Genome-wide changes in expression profile of murine endogenous retroviruses (MuERVs) in distant organs after burn injury

Lee, Young-Kwan; Chew, Alex; Fitzsimon, Lauren; Thomas, Rita; Greenhalgh, David; Cho, Kiho

doi:10.1186/1471-2164-8-440

Table 2 Genomic location, proviral size, primer binding site, and coding potential of putative MuERVs

From: Genome-wide changes in expression profile of murine endogenous retroviruses (MuERVs) in distant organs after burn injury

Virus	Contig number	Subsequence	Chr*	Orientation	Size (bp)	PBS **	*gag*	*pol*	*env*
^a L-1-1.4	NT_039267.6	2466483-2472149	4	+	5667	Q	P	P	-
^a L-1-1.8	NT_078575.5	18237577-18243244	8	+	5668	Q	P	P	-
L-1-2.8a	NT_039460.6	4167673-4158940	8	-	8734	Q	+	+	+
L-1-2.8b	NT_078575.5	12483528-12477141	8	-	6388	Q	+	P	P
L-1-2.9	NT_039472.6	28499787-28493004	9	-	6784	Q	-	+	+
L-1-2.14	NT_039606.6	27905917-27913739	14	+	7823	Q	P	+	+
L-1-2.19	NT_039687.6	54108037-54099311	19	-	8727	Q	+	+	+
^a L-3-2.4	NT_039267.6	3529917-3535228	4	+	5312	Q	+	P	P
^b L-3-9.5	NT_165760.1	8102397-8093731	5	-	8667	P	+	+	+
^b U-1-5.5a	NT_039305.6	7470573-7479554	5	+	8982	Q	P	+	+
^b U-1-5.5b	NT_109320.3	817587-826568	5	+	8982	Q	+	+	+
^b U-1-5.15	NT_039621.6	37681733-37674548	15	-	7186	Q	P	P	+
^b U-1-5.16	NT_039625.6	10813766-10804785	16	-	8982	Q	+	P	P
^b U-1-5.X	NT_039700.6	8642080-8651060	X	+	8981	Q	+	P	+
^b U-1-7.1	NT_078297.5	46243984-46253037	1	+	9054	Q	P	+	+
^a U-3-4.8	NT_078575.5	47244198-47236723	8	-	7476	Q	P	P	+
K-3-3.2	NT_039202.6	12947290-12938249	2	-	9042	Q	P	+	+
K-3-3.3a	NT_039240.6	16281352-16289068	3	+	7717	Q	+	P	P
K-3-3.3b	NT_039240.6	101357871-101366913	3	+	9043	Q	+	+	+
K-3-3.4	NT_109315.3	1334988-1327627	4	-	7362	Q	P	P	-
K-3-3.5a	NT_078458.5	8656480-8663841	5	+	7362	Q	P	P	-
K-3-3.5b	NT_039305.6	6544154-6553194	5	+	9039	Q	+	+	+
K-3-3.5c	NT_109320.3	32960612-32953147	5	-	7466	Q	P	P	-
K-3-3.10a	NT_039490.6	1628826-1619788	10	-	9039	Q	P	P	P
K-3-3.10b	NT_039492.6	15143818-15152862	10	+	9045	Q	+	+	+
K-3-3.11a	NT_096135.4	25877081-25869722	11	-	7360	Q	P	P	-
K-3-3.11b	NT_096135.4	41839881-41848925	11	+	9045	Q	+	+	+
K-3-3.11c	NT_096135.4	52173389-52182429	11	+	9041	Q	+	+	+
K-3-3.11d	NT_165773.1	14484140-14493181	11	+	9042	Q	P	P	+
K-3-3.13	NT_039578.6	10683833-10691619	13	+	7787	Q	+	+	P
K-3-5.13	NT_039589.6	14019544-14010858	13	-	8687	Q	+	+	+
^b K-3-6.4	NT_039258.6	12169957-12163352	4	-	6606	Q	P	P	P
^b K-3-6.5	NT_165760.1	9622092-9631063	5	+	8972	Q	+	P	P
^b K-3-6.6	NT_039343.6	25557034-25549676	6	-	7359	Q	+	P	P
^b K-3-6.7	NT_039428.6	4390808-4399848	7	+	9041	Q	+	+	+
^b K-3-6.8	NT_078575.5	50511987-50519348	8	+	7362	Q	+	P	P
^b K-3-6.12	NT_039551.6	28009046-28018086	12	+	9041	Q	P	+	+
K-4-11.1a	NT_039185.6	8055063-8060808	1	+	5746	Q	+	P	-
^c K-4-11.1b	NT_039189.6	8417864-8426844	1	+	8981	Q	+	P	P
K-4-11.2	NT_039206.6	34645399-34636419	2	-	8981	Q	+	+	+
K-4-11.4a	NT_039264.5	1995942-1986961	4	-	8982	Q	+	P	+
K-4-11.4b	NT_039264.5	8278820-8269838	4	-	8981	Q	+	+	+
K-4-11.7a	NT_039385.6	3682978-3673997	7	-	8982	Q	P	P	-
K-4-11.7b	NT_039413.6	9420528-9429226	7	+	8699	Q	+	+	P
K-4-11.7c	NT_039413.6	10493961-10502941	7	+	8981	Q	+	P	-
K-4-11.7d	NT_039433.6	34095286-34100959	7	+	5764	Q	P	P	P
K-4-11.10a	NT_039492.6	961582-954449	10	-	7134	Q	P	P	P
K-4-11.10b	NT_039492.6	33845187-33854167	10	+	8981	Q	+	+	+
K-4-11.11a	NT_039515.6	5820301-5829280	11	+	8980	Q	+	+	+
K-4-11.11b	NT_165773.1	297443-290657	11	-	6787	Q	+	P	+
K-4-11.12	NT_039548.6	17945382-17951142	12	+	5761	Q	P	P	-
K-4-11.13	NT_039590.6	6969427-6960447	13	-	8981	Q	+	P	+
K-4-11.19	NT_039687.6	31559507-31566568	19	+	7062	Q	P	P	-
K-4-11.X	NT_039706.6	194264-203244	X	+	8981	Q	+	+	+
^c U-4-8.1	NT_039185.6	26088376-26097356	1	+	8981	Q	+	P	+
^c U-4-8.5	NT_039324.6	798268-807248	5	+	8981	Q	P	+	+
^c U-4-8.11	NT_039515.6	3658394-3649425	11	-	8970	Q	+	P	+
^c U-4-8.18	NT_039678.6	472572-481451	18	+	8880	Q	P	+	+
^c U-4-11.1	NT_039185.6	14772777-14781433	1	+	8657	P	+	P	+

Putative MuERVs isolated with 100% homology with respective U3 probes: ^aIsolated in Burn/No Burn, ^bIsolated in No Burn, and ^cIsolated in Burn. The last number of putative MuERVs derived from the same U3 sequences indicates different chromosomal locations, and the letter next to this number represents different virus isolates. The coding potentials for retroviral polypeptides are indicated by ("+" intact/full-length), ("-" defective), and ("P" partial). * chromosome number, **primer binding site, P (tRNA^proline), and Q (tRNA^glutamine).

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ISSN: 1471-2164

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