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💡 Subfamily patterns:

- HERVK: Full polyproteins across several loci

- HERVH: Conserves enzymatic domains, but not structural

- HERVE: Unexpectedly retains protease & RT domains

Young and ancient families both preserve functional fragments!

🧵 3/
💻 Using a reproducible pipeline (HMMER + InterProScan), we identified 17,540 retroviral domains—incl. Gag, RT, RNase H, protease, integrase, and Env.

We then quantified alignment coverage to assess structural conservation.

We also revealed that the use of MALAT1 expression as a surrogate for nuclear content is a promising solution, particularly when raw intronic data is unavailable.
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For example, in the retina, rod cells divide in two groups: high-intronic and low-intronic fraction representing whole cells and nuclei-free cells, respectively.
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