Table 1.
Thirty-Seven Loci Identified in the Human Genome (hg19) Containing a Fragment of 28s rDNA (LSU)
| Chromosome | Coordinates | Size (bp) | Tail Sequence | Strand | LSU Start | LSU End | % ID to LSU | TSD Length | TSD Sequence | EN Sites | Embedded | Adjacent | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A. SINE28 sequences | |||||||||||||||||||||||
| 1p36.11 | chr1:25483509–25483621 | 113 | AT_rich | − | 4921 | 5034 | 91.15 | 12 | TTGTATTT-TAA /TTGCATTTCTAA | TTAGAA | /L1ME3E | ||||||||||||
| 1p34.2 | chr1:42779299–42779471 | 172 | A_rich/T_rich | + | 4819 | 4991 | 83.33 | 11 | TTACTAGACAT | ATAGAA | |||||||||||||
| 1p22.1 | chr1:92972728–92972802 | 74 | A_rich | − | 4960 | 5034 | 90.41 | 8 | TTATGTTT | TAAAAA | |||||||||||||
| 1q23.1 | chr1:157139813–157139887 | 74 | A_rich | + | 4960 | 5034 | 91.78 | 9 | AGACATAAT | TGAGAA | |||||||||||||
| 1q24.2 | chr1:169878692–169878920 | 175 | AT_rich | − | 4848 | 5023 | 81.58 | 11 | ACCTGGCAGAA | TTAAAA | MER5B/ | ||||||||||||
| 2p16.1 | chr2:59830731–59830959 | 220 | A_rich | − | 4814 | 5034 | 83.91 | 5 | GAGTG | TTAAAA | |||||||||||||
| 2q24.1 | chr2:159440392-159440797 | 437 | A_rich | - | 4595 | 5032 | 78.08 | 14 | TGCCAG-GGTATTC / TGCCAGCGGAATTC | TTGGAA | |||||||||||||
| 2q37.1 | chr2:232110068-232110184 | 118 | (TTAGGG)n | + | 4909 | 5027 | 85.14 | 28 | GTCACGCGGGTGTGTTCGTTTGCAGGGA/ GTTACACAAATATGTTAGCTAGAAAGTA | CTAAGA | |||||||||||||
| 3q23 | chr3:142384659-142384747 | 89 | (T)n | - | 4945 | 5034 | 90.91 | 15 | TGATGGAACAATTTT | TTTAAT | |||||||||||||
| 3q26.33 | chr3:179497344-179497506 | 128 | (T)n | + | 4906 | 5034 | 89.84 | 9 | GAAAGGGAG/GAAAGGCAG | AAAGAG | AluSc8/ | ||||||||||||
| 4p16.1 | chr4:7584187-7584364 | 177 | AT-rich | + | 4857 | 5034 | 92.66 | 18 | CAATTAAAGGATATAAAA/ CAATTAAAGGATAAAACA | TTAACA | |||||||||||||
| 4q21.3 | chr4:86968242–86968396 | 155 | T-rich | − | 4879 | 5034 | 83.33 | 14 | {LG}TAGAATAGTACTCT/TAAAATAGTACTCT | TCTAAA | |||||||||||||
| 4q26 | chr4:120158525–120158690 | 166 | AT_rich | + | 4867 | 5033 | 91.52 | 13 | AGAATCAGCCTGT/AGAGTCAGCCTGT | TTATGT | Tigger1 | ||||||||||||
| 8q11.21 | chr8:49375957–49376033 | 76 | A-rich | − | 4958 | 5034 | 93.33 | 16 | G–CTGGCTAAGGTTG/ GGTCAAGCCAAGATGG | TCAAAG | |||||||||||||
| 8q12.1 | chr8:56821654–56822036 | 369 | AT-rich | − | 4613 | 4982 | 69.67 | 12 | ACATTTTCTTTA | AAATGT | /L1PB4 | ||||||||||||
| 8q22.1 | chr8:98577734–98577938 | 187 | (TAAA)n | + | 4847 | 5034 | 82.57 | 6 | GGGACA | ACAGAA | |||||||||||||
| 9q21.13 | chr9:79186649–79186950 | 335 | A-rich | + | 4699 | 5034 | 85.37 | 13 | AATAATAATGAGA/AATAATAATAATA | AAGAAA | |||||||||||||
| 9q33.3 | chr9:126813738–126813813 | 75 | A-rich | − | 4959 | 5034 | 93.33 | 14 | AAATCATCATCTC/GAATCACCATCTCA | CTAAAA | |||||||||||||
