequence of the gene. There you can find out the exact location by copying from the 1000 genome location (some 10 nucleotides) and finding in the ensemple.
Yes the exact location you need to find out manually.
Although you can easily find out through nucleotide search in NCBI's home page.
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/
Your position chr14:23851239 in NCBI's current assembly GRCh38 is within a gene-free section between DHRS2 (~23.6 Mbp) and DHRS4 (~23.9 Mbp). Other assemblies will vary, even within NCBI.
Someone mentioned MYH6 (~23.4 Mbp in GRCh38). Is that your gene? It seems almost always to have 37 exons, except when mutated. COL11A1 (for one) exhibits alternate splicing, and can make mRNA using either 66 or 67 exons.
So absolute address variability and alternative splicing really make it impossible to get just one answer to questions of this type, whether by hand or by program.
Thanks to all of you for the answer and suggestions,
Dear Jie Li, Thanks for your suggestion, it might be helpful, if i could make such algorithm but I am not a computer application person that's why posted this question in this forum.
Dear Michael,
Yes there is update of databases, but the gene is MYH6 only, as compared to previous database hg18. It was just an example, Actually I am more concerned about finding which gene, exon or intro that mutation is present and if exon what will be the amino acid change if I have any chromosome location and chromosome number, rather going manually there is some software available or not.
Thanks
In my case I used the Integrative Genomic Viewer (IGV). It is a software that is available online for free. You can navigate by writing the chromosome location and the position such as (chr14:23851239) in your case, then you will have a look where the SNP's position on the gene.
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