Table 1 Low-complexity regions (LCRs) in monkeypox virus (MPXV) genome sequence 353R

From: Monkeypox virus genomic accordion strategies

Name	Location start^a	Location end^b	Repeat unit^c	Pattern^d	Nearest OPG^e	Type of LCR^f	Relative position to the OPG^g	Distance in bp^h	Copenhagen notationⁱ	Vaccinia virus (VACV) notation^j	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
LCR8	147,655	147,718	5 + 7		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.

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Table 1 Low-complexity regions (LCRs) in monkeypox virus (MPXV) genome sequence 353R

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