Mitochondrial DNA-like sequences in the nucleus (NUMTs)1

Chromosome 1

Celera Scaffold and Genbank accession numbers are indicated for each NUMT-containing contig. Nucleotide positions of NUMTs in contigs are color-coded according to the analyzed contig. To avoid redundancy, when both Celera and Genbank contigs are available for a given NUMT, repeat information is provided for one of the contig types. (1A): 1 NUMT within a repeated element in the corresponding contig; (1B): 1 NUMT within 1-15bp of a repetitive element in the corresponding contig; (1C): 1 NUMT 15-150bp away from a repetitive element in the corresponding contig; (1D): 1 NUMT more than 150bp away from a repetitive element; (1E): 1 NUMT solely truncated by repeats in the corresponding contig. {39% GC} � average GC content in 100 KB region encompassing the NUMT or NUMTs.

Map	Band Type	Celera Scaffold and Genbank accession numbers	Position in the Contig	% similarity	Region of similarity to Cambridge sequence
1p36.3 (1C)	R {39%GC}	GA_x5J8B7P0VAE:1..500000 Also in Genbank: AL663100.12	402617-402926 403225-403024 403234-403437	82	!AluY 910-1123 Charlie4a(Mer1)
1p36.3 (1D)	R {50%GC}	GA_x5J8B7P0VAE:4000001..4500000 Also in Genbank: AL356693.37	134519-134728	90	2466-2675
1p36.3 (1B)	R {45%GC}	GA_x5J8B7P0VAE:1000001..1500000 Also in Genbank: AL139415.10	67560-67686 67760-67922 67938-68046 68227-68065 68234-68291 68292-68600 68601-68612 68613-68738 68739-68962		L2(np2481-2611) !AluSx L2(np2725-2833) 8040-8202 LTR16A(np442-385) !AluSc !LTR16A(np385-373) !L1PB2 !LTR16A(np374-145)
1p34.3 (1D)	R {43.5% GC}	GA_x5L2HTVAVSK:8500001..9000000 Also in Genbank: AL513220.9	488658-488731	100	8934-9007
1p32 (15q26) (1A)	R (R) {38%GC}	GA_x54KRE9971S:1..3319 AL645730.10	2-358 364-751 77023-77460 77459-77868 77874-78236	78   77	4666-5022 L1Pa15 L1PA5(np5360-5801) 4612-5022 L1PA5(np5782-6133)
1p31 (1C)	G {35% GC}	GA_x5HB7VCJ5FA:3500001..4000000 Also in Genbank: AC096951.2	467872-467706 467904-467988	89	16401-16567 L1ME
1p13 (1D)	R (35% GC}	AL627169.8	10559-7110	74	5855-9316
1p22 (1B)	R {40% GC)	AL117351.12	45203-45528 45584-45700 45702-47060 47060-47390 47385-48225 48227-49037 49037-49172 49190-49513 49502-49721 49726-49781 49782-50095 50096-50418 50419-50460 50461-54817 54818-55160 55161-55991 55921-56076   56087-56345 56354-56450   56441-56831 56881-56954   56958-57257 57258-57351   57354-57510   57560-58050 58035-58076   58095-58268   58350-58558 58612-59265 59337-59470 59607-59910 59910-60877   60882-61158 61164-61193 61190-61485 61485-61693   61703-62490     62052-62075 62508-62625 62639-62666 62689-62756 62757-63055 63052-63280	69       66   75 68             71 75       75   70 77     65   80   67 88   70     70   69       72 67   73           78 72	L1ME AT_Rich 1721-3106 Tigger1(Mer2type_np 2418-2082) Tigger1(Mer2type_np 1766-910) 4572-5438 (blue whale mtDNA NC_001601.1) FLAM_C(Alu) 5566-5892 5767-5990(blue whale mtDNA NC_001601.1) !L1PB1 (np6151-6096) !AluSx !L1PB1 (np6096-5774) (TA)n !L1PB1 (np5774-1436) MSTA(LTR/MaLR) 6841-7680 7065-7226(CO2) (NC_001779.1, Rhinoceros mtDNA) AluSq 4530-4620 (NC_001950.1, mtDNA of spotted catshark) 7863-8246 7753-7826 (NC_001779.1, Rhinoceros mtDNA) !AluJb 7768-7861 (NC_001665.1, Rat mtDNA) 7924-8071 (NC_001779.1, Rhinoceros mtDNA) 8688-9191 8579-8620 (NC_002009.1 Fruit eating bat mtDNA) 8697-8875 (NC_001821.1armadillo mtDNA) !AluJb 9921-10579 FLAM_A(Alu) !AluJb 10915-11904 (blue whale mtDNA NC_001601.1) !AluSx (CAAAA)n 12032-12340 12665-12897 (NC_001602.1 mtDNA of the gray seal) XM_015980.4 (Human 16.7Kd protein-removed from Genbank) (CAG)n FLAM_C(Alu) (A)n 12586-12653 !AluSx 12639-12875
1p11 (1B)	Centromere {39% GC}	AC022192.3	103004-103534 103535-103832 103833-103886 104418-103878 104487-104441 105835-104485 105846-106807 106584-106643 106810-107498	82 80 74 73	SATR1(np969-492) !AluY SATR1(np492-1) 987-1534 15042-15087 5604-6979 9394-10319 (TA)n SATR1(np779-1)
1q12 (1B)	Grey {42% GC}	GA_x54KRE8AV33:1..500000 Also in Genbank: AC068398.3	79526-79415 14706-15623 16596-15626 15791-15850 16595-17950 18017-18555 18548-18581NNN	88 74 74 83	6870-6981 SATR1(np1-1028) 9386-10319 (TA)n 5596-6979 987-1526 SATR1(np216-250)
1q24 (1C)	G {40% GC}	GA_x54KRE8EL5L:6500001..7000000 Also in Genbank:AL160059.7	290898-291033 291093-291486 291598-291644 291662-291724	76	MIR(np82-226) 12143-12536 MIR(np216-262)MIR3
1q43 (1B)	G(39% GC}	GA_x5J8B7NYNCY:4000001..4500000 Also in Genbank: AL590396.13	299067-309581 42076-42201 42298-42371 48098-42476 48101-48143 48613-48705 49016-48776 53428-49033	81   78   70 72	12562-6189 MER117(Mer1_type) MIR 573-6196 (TA)n (CGTG)n 12-244 12156-16563
1q43 (1B; 1A)	G {43% GC}	GA_x5J8B7NYNCY:6500001..7000000 Also in Genbank:AL451068.13	219597-224583 241914-241006 112001-112272 112298-112442 112436-113344 113336-113344 113345-113426 113427-113469 129666-129714 129744-12980 134797-129811 134814-135001	74 71 71         74	9771-14799 14796-15722 AluJo THE1b(LTR/MaLR) 14796-15722 (CATATA)n !L1PA17 (CATATA)n Alu !AluSx (np290-233) 9771-14799 !AluSx (np249-62)

1 Data from Supplemental material, Mishmar, D., Ruiz-Pesini, E., Brandon, M., and Wallace, D.C. 2004. Mitochondrial DNA-like sequences in the nucleus (NUMTs): insights into our African origins and the mechanism of foreign DNA integration. Human Mutation 23(2):125-133.