Spreadsheet: 0507db5b-e666-4115-bd89-76b0a88fadd8
Sheet: Sheet1

Supplementary data | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14
Table 1. Chimpanzee-specific L1 insertion-mediated deletion loci in Han et al. 2005b
Name | Forward primera | Reverse primera | HS reverse primerb | A. T.c | Chr. loc. in chimpanzeed | Human Size | Chimp Size | L1 familye | L1 size (bp) | Deletion size (bp) | L1 features | Genes ± 2MB | Genes ± 1MB | Genes ± 0.25MB
LC1 | GGACTGAATCCTTATGGGATATAAAA | CCTGGCAAAACCTTAAATACATCT |  | 57.9 | chr10:104399299-104401507 | 197 | 800/198 | L1PA2 | 609 | 8 | 5' truncation | 36 | 12 | 4
LC3 | TTGGAAGTACAGGATACCAGCA | AGCCATTCCCTACACATACCTC |  | 60 | chr11:55834359-55836471 | 187 | 697 | L1PA2 | 525 | 15 | 5' truncation | 19 | 12 | 0
LC4 | CACATGGTTTGGTTTTCAAGTTT | GGCTTTGGTATGAGAATGATGC† | TGATAGAATTAGAATATGCTCAACGTG | 60 | chr14:74886199-74890106 | 828 | 454 | L1PA2‡ | 2993 | 683 | 5' truncation | 4 | 2 | 6
LC5 | CTGGTTGATGCAGTCCTCAGA | TTGGGAACCACTGGTATGGTAT |  | 60 | chr14:94032570-94034007 | 667 | 505 | L1PA2 | 403 | 565 | 5' truncation | 30 | 17 | 2
LC7 | GGAGGGGACATGCTTTACTTTA | ATGTTGCCTCATCCTTACAAGC |  | 60 | chr15:46267027-46268760 | 253 | 379 | L1PA2 | 139 | 13 | 5' truncation | 4 | 3 | 1
LC8 | CTATTAGCACACAAAGCCAGCA | CCTGCATACCATAGGCTCTTCT |  | 60 | chr15:97328742-97330464 | 166 | 288/166 | L1PA5 | 140 | 18 | 5' truncation | 16 | 9 | 1
LC9 | CATCTGACTGGAGGATACATGC | TGAAATGATTTAACTTGTTTTTGAA |  | 48 | chr16:31108029-31109719 | 195 | 282/195 | L1PA2 | 104 | 17 | 5' truncation | 37 | 32 | 3
LC13 | ATGTTGATGTTTGGTTCCTGTG | GAAAGGCTACAATGCCTTCTTT |  | 58 | chr2:171915085-171917050 | 438 | 805 | L1PA2 | 383 | 16 | 5' truncation | 10 | 7 | 0
LC14 | TCTGGATCCAAATGCTTTTACC | ATGACCCGGTGAATTACCATAG |  | 55 | chr3:199854482-199856243 | 208 | 372 | L1PA2 | 176 | 12 | 5' truncation | 4 | 1 | 0
LC15 | TATATTCAGGCCTGCCTCTCTC | AACAGCTGCATAGGCAGTATCA |  | 55 | chr4:123226970-123228727 | 488 | 650 | L1PA2 | 581 | 419 | 5' truncation | 16 | 1 | 0
LC16 | CTTAAAGAACTTTACCTTCCAATTTTT | TGCCACAATTTCAGATCCTGT† | TGCAGTGAAAAGGTATCCATGA | 55 | chr4:136405599-136409514 | 796 | 395 | L1PA2 | 3028 | 716 | 5' truncation | 27 | 8 | 0
LC17 | AGCTGGAAACCTTCATTCTCAG | TGAAAGTCATTATTTGCCATAACA |  | 55 | chr5:104545228-104546827 | 427 | 543 | L1PA2 | 247 | 126 | 5' truncation | 4 | 1 | 2
