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Viewing gene records

Use the less command to view the file:

less -S gencode.v41.annotation.gff3

You can scroll around and have a look in there. You should see some metadata lines at the top (they start with #). They look like this:

##gff-version 3
#description: evidence-based annotation of the human genome (GRCh38), version 41 (Ensembl 107)
#provider: GENCODE
#contact: gencode-help@ebi.ac.uk
#format: gff3
#date: 2022-05-12
##sequence-region chr1 1 248956422

...and include information on the human genome assembly used (GRCh38, what's known as 'build 38') and other things.

This is followed by some data rows, that look like:

chr1    HAVANA  gene    11869   14409   .       +       .       ID=ENSG00000223972.5;gene_id=ENSG00000223972.>
chr1    HAVANA  transcript      11869   14409   .       +       .       ID=ENST00000456328.2;Parent=ENSG00000>
chr1    HAVANA  exon    11869   12227   .       +       .       ID=exon:ENST00000456328.2:1;Parent=ENST000004>
chr1    HAVANA  exon    12613   12721   .       +       .       ID=exon:ENST00000456328.2:2;Parent=ENST000004>

When you want to quit less, press q.

Tip

What's the -S for in that less command? Well try it without and you'll see:

less gencode.v41.annotation.gff3

The -S tells less to extend all the lines off the right of the screen - without it they wrap around which makes reading the file pretty difficult.

So, what does all that data mean? This file format is one of those annoying ones that includes no column names. To figure out what they mean, you have to look at the GFF3 specification. You can find this on the GENCODE site or a similar description on Ensembl.

Question

Look at the first 'gene' in the file. By manually looking at the file and comparing to the file specification, can you figure out:

  • which chromosome is it on?
  • which strand is it transcribed on?
  • what type of gene is it - is it protein-coding? (Hint: look for the gene_type attribute. It can be looked up in the list of biotypes.)
  • how many transcripts does the gene have?

Note that to answer this last question, you'll need to look at how the different rows in the file are related to each other. In short:

  • each row has an ID attribute
  • some rows also have a Parent attribute

these attributes make the records in the file into a tree. So conceptually the structure looks something like

            gene
           /    \      
 transcript1   transcript2  ...

i.e. each transcript has a parent gene - which means that it represents an observed or predicted RNA transcript of that gene. Transcripts themselves have exons - the parts of the transcript that actually make it to mature messenger RNA - so actually it is more like this:

             gene
            /    \      
  transcript1   transcript2  ...
   /      |      |       \
exon1  exon2    exon1    exon2
Question

There are also coding sequence records (type=CDS). Can you tell what these have as parents - exons, transcripts or genes?