Additional Major Indels Between the PGF and COX Haplotypes
Indel family | Indel type | Additional DNA present in | Context |
|---|---|---|---|
| Simple repeat | (CTTT)n(CCTT)n(CTTT)n | PGF | Satellite repeat of CC/TTT at position where COX has six copies of an ATTT repeat. Positioned ∼5 kb telomeric of 5′ C6orf101 |
| LINE | L1PA2 | PGF | Clean indel positioned ∼35 kb centromeric of 5′ HLA-DRB1 and ∼12 kb telomeric of 5′ HLA-DQA1 |
| LIM2 | COX | Clean indel positioned ∼37 kb centromeric of 5′ HLA-DRB1 and ∼11 kb telomeric of 5′ HLA-DQA1 | |
| BL1PA4 | COX | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 | |
| SINE | AluYa5/8 | PGF | Clean indel. Positioned ∼450 bp telomeric of 5′ OR12D2 |
| AluYb8 | COX | Within a MER65-int element. Between exon 2 and exon 3 of a variant of C6orf12 (HTEX4.3) | |
| AluSg | COX | Within a LTR10E element. Positioned ∼57 kb centromeric of 5′ HLA-C and ∼25 kb telomeric of 3′ HLA-B | |
| AluYb8 | PGF | Within L2 element. Within C6orf10 (TSBP like) intron 8, ∼4 kb from centromeric exon 8 and ∼3 kb from telomeric exon 9 | |
| AlYa5 | PGF | Within an LTR12 element. Within HLA-DRB1 intron 5, ∼100 bp from centromeric exon 5 and ∼700 bp from telomeric exon 6 | |
| AluY | PGF | Clean insertion positioned ∼14 kb centromeric of 5′ HLA-DRB1 and ∼33 kb telomeric of 5′ HLA-DQA1 | |
| AluY | PGF | Clean indel positioned ∼36 kb centromeric of 5′ HLA-DRB1 and ∼11 kb telomeric of 5′ HLA-DQA1 | |
| BAluSx | PGF | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 | |
| BAluSx | PGF | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 | |
| AluY | COX | Within HLA-DQB1 intron 2 ∼2 kb centromeric of exon 3 and ∼1.2 kb telomeric of exon 2 | |
| AluYa5 | COX | Positioned ∼8.5 kb centromeric of HLA-DQB3 and ∼1.2 kb telomeric of 5′ HLA-DQA2 | |
| AluY | PGF | Positioned ∼18 kb centromeric of 5′ HLA-DQB2 and ∼30 kb telomeric of 3′ HLA-DOB | |
| AluYb8 | PGF | Clean indel within intron 2 of HLA-DPB2 pseudogene, positioned ∼8 kb centromeric of exon 2 and ∼2 kb telomeric of exon 3 | |
| HERV | HERVK9 | PGF | Within a MER9 element. Positioned ∼24 kb telomeric of MICF and ∼6 kb centromeric of 5′ end HLA-H |
| HERVCK4 | PGF | Within C4B intron 9, ∼300 bp from telomeric exon 9 and ∼130 bp from centromeric exon 10 | |
| LTR | BLTR5 | PGF | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 |
| MER | BMER11C | PGF | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 |
| SVA | SVA | PGF | Clean indel. Positioned ∼8 kb telomeric of HLA-A |
| SVA | PGF | Positioned ∼52 kb centromeric of POU5F1 and ∼23 kb telomeric of HLA-C | |
| SVA | COX | Within an HERV1 element. Positioned ∼57 kb centromeric of 5′ HLA-C and ∼25 kb telomeric of 3′ HLA-B | |
| SVA within which there are two copies of a 38-mer | PGF | Within an L14MC element. Positioned ∼6.5 kb telomeric of 5′ HCP5, between MICA and MICB | |
| Combination indels | SVA and (TCTCCC)×38 | PGF | Clean indel between Charlie9 repeat and MLT1E3 repeat. Positioned ∼3 kb telomeric of 5′ HLA-F |
| AluSp and L1PA13 | PGF | Positioned ∼52 kb centromeric of 5′ HLA-C and ∼28 kb telomeric of 3′ HLA-B | |
| AluSq and AluY | COX | Within an L2 element. Within HLA-DRB1 intron 1, ∼2.5 kb from centromeric exon 1 and ∼3.5 kb from telomeric exon 2 | |
| SVA and other sequence | PGF | Positioned ∼4.5 kb centromeric of 5′ HLA-DRB1 and ∼41 kb telomeric of HLA-DQA1 | |
| L1PA4 and (A)n stretch | COX | Positioned ∼2 kb centromeric of 3′ HLA-DQA1 and ∼14 kb telomeric of 3′ HLA-DQB1 | |
| BL1PA6 and AluY | PGF | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 | |
| BT-rich repeats and SVA | COX | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 | |
| L1MC5 with LTR42 in middle | PGF | Positioned ∼47 kb centromeric of 5′ HLA-DQB2 and ∼700 bp telomeric of 3′ HLA-DOB | |
| Complex indels | CSome non-repeat sequence, MIR, MER41B, MER115, AluSx, Flam_C, AluSg, AluY, AluSx and L2 with MER38 in middle | PGF | Probable recombination between two nearby Alus: PGF has AluSc bordering the telomeric end of the indel and an AluSx bordering the centromeric end. Positioned ∼600 bp centromeric of 5′ of RFP, and ∼15 kb telomeric of C6orf100 |
| ∼4 kb indel containing a possible CpG island through the centromeric 2 kb. EST matches are observed around the CpG island. One match is observed to a small ∼260-bp fragment of the KIAA1545 cDNA | COX | Positioned ∼16 kb centromeric of 3′ HLA-G and ∼5.5 kb telomeric of MICF pseudogene | |
| ACompared with PGF, COX has part of the sequence inverted and two inserted sequences either side of the inversion | COX | Positioned ∼50 kb centromeric of C6orf205 | |
| L2, Tigger4, and MER20 each separated by non-repeat element sequence | COX | Located within an MER53 element in HLA-DRB1 intron 1, ∼5 kb from centromeric exon 1 and ∼900 bp from telomeric exon 2 | |
| BHAL1 with an AluY and an AluYc in it | PGF | Centromeric of HLA-DQA1 and telomeric of HLA-DQB1 |
[i] SVA repeats contain several Alu sequences and a fragment of LTR5. Dot-matrix comparisons of PGF and COX sequences over indels marked with superscript A and B are shown in Figures 3A and 3B, respectively. See Supplemental Table 4 for genomic locations of each indel.