[NAME] | TGCTGTTTCCATTATTGCCTAA | CACCAATTATGAACTAAGCAGGA |  | 55 | chr6:89308800-89310662 | 198 | 458/198 | L1PA2 | 270 | 10 | 5' truncation | 18 | 7 | 0
LC19 | TGACCAGAAAAATGTCTGTATTCAA | CAAGGTGATTAGCATAAAAGGCTAT |  | 55 | chr6:127162130-127164632 | 216 | 1112 | AAG/A | 908 | 11 | 5' truncation | 18 | 5 | 2
LC22 | TGCCTCCTTTGGTCTCATATCT | AGCAATTAAGGTGAGGACGAAG |  | 55 | chr8:69095404-69097387 | 245 | 629 | L1PA2 | 398 | 14 | 5' truncation | 16 | 3 | 2
LC23 | ATAAGGTGCAGTTGGCAGAGAT | CCTGGGTGTGTCCATTAATTCT |  | 55 | chr9:4760239-4762311 | 181 | 635 | L1PA2 | 466 | 12 | 5' truncation | 140 | 59 | 30
LC24 | GAACACTGAAGAGCTTGCAGAA | TGTACATGAGCAACTTGTGAGG |  | 55 | chr9:29436211-29438410 | 225 | 831 | L1PA2 | 618 | 12 | 5' truncation | 18 | 3 | 1
LC25 | TCCTCTTCATCTCACAGAGCAA | ATTTTCTCTGATGGCCAGTGAT† | AGCAATTCAAGGAAGGAACTATTG | 55 | chrX:39922648-39925088 | 312 | 426 | L1PA2‡ | 841 | 19 | 5' truncation | 29 | 13 | 1
LC26 | AGCTGCTGCTTGCTGCTATTA | TTGCCATTCTAACTGGTGTGAG† | [NAME] | 60 | chr22:22072775-22075164 | 420 | 881 | L1PA2 | 1407 | 2973 | 5' truncation/inversion | 8 | 5 | 2
LC27 | TAAAGAGCTTCTGCACAGCAAA† | GGATCTTCTGCTTAGTGGTCCA | TCACCATATCATATAAGGCCATTG* | 60 | chr2:170712230-170714666 | 534 | 665 | L1PA2 | 1460 | 1175 | 5' truncation/inversion | 11 | 4 | 1
LC28 | CCAGTTTTTGCCCATTCAGTAT† | TTGAGTTCATTGTTGATTCTGG | TTCAAGCTGATTTGGTTCATGT* | 63/60 | chr5:125439254-125443507 | 798 | 406 | L1PA2‡ | 3241 | 719 | 5' truncation | 12 | 9 | 5
[NAME] | AGGCCTATAAATCATGCTGCTA† | TGCACAAGTATCCCAGACCTTA | AACCCCTTGGGTGATTACAAAT* | 60/57.4 | chr5:148162097-148167041 | 394 | 589 | AAG/A | 3689 | 1350 | 5' truncation | 20 | 11 | 1
LC30 | GTTGCTCCTGAACTCTGATTGA | GGACATGGATGAAATTGGAAAT† | TAAGCAAACTGGTACAGCCAGA | 60 | chr7:64411160-64412785 | 607 | 477 | L1PA2 | 572 | 2064 | 5' truncation | 17 | 9 | 3
LC31 | ATGGAGACCAACTGTGCATGT | TTGTGCTCTAAGAATACTTAACATGAG |  | 57.4 | chr8:130854472-130856759 | 1055 | 1484 | L1PA2 | 1407 | 978 | 5' truncation | 18 | 11 | 1
LC32 | CTCCTGTGCCTAAATTTGTTCC† | TCAGACGCATGTTTAACTTTGG | CGACTAGAGTTGACTTCCTCAAA* | 60 | chr9:23037637-23038986 | 562 | 446 | L1PA2 | 292 | 1791 | 5' truncation | 8 | 6 | 2
LC33 | ACCCAAAAAGGTGAACACAAGT | TGTGATTATTCAAGGTGCAAGG |  | 55 | chr9:116343239-116344885 | 1270 | 217 | L1PA2 | 134 | 1187 | 5' truncation | 26 | 8 | 1
a(†) | Chimpanzee specific primer.
b(*) | Human specific forward primer.
c | Annealing temperature (Chimpanzee/Human).
d | Chromosomal location.
e(‡) | Including gap.