| 10q21.3 | chr10:68805211–68805496 | 309 | (CAA)n/AT-rich | – | 4725 | 5034 | 87.5 | ND | TTTAAA | /MIRc | |||||||||||||
| 10q25.3 | chr10:115461374−115464039 | 101 | T-rich | – | 4918 | 5019 | 90.32 | 8 | AAAGGTGA/AAAGTTTA | ACAGAA | Tigger1 | ||||||||||||
| 12q24.32 | chr12:127650453–127650987 | 424 | (AAAAAT)n | − | 4610 | 5034 | 93.84 | 16 | AAAAA-ATCAGATCCC/ AAAACCATCAGATCCC | TTAAAA | |||||||||||||
| 17q25.2 | chr17:75158032–75158389 | 417 | (AAAAAT)n | − | 4617 | 5034 | 72.58 | 25 | TCAGCCATGGGGATCTGATGGTTTT/ TCAGCCAATGGGATCTGATT-TTTT | AAAAGT | |||||||||||||
| 18q11.2 | chr18:21191674–21191827 | 130 | A-rich | + | 4904 | 5034 | 87.42 | 9 | CCATTGATA | GAAAAC | |||||||||||||
| 18q23 | chr18:77772847–77773065 | 215 | A-rich | + | 4818 | 5033 | 93.12 | 19 | AAATTTTTTTTTTTTTTTT | CCATTA | /AluY | ||||||||||||
| 22q11.22 | chr22:22210671–22210856 | 211 | A_rich | + | 4823 | 5034 | 69.75 | 6 | CAGATA | ACAAAA | |||||||||||||
| Xq25 | chrX:121106711–121106776 | 65 | A_rich | + | 4963 | 5028 | 95.38 | ND | ATGAAA | L1MA8 | |||||||||||||
| Xq27 | chrX:139858393–139858607 | 215 | ND | + | 4821 | 5035 | 84.7 | ND | AAACAT | L1P3 | |||||||||||||
| B. Segmental duplications of LSU fragment/Alu clusters (sd28alu) | |||||||||||||||||||||||
| 4q21.1 | chr4:76807176–76807697 | 522 | AT-rich | + | 4511 | 5033 | 82.8 | ND | AluSq/ | ||||||||||||||
| 8q11.1 | chr8:46951571–46952097 | 534 | ND | − | 4501 | 5035 | 78.32 | ND | /AluSq2 | ||||||||||||||
| 12p11.1 | chr12:34372315–34372728 | 515 | ND | − | 4513 | 5028 | 94.05 | ND | /AluSq2 | ||||||||||||||
| 12q12 | chr12:38531458–38531930 | 539 | ND | + | 4495 | 5034 | 82.55 | ND | AluSx1/ | ||||||||||||||
| 19q13.31 | chr19:43911666–43912167 | 555 | ND | + | 4480 | 5035 | 79.21 | 7 | CTTCGCA | AluSq/ | |||||||||||||
| 21q11.2 | chr21:15456973–15457500 | 527 | ND | − | 4501 | 5028 | 81.8 | ND | /AluSq2 | ||||||||||||||
| Yq11.221 | chrY:19691914–19692439 | 527 | ND | − | 4501 | 5028 | 79.19 | ND | /AluSx1 | ||||||||||||||
| Yq11.222 | chrY:20487334–20487859 | 527 | ND | + | 4501 | 5028 | 79.19 | ND | AluSx1/ | ||||||||||||||
| C. 3′-LSU fragments of larger size than predicted for a SINE | |||||||||||||||||||||||
| 2q21.2 | chr2:133036251–133039236 | 3,232 | Acro1 | − | 1736 | 4968 | 83.38 | ND | |||||||||||||||
| 19q13.2 | chr19:42069990–42070694 | 771 | (TTTA)n | − | 4253 | 5024 | 78.73 | ND | |||||||||||||||
Sequences given in bold indicate 100% identity across annotated TSD sequence. Sequences given in italics indicate 85–99% identity across TSD sequence, both 5′- and 3′-TSDs are included (separated by slash) with gaps in alignment between them indicated by a hyphen. EN sites: endonuclease recognition sequence. ND, not detected.