NCBI retrieve genome assembly with splicing or "modifications"

Question

I am trying to fetch genome assemblies that include splicing information.
E.g. Here, is a genome assembly of a yeast, where genes show variants like this: join(5928..7626,7685..7785,7857..7982).

I am retrieving the information from NCBI with the following commands:
efetch -db nuccore -id CP003820.1 -format tabular. I tried different formats and it changes but I don't get the join(...)

1) Am I correct and the join(...) indicates "splicing-like" modifications in yeast?
2) How can I get the join(...) (any other format is fine too) with efetch?

Answer 1

The page you link to is a GenBank Flat file, the default format used by GenBank. So, to get that format, which includes the join lines, use:

./efetch -db nuccore -id CP003820.1 -format gb

The join() lines give the different ways in which a sequence can be built from this gene. For example, one mRNA sequence produced by the locus you mention (CP003820) is:

  mRNA            complement(join(100..1497,1556..1767,1823..2274,
                 2322..2782,2846..3126,3206..3890,3958..5263,5322..5422,
                 5494..>5645))

The corresponding coding sequence is for the mRNA above is:

 CDS             complement(join(168..1497,1556..1767,1823..2274,
                 2322..2782,2846..3126,3206..3890,3958..5263,5322..5422,
                 5494..5645))

These aren't necessarily splicing "modifications", and aren't "variants", they are simply the way that the exons are joined to make an mRNA.

Note that since CP003820.1 is "Cryptococcus neoformans var. grubii H99 chromosome 1, complete sequence", there are multiple genes described in there and each will have its own (or multiple, if there is alternative splicing) join statements. Specifically, I see 1014 genes described in the file:

$ grep -Pc '^\s+gene\s+' CP003820.gb 
1014

950 mRNAs:

$ grep -c 'mRNA.*join(' CP003820.gb 
950

And 955 proteins:

$ grep -Pc 'protein_id=' CP003820.gb 
955