Skip to main content

Table 1 Motifs used in the screening of DRB1-e2.

From: Sequence features of HLA-DRB1 locus define putative basis for gene conversion and point mutations

Motif description Motif sequence Reference
Polypurine/-pyrimidine tract 5'-RRRRR-3'/5'-YYYYY-3' [47, 19, 48, 49]
Alternating purine-pyrimidine tract 5'-RYRYR-3'/5'-YRYRY-3' [19, 50]
Immunoglobulin heavy chain class switch repeats 5'-GAGCT-3'/5'-AGCTC-3' [51, 49]
  5'-GGGCT-3'/5'-AGCCC-3'  
  5'-GGGGT-3'/5'-ACCCC-3'  
  5'-TGGGG-3'/5'-CCCCA-3'  
  5'-TGAGC-3'/5'-GCTCA-3'  
DNA polymerase arrest site 5'-WGGAG-3'/5'-CTCCW-3' [49]
Deletion hotspot consensus 5'-TGRRKM-3'/5'-KMYYCA-3' [28, 49]
Heptamer recombination signal 5'-CACAGTG-3'/5'-CACTGTG-3' [22]
Nonamer recombination signal 5'-ACAAAAACC-3'/5'-GGTTTTTGT-3' [22]
Chi-like sequence 5'-GCTGGGG-3'/5'-CCCCAGC-3' [40, 52]
Chi-like sequence 5'-CCAG-3'/5'-CTGG-3' [53, 54]
Chi-like sequence 5'-GCWGGWGG-3'/5'-CCWCCWGC-3' [55]
Topoisomerase I consensus cleavage sites 5'-CAT-3'/5'-ATG-3' [56]
  5'-CTY-3'/5'-RAG-3'  
  5'-GTY-3'/5'-RAC-3'  
DNA polymerase A pause site core sequence 5'-GAG-3'/5'-CTC-3' [57]
  5'-ACG-3'/5'-CGT-3'  
DNA polymerase A/B frameshift hotspots 5'-TGGNGT-3'/5'-ACNCCA-3' [58, 59]
Vertebrate topoisomerase II consensus cleavage site 5'-RNYNNCNNGYNGKTNYNY-3'/ [60, 61]
  5'-RNRNAMCNRCNNGNNTNY-3'  
Human hypervariable minisatellite core sequence 5'-GGGCAGGANG-3'/5'-CNTCCTGCCC-3' [62]
DNA polymerase A frameshift hotspots 5'-TCCCCC-3'/5'-GGGGGA-3' [59, 63]
DNA polymerase B frameshift hotspots 5'-TTTT-3'/5'-AAAA-3' [58]
Indel hotspot 5'-GTAAGT-3'/5'-ACTTAC-3' [64]
Hotspot motif 5'-CCTCCCT-3'/5'-AGGGAGG-3' [63]
Repeat element motif 5'-CCCCACCCC-3'/5'-GGGGTGGGG-3' [63]
Double strand break-generating motif 5'-TGGGGG-3'/5'-CCCCCA-3' [63]
  1. The sequences of the complementary strands are separated by "/". The ambiguity code symbols are: R = A/G, Y = C/T, K = G/T, M = A/C, S = G/C, W = A/T, N = A/C/G/T.