Incorrect exon number in NCBI RefSeq (GRCh38)

[Alexis Praga]

Hi,

In GRCh38, SHANK3 is shown as having 25 exons on NCBI Refseq. Zooming in reveals exon 13 is actually a "micro-exon".

However, RefSeq with the same accession number has only 23 exons: https://www.ncbi.nlm.nih.gov/gene/85358. So it does not look like an alignment issues.

On NCBI, only one exon is shown

I'm aware of differences between UCSC and NCBI Refseq for SHANK3 ( https://groups.google.com/a/soe.ucsc.edu/g/genome/c/yMxAt00XVHs/m/I4vamnA7BwAJ ) but this happens on the NCBI Refseq track.

RefSeq helpdesk advised to see with you to get to the bottom of the matter so any pointer would be great

Thanks,

Alexis

[ale...@praga.dev]

Hi,

After exchanging with Refseq, they told me the transcript is fine but there are alignement issues in GRCh38 with the CDS of SHANK3.

Using a "fix" in the reference genome shows the proper number of exons ( chr22_KQ759762v2_fix:8917-69331 ).

This is actually the first result using the search for SHANK3.

Best,

Alexis

On 2025-05-08T23:12:39.000+02:00, Alexis Praga <alexis...@gmail.com> wrote:

Hi,

In GRCh38, SHANK3 is shown as having 25 exons on NCBI Refseq. Zooming in reveals exon 13 is actually a "micro-exon".

micro-exon.png

However, RefSeq with the same accession number has only 23 exons: https://www.ncbi.nlm.nih.gov/gene/85358. So it does not look like an alignment issues.

On NCBI, only one exon is shown

refseq.png

I'm aware of differences between UCSC and NCBI Refseq for SHANK3 ( https://groups.google.com/a/soe.ucsc.edu/g/genome/c/yMxAt00XVHs/m/I4vamnA7BwAJ ) but this happens on the NCBI Refseq track.

RefSeq helpdesk advised to see with you to get to the bottom of the matter so any pointer would be great

Thanks,

Alexis

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[Gerardo Perez]

Hello, Alexis.

Thank you for your interest in the UCSC Genome Browser and for your question regarding SHANK3.

We appreciate you reaching out to the RefSeq helpdesk and bringing the alignment issue with the SHANK3 CDS in hg38/GRCh38 to our attention. We can confirm that the alignment to the fix patch sequence chr22_KQ759762v2_fix:8,917–69,331 appears in the results and correctly displays 23 exons for SHANK3.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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