This track shows the L1-HS (human-specific LINE-1) retrotransposon copies that are already present in the human reference genome, as catalogued by euL1db. Unlike the companion euL1db Insertions track, which shows polymorphic insertions not present (or variably present) in the reference, the items here are the L1-HS copies that the reference genome already contains. Together, the two tracks provide a comprehensive view of L1-HS positions in the genome — both the "fixed" reference set and the variants segregating in the human population.
Each item is a single reference L1-HS element. The name shows the L1HS sub-group. Items are coloured by sub-group:
L1HS-Ta — youngest, currently active L1-HS subset
L1HS-PreTa — older L1-HS subset, ancestral to Ta
L1HS-undef — sub-group not assigned in euL1db
The detail page for each element shows the element length, its integrity (full-length, 5′-truncated, 3′-truncated, internal_fragment), and its position on the L1HS consensus sequence. Filters are provided for sub-group and integrity.
The reference L1-HS catalogue was assembled by the euL1db curators by aligning the L1HS consensus sequence to the hg19 reference genome and classifying each match into one of the L1HS sub-groups. See Mir et al. 2015 for further details.
Track files were generated from the euL1db v1.00 ReferenceL1HS.txt table (data dump downloaded March 2018) using the script meiEul1dbRefToBed.py. The hg19 BED was lifted to hg38 with liftOver; of 1,544 hg19 elements, 1,540 lifted successfully. For details see hg19/mei.txt and the scripts directory src/hg/makeDb/scripts/mei.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our REST API, track=meiEul1dbRef.
For automated download and analysis, the annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called eul1dbRef.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed.
The original annotation source data can be downloaded from eul1db.unice.fr via the Download tab.
Thanks to Gaël Cristofari and colleagues at IRCAN (Nice, France) for making the euL1db data freely available. Track built at UCSC by the Genome Browser group.
Mir AA, Philippe C, Cristofari G. euL1db: the European database of L1HS retrotransposon insertions in humans. Nucleic Acids Res. 2015 Jan;43(Database issue):D43-7. PMID: 25352549; PMC: PMC4383891