Ac	long interspersed nucleotide element
AID	activation-induced deaminase
AP	apurinic
BER	base excision repair
BFB	breakage-fusion-bridge cycle
CDS	coding sequence
CDT	cytolethal distending toxin
CNV	copy number variation
CRISPR	clustered regularly interspaced short palindromic repeats
DDR	DNA damage response
DGR	diversity-generating retroelement
dPRL	decidual prolactin
Ds	Dissociator transposon
DSB	double-strand break
ENV	envelope protein (retrovirus)
ERV	endogenous retrovirus
ESC	embryonic stem cell
HERV/hERV	human ERV
HGT	horizontal gene transfer
HR	homologous recombination
Indel	insertion plus deletion
IPSC	induced pluripotent stem cell
IR	inverted repeat
lincRNA	long intergenic non-coding RNA
LINE	long interspersed nucleotide element
lncRNA	long non-coding RNA
LSG	lineage-specific gene
LTRs	long terminal repeats
MaLR	mammalian apparent LTR-retrotransposon
MER	mammalian endogenous repeat
mERV	mouse endogenous retrovirus
MIR	mammalian-wide interspersed repeat
miRNA	microRNA
MMR	mutagenic mismatch repair
mRNA	messenger RNA
MT	mouse transposon
NAHR	non-allelic homologous recombination
NCLDV	nucleocytoplasmic large DNA virus
NEE	novel enriched environment
NER	nucleotide excision repair
NGE	natural genetic engineering
NHEJ	non-homologous end-joining
ORF	open reading frame
ORR	origin region repeat
RAG	recombination-activating gene, transposase activity needed for V(D)J recombination in adaptive immunity
RIDL	repeat insertion domains of lncRNA
RLEs	retrovirus-like elements
ROS	reactive oxygen species
SINE	short interspersed nucleotide element
SOS	DNA damage signal-inducible repair response in bacteria
SSB	single-strand break
SSR	simple sequence repeat
SVA	a hominid retrotransposon containing SINE, VNTR and Alu components
TE	transposable element
WGD	whole genome duplication