Table 2. Human specific L1 insertion-mediated deletion loci in Han et al. 2005b
Namea | Forward primerb | Reverse primerb | CS reverse primerc | [NAME] | Chr. loc. in chimpanzeee | Human Size | Chimp Size | L1 family | L1 size (bp) | Deletion size (bp) | L1 features | Genes ± 2MB | Genes ± 1MB | Genes ± 0.25MB
LH1 | ACCAACTTTGTTGGAACTTAGGA | GCAATAAATCAATCCTGCCACT |  | 57.4 | chr11:20881246-20882745 | 447 | 346 | L1PA2 | 116 | 15 | 5' truncation | 21 | 7 | 2
LH4‡ | - | - |  | - | chr16:7864291-7865840 | - | - | Ta | 250 | 107 | 5' truncation | 13 | 9 | 1
[NAME] | ATTTGTGGAAGACCAGAGCATT | ACACCGGATCTAACACACCAC |  | 60 | chr1:29797904-29800103 | 890 | 101 | L1PA2 | 800 | 11 | 5' truncation | 46 | 9 | 1
LH7 | CTGCCTAGGGCTATTCAACAAC | ATCATCACAGGGTCAGGACTTT |  | 54 | chr1:232523876-232525975 | 763 | 106 | L1PA2 | 669 | 12 | 5' truncation | 31 | 20 | 5
LH8 | GTGTACAATGGAAGGTGCTGAA | TGAGAAGTGTCTGCTCATGTCC† | GGAGCCTTGTTAGGGCTTTTTA | 60/55 | chr2:5140075-5142574 | 403 | 214 | L1PA2 | 1092 | 19 | 5' truncation | 22 | 10 | 5
LH9 | AATCTAGGTATAAATGCCTGTTAATGA | GACATGGTTAAACTGTCAATTTTCT |  | 55 | chr2:77382121-77384170 | 803 | 172 | L1PA2 | 641 | 10 | 5' truncation | 10 | 1 | 0
LH10 | GATTGTGGAATGACTGAATAAGC | TCCTTGTTCTTACACCTTTTGC |  | 55 | chr3:98391272-98392821 | 272 | 134 | L1PA2 | 149 | 11 | 5' truncation | 20 | 11 | 2
[NAME] | TGAATTCTTGCTGACCTCTTCA | TGTTGACAGTGGGGTGTTAAAG† | TGATGGGAAGTGATTGgATCAT | 55/55 | chr4:12019991-12025290 | 461 | 366 | L1PA2 | 4044 | 64 | 5' truncation | 13 | 3 | 0
LH14 | TGACTGGCTCTGTAAGGTTTGA | CTGTGAATCCATCTGGTCCTG† | GTCCTACCAACACCCTGATCTC | 55/55 | chr4:19012156-19016455 | 398 | 169 | L1PA2 | 2921 | 11 | 5' truncation | 12 | 2 | 0
LH15 | GGAAATTGCTAGATTGGTGGAA | CTCTGCTGACCACAAACAAATC |  | 55 | chr4:58727217-58729666 | 199/1241 | 199 | Ta | 1054 | 12 | 5' truncation | 21 | 4 | 1
LH16 | TGTCTCAAATTTGTCTATGCAACA | TTCAGCAATACAAAGAAATGAAGT |  | 55 | chr4:127193845-127195551 | 592 | 281 | L1PA2 | 325 | 14 | 5' truncation | 11 | 3 | 0
LH17 | TATGGTCGTATGCCTGTATTGC | GAGTGTTTTCCAACTTGGTTCC† | CCTAGGGCATATCCCATGTAGA | 55/55 | chr5:144072412-144078261 | 390 | 612 | GCG/A | 4895 | 474 | Chimeric (non-inverted) | 17 | 5 | 1
