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. 2024 Apr 18;15:3059. doi: 10.1038/s41467-024-46949-7

Table 1.

Low-complexity regions (LCRs) in monkeypox virus (MPXV) genome sequence 353R

Name Location starta Location endb Repeat unitc Patternd Nearest OPGe Type of LCRf Relative position to the OPGg Distance in bph Copenhagen notationi Vaccinia virus (VACV) notationj Comments
LCR1 5369 5624 16 [AACTAACTTATGACTT]n OPG003 (ITR) STR Downstream 72 Cop-C19L NA
LCR1 5369 5624 16 [AACTAACTTATGACTT]n OPG015 (ITR) STR Upstream 35 CPXV-017 NA
LCR2 174,063 174,112 2 [ATAT]n NA STR Downstream 46 Cop-B16R B14R
LCR3 179,872 180,345 9 ATAT [ACATTATAT]n OPG208 STR ATG Start/Promoter 21 Cop-K2L B19R SPI-1 apoptosis inhibition
LCR4 193,504 193,759 16 [AAGTCATAAGTTAGTT]n OPG003 (ITR) STR Downstream 72 Cop-C19L NA
LCR4 193,504 193,759 16 [AAGTCATAAGTTAGTT]n OPG015 (LITR) STR Upstream 35 CPXV-017 NA
LCR5 133,895 133,918 1 [T]n MPXVgp137 homopolymer Upstream 889 Cop-A25L A27L Fragmented gene area
LCR6 133,980 133,989 10 [CAATCTTTCT]n MPXVgp137 STR Upstream 818 Cop-A25L A27L
LCR7 137,319 137,375 3 [ATC]n OPG153 STR Inside ORF NA Cop-A28L A26L Attachment MVs/laminin
LCR8 147,655 147,718 5 + 7 [ATATTTT]n [ATTTT]n [ATATTTT]n [ATTTT]n [ATATTTT]n [ATTTT]n [ATATTTT]n OPG171 STR Upstream 75 Cop-A42R A42R
OPG170 STR Upstream 70 Cop-A41L A41L
LCR9 151,350 151,417 9 [TATGAAG]n [GATATGAT]n [GATATGATG]n [GATATGAT]n OPG176 STR Upstream 12 Cop-A46R A47R
LCR10 197,830 197,842 1 [T]n OPG001 (ITR) homopolymer Downstream 225 NA NA
LCR11 1286 1298 1 [T]n OPG001 (ITR) homopolymer Downstream 225 NA NA
LCR12 29,326 29,364 1 [A]n OPG044 homopolymer Inside ORF NA Cop-K7R B15R C-terminal position
LCR13 76,896 76,904 1 [T]n OPG097 homopolymer Inside ORF NA Cop-L3L/L4R L3L/L4R
LCR14 81,658 81,666 1 [T]n OPG104 homopolymer Inside ORF NA Cop-J5L L5L Essential for viral replication
LCR15 140,911 140,977 9 [ATAACAATT]n [ATAATTGTT]n [ATAATAATT]n [ATAATTGTT]n OPG159 STR Inside ORF NA Cop-A31L A33L PKR inhibitor candidate? / C-terminal position
LCR16 153,457 153,465 1 [A]n OPG180 homopolymer Upstream 15 Cop-A50R A50R
LCR17 163,979 164,003 4 [TAAC]n OPG188 STR Downstream 82 Cop-B2R B4R
LCR18 166,865 166,920 7 [AATAATT]n OPG190 STR Downstream 15 Cop-B5R B6R
LCR19 170,508 170,563 6 [GATACA]n OPG197 STR Inside ORF NA Cop-B11R B11R Hypothetical protein
LCR20 172,868 172,876 1 [T]n OPG199 homopolymer Downstream 56 Cop-K2L SPI-2/B12R
LCR21 175,299 175,357 6 [GATGAA]n OPG204 STR ATG Start/Promoter NA Cop-B19R B16R Alternative ATG repeat start

Short tandem repeats (STRs) are described using nucleotide base-pair coordinates with reference to the high-quality genome (HQG) sequence (ENA Accession #OX044336). Listed are the number of repeat units, description of the sequence (with n = number of repeats for this particular genome), identification of the nearest annotated orthologous poxvirus gene (OPG), type of LCR (STR or homopolymer), position of the LCR to the nearest gene, and distance of the LCR to the nearest gene. OPG notations follow the standardized nomenclature32; vaccinia virus (VACV) Copenhagen strain and classical VACV gene notations are shown in addition to enable comparisons. NA not applicable.

anucleotide base coordinate in reference HQG (Genbank #OX044336).

bnucleotide base coordinate in reference HQG (Genbank #OX044336).

cnumber of repeat units in the HQG (Genbank #OX044336).

ddescription of the pattern of the LCR in representative MPXV, in which n is the number of repeats for this particular genome.

eidentification according to Senkevich et al. of nearest identified gene; new notation.

ftype of LCR: short tandem repeats or homopolymer.

gposition of the LCR to the nearest gene.

hdistance of the LCR to the nearest gene.

inotation of the gene in the VACV Copenhagen strain.

jnotation of the gene in the VACV Western Reserve strain.