Question: Difference Between Ensembl Translated Exons And Exons?
1
gravatar for user
5.0 years ago by
user770
United States
user770 wrote:

I'm trying to figure out what Ensembl means by translated exons, when these are annotated for a gene based on Ensembl API. I notice that the translated exons associated with a transcript are sometimes different from the exons in the transcript. Why is that? Why aren't the translated exons of a transcript a strict subset of the exons in the transcript? Thanks.

ensembl annotation ucsc • 2.0k views
ADD COMMENTlink written 5.0 years ago by user770
1

can you provide a specific example - a pair of links in Ensembl?

ADD REPLYlink written 5.0 years ago by Jeremy Leipzig17k
5
gravatar for Malachi Griffith
5.0 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith15k wrote:

Similar to JC's answer.

In some gene annotation schemes a distinction is made between: (1) exon coordinates of a transcript without regard to coding, and (2) exon coordinates for only the coding portion (i.e. the translated portion).

If the ORF starts within the boundaries of an exon (not right at the beginning), and you represent the coding/translated blocks independently of the exon blocks, you will have the first and last coding exon sharing one but not two coordinates with transcript exons. For all internal exons the coordinates will match up.

This concept, used in Ensembl is similar to that of the GTF file format. Perhaps examining the coordinates of a simple gene in GTF format will be helpful. Four types of coordinate blocks are defined: 'exon' (full exon), 'CDS' (coding portion of exon), 'start' (start codon), and 'stop' (stop codon). Note how for exons 1 and 6 the coordinates for 'exon' and 'CDS' match at only one end. For exons 2-5, the coordinates for 'exon' and 'CDS' match at both ends.

chr3 hg19_refGene exon  124449213 124449474 0 + . exon "1"; gene_id "NM_000373";
chr3 hg19_refGene CDS   124449319 124449474 0 + 0 exon "1"; gene_id "NM_000373";
chr3 hg19_refGene start 124449319 124449321 0 + . exon "1"; gene_id "NM_000373";
chr3 hg19_refGene CDS   124453940 124454093 0 + 0 exon "2"; gene_id "NM_000373";
chr3 hg19_refGene exon  124453940 124454093 0 + . exon "2"; gene_id "NM_000373";
chr3 hg19_refGene CDS   124456415 124457086 0 + 2 exon "3"; gene_id "NM_000373";
chr3 hg19_refGene exon  124456415 124457086 0 + . exon "3"; gene_id "NM_000373";
chr3 hg19_refGene CDS   124458871 124459046 0 + 2 exon "4"; gene_id "NM_000373";
chr3 hg19_refGene exon  124458871 124459046 0 + . exon "4"; gene_id "NM_000373";
chr3 hg19_refGene CDS   124460999 124461113 0 + 0 exon "5"; gene_id "NM_000373";
chr3 hg19_refGene exon  124460999 124461113 0 + . exon "5"; gene_id "NM_000373";
chr3 hg19_refGene CDS   124462762 124462928 0 + 2 exon "6"; gene_id "NM_000373";
chr3 hg19_refGene stop  124462929 124462931 0 + . exon "6"; gene_id "NM_000373";
chr3 hg19_refGene exon  124462762 124468119 0 + . exon "6"; gene_id "NM_000373";
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Malachi Griffith15k
3
gravatar for Jeremy Leipzig
5.0 years ago by
Philadelphia, PA
Jeremy Leipzig17k wrote:

5' and 3' UTRs are considered exonic because they are not explicitly spliced out.

enter image description here

ADD COMMENTlink written 5.0 years ago by Jeremy Leipzig17k
0
gravatar for JC
5.0 years ago by
JC6.2k
Mexico
JC6.2k wrote:

Because biology says that. When a gene is transcribed, a typical mRNA includes the coding exons and other segments as signals and regulatory elements. Those elements are not transcribed into protein, but are exonic elements too.

ADD COMMENTlink written 5.0 years ago by JC6.2k

No. The case I'm referring to is one where the exons that are translated share one but not two coordinates with an exon in the transcript. The transcript is coding. How do you explain this?

ADD REPLYlink written 5.0 years ago by user770

exon skiping? can you give more details and Ensembl IDs

ADD REPLYlink written 5.0 years ago by JC6.2k
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