Why does Txdb transcript length not always match to transcript end-start position?

Question

[Sora Yoon]

I have just found an example that biomart's transcript_length is not identical with transcript_end - transcript_start.

ensembl_gene_id mgi_symbol chromosome_name strand start_position end_position   gene_biotype transcript_start transcript_end strand.1 transcript_length
128537 ENSMUSG00000037860       Aim2               1      1      173178445    173293606 protein_coding        173178445      173293606        1              2839
128538 ENSMUSG00000037860       Aim2               1      1      173178445    173293606 protein_coding        173246762      173255347        1               383
128539 ENSMUSG00000037860       Aim2               1      1      173178445    173293606 protein_coding        173248164      173287285        1               744

Does anyone know why such discrepancy happen??

Thanks

Answer 1

[Pierre Lindenbaum]

Does anyone know why such discrepancy happen??

Life

[Sora Yoon]

Thanks. Then, it means that a great portion is intron in Aim2 gene.

[i.sudbery]

Yes, this is almost always the case. Exons make up 2% of the human genome, but transcripts, including introns, cover 40% of the human genome (ref)

Answer 2

[i.sudbery]

transcript_end - transcript_start encompases the full length of the genomic region associated with the transcript, including intronic sequence, where as "transcript" length is the length of the mature RNA transcript (i.e. just the length of the exonic sequences, after removal of the introns by splicing).

[Sora Yoon]

Thanks, that makes sense!!