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Definition of the different DNA regions
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Nancy M. Bennetts ?
Definition of the different DNA regions
We can take a look at the following picture (from wikipedia):
The regions are then:
intergenic: everything outside of the shown gene region
<5 Kb downstream: outside of the transcribed region, but possibly part of the promoter or an enhancer (yellow boxes before coding region).
UTR 5′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box before coding region).
intronic: In the Introns, as shown in the picture (grey boxes)
intragenic: These have to be mutations inside the coding region (red boxes), which is confusing since the authors specifically describe them as 'non-coding' mutations. If you read that as 'mutations that don't change the protein sequence', these could be silent mutations
UTR 3′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box after coding region)
<5 Kb upstream: outside of the transcribed region, but possibly part of an enhancer (yellow boxes after coding region)
We can take a look at the following picture (from wikipedia):
The regions are then:
intergenic: everything outside of the shown gene region
<5 Kb downstream: outside of the transcribed region, but possibly part of the promoter or an enhancer (yellow boxes before coding region).
UTR 5′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box before coding region).
intronic: In the Introns, as shown in the picture (grey boxes)
intragenic: These have to be mutations inside the coding region (red boxes), which is confusing since the authors specifically describe them as 'non-coding' mutations. If you read that as 'mutations that don't change the protein sequence', these could be silent mutations
UTR 3′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box after coding region)
<5 Kb upstream: outside of the transcribed region, but possibly part of an enhancer (yellow boxes after coding region)
The Sequence Ontology project defines an intragenic variant as "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." source
Intragenic means the variant is located within the same gene, which only implies that the sequence analysis assigned a certain variant to a gene. So, there is incomplete data regarding the gene product (such as different splice forms).
The Sequence Ontology project defines an intragenic variant as "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." source
Intragenic means the variant is located within the same gene, which only implies that the sequence analysis assigned a certain variant to a gene. So, there is incomplete data regarding the gene product (such as different splice forms).
We can take a look at the following picture (from wikipedia):
The regions are then:
We can take a look at the following picture (from wikipedia):
The regions are then:
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You can look up the mutation locations here: http://grch37.ensembl.org/index.html
You can look up the mutation locations here: http://grch37.ensembl.org/index.html
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The Sequence Ontology project defines an intragenic variant as "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." source
Intragenic means the variant is located within the same gene, which only implies that the sequence analysis assigned a certain variant to a gene. So, there is incomplete data regarding the gene product (such as different splice forms).
The Sequence Ontology project defines an intragenic variant as "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." source
Intragenic means the variant is located within the same gene, which only implies that the sequence analysis assigned a certain variant to a gene. So, there is incomplete data regarding the gene product (such as different splice forms).
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