The UCSC Repeat Browser lifts sequence from a repeat region annotated by RepeatMasker on the human genome to the Dfam consensus of that repeat family. Occasionally there is not a Dfam consensus for the RepeatMasker annotation. This can occur for several reasons:
- RepeatMasker builds the full annotation from smaller subparts of elements (e.g. some LINE elements are built from 5′, 3′ and ORF regions). In these cases, we have built our own consensus and lifed from the genomic instance to our consensus. Please see the Sequences page for a full list of Dfam & Repeat Browser sequences.
- RepeatMasker assigns the annotation to a larger group instead of a specific family. For instance many elements receive a general “Alu” classification instead of a specific subfamily (e.g. AluYc5, AluYa8). In this case we built a consensus, but it should be taken with a mound of salt. It represents a “consensus” of elements that RepeatMasker was not able to assign to a specific family.
- Occasionally the nomenclature changes between RepeatMasker and Dfam. For instance, HERVI-int in RepeatMasker is HERVI in Dfam. In these cases, we simply use the key on the Sequences page.
- A few RepeatMasker elements use a single Dfam consensus (e.g. MLT1F-int in Dfam and RepeatBrowser is the consensus sequence for multiple RepeatMasker annotations: MLT1F2-int, MLT1F-int, MLT1E2-int, MLT1F1-int, MLT1E1A-int, MLT1E1-int, MLT1E3-int, MLT1E-int, MLT1M-int).