LH18 | AAACAGCAGGGACAGAGAGAAG | CTCAGGCTCCAGCTAGTCCTAC |  | 55 | chr6:105815573-105816972 | 386 | 400 | L1PA2 | 128 | 142 | 5' truncation | 14 | 7 | 4
LH19 | TGAAGGAAACGTCATACAATGAA | TGCACAAATATTGCTCTTCAAA |  | 60 | chr7:11333905-11335554 | 734/504 | 504 | preTa | 251 | 20 | Chimeric (non-inverted) | 12 | 7 | 1
LH20 | TGAAAACTGGTAGCACTTGCAT | GCTACTGCCGTGTTTTACAAAG |  | 60 | chr7:14401904-14403453 | 386 | 241 | ACG/A | 165 | 21 | 5' truncation | 11 | 4 | 1
LH22 | AAGCTTTGGCACAGAGTTGTTA | ACTCCCTTTACATTTCGCCACT |  | 55 | chr8:97978992-97980591 | 546 | 345 | Ta | 211 | 10 | 5' truncation | 26 | 14 | 1
[NAME] | [NAME] | TTTTGTGAGGGAGAGTGAAAGT |  | 55 | chr8:100259150-100260699 | 403 | 249 | Ta | 166 | 11 | 5' truncation | 32 | 12 | 3
LH24 | CCTGGAGCAGACACAAATAGG | TTTGAATATATTGGGAAAGCCATA† | [NAME] | 48/60 | chr10:111067828-111070327 | 522/700 | 700 | Ta | 304 | 2208 | 5' truncation | 14 | 6 | 0
LH26 | CTGGAATACTCAATATTGCTAAGATG | CAATTCTGTGAAGAAAGTCATTGG† | gcctttccaaaggataggtaga | 57.4/55 | chr11:42192341-42195390 | 225/448 | 374 | GAG/G | 1915 | 1763 | Chimeric (non-inverted) | 13 | 1 | 1
LH27 | TAGGAAGTCATCCAGGAGGAAA | TATCACACTCTGGGAACTGTGG† | gtagctgccagcaatacttgg | 55/55 | chr11:126661803-126664502 | 429 | 465 | L1PA2 | 1904 | 2611 | 5' truncation | 37 | 8 | 0
LH28 | GGAACAGGGAAAGGTACTGACA | ACTTCTTTGCCTTTGGTTTGAA† | [NAME] | 60/60 | chr12:91811706-91818455 | 555/876 | 879/612 | L1PA2 | 5174 | 4848 | 5' truncation | 26 | 13 | 4
LH29 | TAACAgAAGGGGAGGAAACAAA† | GGCTACAAATAAAGGGACCTCA | tgtctgtgaacaacagccagac* | 60/60 | chr18:67553158-67554257 | 397 | 487 | /A | 60 | 2404 | 5' truncation | 11 | 2 | 0
LH30 | CAAGAATGAATTGGTGAACAGG | TGACCTTGCCTTGGAGAA |  | 55 | chr1:174109124-174110723 | 598 | 1345 | L1PA2 | 513 | 1260 | 5' truncation | 20 | 7 | 3
LH31 | ttatccaatttgccagtctgtg† | AATGTATTGACAACAGGGTTATTTTT | CTCCCCAGATGAATTCTGTCAT* | 55/60.3 | chr4:98147081-98151880 | 444 | 1798 | L1PA2 | 3991 | 1613 | Chimeric (non-inverted) | 9 | 3 | 2
a(‡) | No amplification
b(†) | Human specific primer.
c(*) | Chimpanzee specific forward primer.
d | Annealing temperature (Human/Chimpanzee).
e | chromosomal location.