How to batch get/create all NCBI transcripts (NM_)

[ejwinter]

I am trying to create a repository of all ncbi transcripts (e.g. NM_000038.5) that contains all the exons (including UTRs and CDS ranges).

I was first surprised there is no such repository. I then tried to create my own using the mRNA_Prot and CCDS datasets but I found that the entries there don't match the entries in UCSC Genome Browser.

I hope someone can point me to such a repository or how I can use some available datasets to create a gff/gff3 with all features of the transcript defined.

Thank you,
Eric

[GenoMax]

Can you clarify if you are doing this for a specific genome (e.g. human) or for entire RefSeq?

If you only need human then how about using this: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ You will find additional genomes (and the gff files) at the top level link: ftp://ftp.ncbi.nlm.nih.gov/genomes/