Question about ASM track and genomic coordinates of ICRs in bosTau9

[Jéssica Macedo Rafael de Arruda]

Dear UCSC Genome Browser team,

My name is Jéssica, and I am a graduate student working with genomic imprinting in cattle. While exploring the bosTau9 assembly in the UCSC Genome Browser, I noticed the red peaks in the ASM track (Allele-Specific Methylation averaged across all samples in bosTau9).

Could you please clarify:

1. Do these ASM peaks represent candidate regions of allele-specific methylation that could correspond to known or potential Imprinting Control Regions (ICRs)?

2. Is there any way to obtain or view the genomic coordinates of catalogued ICRs directly through the UCSC Genome Browser?

3. Is there a direct annotation linking these peaks to experimentally validated ICRs, or are they only indicative of allele-specific methylation events?

Thank you very much for your attention and for maintaining such an important resource for the scientific community.

Best regards,
Jéssica M. Rafael Arruda
MSc student – UENF

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Jéssica Macedo Rafael de Arruda

Licenciada em Pedagogia e Ciências Biológicas

Especializada em Pedagogia Social / Alfabetização e Letramento

Mestranda em Biociências e Biotecnologia (UENF)

(28) 99988-4323

[Matthew Speir]

Hello, Jéssica.

Thank you for your question about ASM data in the UCSC Genome Browser. 

From your screenshot, it looks like you are using data from the MethBase2 track hub. This hub is maintained by the Smith Lab at USC: https://smithlabresearch.org. I've cc'd the PI, Andrew Smith, to see if he has any details to share about imprinting control region (ICR) data in the MethBase2 hub.

Additionally, you can always read the track description pages for more detail about how data were generated. You can access this by clicking the gray bar to the left of the track or by clicking the track name below the image:

I hope this is helpful. 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.

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Matthew Speir

UCSC Genome Browser, User Support

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