Hi all friends,
I have a dumb question, sorry for it. I focus on a gene with multiple transcripts from human, I want to know the position (start and stop points) of each transcript in the genomic sequence of the gene. Could you please help me what I can do?
Thank you
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seta
That information is contained in the annotation files (GTF or GFF) associated with the genome. For a single gene, it's probably easiest to use ENSEMBL's BioMart tool.
Ah, yea you can find gene information here too. The question was a little ambiguous, but if you are only interested in the positions of known or predicted genes for a genome, then the gtf is the way to go.
You can pull them from here: http://genome.ucsc.edu/cgi-bin/hgTables
For a single gene just search for it in Ensembl and then click on "show transcript table". To see the start and end you have to click on the Ensembl Transcript ID in the table.
Much faster than my answer. Thumbs up !
PS : in the end, not so fast depending on the number of alternative transcripts that you have to click one by one ^^
These are the links to the Ensembl annotation in GTF and GFF3. BioMart is available as a web interface. You can access it programmatically if you know R (biomaRt), through the (BioMart Perl API) and/or the BioMart RESTful access.
1) Get the data
2) Open it in Excel, R or whatever you like and substract the gene START and END to the transcripts START and END to get the position of transcripts relatively to the full gene. Done.
PS : Note that the START position is only the real start (like transcription start site) if the strand is +. When its on the minus strand, then the END position is the TSS.
Thank you for your complete response. I did it and all transcripts were on the minus strand. Just for making sure, with below information, please kindly tell me the position of "ENST00000346798" relative to the full gene.
Ensembl Gene ID Ensembl Transcript ID Gene Start (bp) Gene End (bp) Transcript Start (bp) Transcript End (bp) Strand
ENSG00000142192 ENST00000346798 25880550 26171128 25880550 26170654 -1
Thank you
What do you mean by "full gene"? The longest transcript? The most 5' and 3' transcript ends (which may be derived from different isoforms)? The most 5' and 3' exon endpoints?
Each annotation contains information for one transcript (including 5' and 3' UTRs) and corresponding coding sequence (gene). In your example, the transcript begins 474 nucleotides (26171128 - 26170654) before the gene, and both end at the same position (25880550).
I came to the same results with that gene and transcript.
I guess "full gene" is the most 5' and 3' transcript ends or at least this is my understanding of how genes are annotated.
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I assume you have a sam file of the alignments? Here is the pdf for the format: https://samtools.github.io/hts-specs/SAMv1.pdf
Column 4 holds position information of the aligned read, and length of the read can be obtained from column 10. This should be enough information to filter all reads from a given position on a genome.
Hope that helps!
This is not providing an answer for the question asked in the original post. I have moved this post to a comment.