Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells

Table 1 List of candidate genes with TE-derived exons

Gene	TE ID and Location
Gene	TE	Location	Type of exon
PARP9	L1_Canid	Exon	constitutive
GBP1	L1M5	3’UTR	StringTie alternative; ncbi constitutive
DDX60	MER92B	3’UTR	constitutive
NLRC5	Multiple (3 TEs)	Alternative TSS, regulatory elements	constitutive
CS012	LTR10A_ML	3’UTR	StringTie alternative; ncbi constitutive
XAF1	L1MD	3’UTR	constitutive
SLFN5	Ves	E2 (5’UTR)	constitutive - truncated in some isoforms
IFITM2	LTR1D_ML	3’UTR	StringTie constitutive (missing in ncbi)
PLAT3	Ves2_ML	Last Exon + 3’UTR	constitutive
PLAT3	MLT1M	E2	constitutive
SP140L	L1-2a_EF	E7 - 3’UTR	alternative
SP140L	LTR18C_ML	E6 - 3’UTR	alternative

Transposable element (TE) exonization events were predicted by intersecting coordinates of annotated TEs and de-novo transcriptome assembly of RNA-seq data for Myotis lucifugus. Each candidate was inspected in our custom UCSC genome browser track (https://genome.ucsc.edu/s/GiuliaPasquesi/myoLuc2_HiC) and selected if it showed multiple lines of support (RNA expression, chromatin profile, additional gene/isoform annotation)

ISSN: 1759-8753