What does a gene's "aligned length" represent in the NCBI gene database? I can understand that CDS length represents the length of the coding sequence (the number of amino acid residues + 1 and then multiplied by 3), but I really can't understand what aligned length is.
1 answer
It is the length of the transcript
In this case, yes. But really, it is the length of the transcript that aligns to the genome. For example, take a look at the human gene CDKN1C and the transcript NM_000076.2.
As you can see, the aligned length and sequence length are different here. If you look at the sequence of NM_000076.2 you will notice that this transcript has a polyA tail that does not _align_ to the genome. Hence the difference.
Manually curated RefSeq transcripts are based on a cDNA sequences that were submitted to GenBank. If one such sequence has a polyA tail, a curator can choose to retain it in the final RefSeq. Not all RefSeqs will have a polyA tail though.
The aligned sequence length and the transcript length can also differ when the RefSeq transcript sequence and the genome sequence are not completely identical.
Thanks a lot! That's very clear!
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Can you show us an example of where you see this?
Sure, I'll add a link. SNCA synuclein alpha Homo sapiens (human) If you put the mouse pointer on the transcript map of this gene (without clicking), you can see the "aligned length" information mentioned in my question. It would help me a lot if you could answer what this means. Thanks!
It's the length of the exons, compared to the genomic length which would be exon+intron, called the span in the hover menu.
It is the length of the transcript
Entry in GenBank/Nuccore
Corresponding entry in Ensembl
I see! Thanks a lot!