What does a gene's "aligned length" represent?
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9 months ago
Ethan Lee • 0

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.

alignment • 2.1k views
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Can you show us an example of where you see this?

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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!

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It's the length of the exons, compared to the genomic length which would be exon+intron, called the span in the hover menu.

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It is the length of the transcript

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Entry in GenBank/Nuccore

nuccore

Corresponding entry in Ensembl

Ensembl

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I see! Thanks a lot!

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9 months ago
vkkodali_ncbi ★ 3.7k

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. enter image description here

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.

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Thanks for the clarification. I guess would be somewhat dependent on submissions people have done. There being no poly-A in the genome after the end of alignable sequence.

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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.

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Thanks a lot! That's very clear!

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