Description
This track collection shows Mobile Element Insertions (MEIs) in the
human genome. Mobile elements are stretches of DNA that have copied themselves
into new genomic locations during evolution, and a few families remain
active enough to keep producing new insertions in the human population
today. The three element classes responsible for almost all MEIs in
humans are Alu (~300 bp SINE retrotransposons), L1/LINE-1
(typically 6 kb autonomous retrotransposons) and SVA (composite
elements of ~700-3000 bp). Polymorphic MEIs - sites where some individuals
carry the inserted element while others do not - are an important source
of structural variation, can disrupt or alter gene expression, and have
been implicated in a number of human diseases.
Tracks in this collection report MEI calls from several sources: long-read
genome assemblies, short-read whole-genome sequencing, and curated
aggregations of published insertion calls. Items are colored by element
class. Because the callsets differ in cohort, sequencing technology and
caller, the same insertion site may be present in one subtrack and absent
from another.
Available subtracks
- HGSVC3 65 MEIs -
mobile element insertions identified in 65 diverse long-read
assembled samples relative to the reference assembly
(HGSVC3, Logsdon et al. 2025, Nature). Available on
both GRCh38/hg38 (12,642 MEIs) and T2T-CHM13/hs1 (12,919 MEIs).
- HMEID 5675 MEIs -
36,699 mobile element insertions called by MELT (Gardner et al.
2017) on 5,675 samples from the NyuWa Chinese cohort and the 1000
Genomes Project, with per-cohort and per-super-population allele
frequencies (Niu et al. 2022, Nucleic Acids Res). hg38 only.
- SweGen 1000 MEIs -
18,090 mobile element insertions called by MELT v2.0.2 on the
1,000 SweGen Swedish whole-genome samples (Ameur et al. 2017,
Eur J Hum Genet), lifted from GRCh37 to hg38. The
short-variant frequencies for the same cohort are in the
SweGen subtrack of
SNV Frequencies. hg38 only.
- euL1db Insertions -
curated L1-HS insertion polymorphisms aggregated from 32 published
studies covering 943 samples (euL1db, Mir et al. 2015,
Nucleic Acids Res), lifted from hg19. Available on hg19
and hg38.
- euL1db Ref L1HS -
the L1-HS copies already present in the reference genome, as
catalogued by euL1db from the RepeatMasker annotation. The
companion to the euL1db Insertions track. Available on hg19 and
hg38.
Related: Long-read Structural Variants
contains the parent SV callsets from which several of these MEI tracks
are derived. RepeatMasker shows
all annotated mobile elements in the reference genome (regardless of
whether they are polymorphic).
Display Conventions and Configuration
In the three insertion callsets (HGSVC3, HMEID and SweGen) each
MEI is shown as a 1-bp anchor block at the position where the insertion
attaches to the reference, colored by element class:
- Alu — SINE (Short INterspersed Element)
- L1 — LINE-1 (Long INterspersed Element-1)
- SVA (SINE-VNTR-Alu) — composite retrotransposon
- HERVK (Human Endogenous Retrovirus K) — endogenous retrovirus
- snRNA — small nuclear RNA
The two euL1db subtracks differ. Their items span real genomic intervals
rather than a 1-bp anchor, and they are colored on a different basis:
euL1db Insertions by the lineage of the contributing insertion calls
(germline, somatic, both, or unknown) and euL1db Ref L1HS by L1HS
sub-group. Each of those pages describes its own color scheme.
Filters available on the subtrack configuration page allow restricting
the displayed items by element class, insertion length, allele frequency,
number of carrier samples, the number of MEI callers that supported the
call, validation by L1ME-AID or PALMER, and overlap with reference
segmental duplications and tandem repeats.
Data Access
Each subtrack has its own description page with details on file location,
the autoSql schema, citation and download instructions.
References
Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri AK, Lundin P, Che H
et al.
SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish
population.
Eur J Hum Genet. 2017 Nov;25(11):1253-1260.
PMID: 28832569; PMC: PMC5765326
Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project
Consortium, Devine SE.
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.
Genome Res. 2017 Nov;27(11):1916-1929.
PMID: 28855259; PMC: PMC5668948
Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo
D et al.
Complex genetic variation in nearly complete human genomes.
Nature. 2025 Aug;644(8076):430-441.
PMID: 40702183; PMC: PMC12350169
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
Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T et al.
Characterizing mobile element insertions in 5675 genomes.
Nucleic Acids Res. 2022 Mar 21;50(5):2493-2508.
PMID: 35212372; PMC: PMC8934628