Table 2

Motifs previously identified in other genes found in the DRB1-e2

Motif description

Motif sequence

Position

Not present in

Polypurine tract

5'-RRRRR(RRR)-3'

88–95

121–125a

178–184

246–250

Polypyrimidine tract

5'-YYYYY-3'

5–10

36–41

Immunoglobulin heavy chain class switch repeat

5'-GAGCT-3'

141–145

DRB1*0328

248–252

DRB1*0452

5'-TGGGG-3'

145–149

DRB1*07

Deletion hotspot consensus

5'-TGAAGA-3'

37–42b

5'-TGRRKM-3'

145–150

DRB1*07

250–255b

Chi-like sequence

5'-GCTGGGG-3'

143–149

DRB1*07

5'-CTGG-3'

144–147b

DRB1*07

167–170b

DRB1*0705

176–179

Topoisomerase I consensus cleavage site

5'-CTY-3'

38–40

251–253

DRB1*0423, *0452

5'-GTY-3'

4–6

31–33

47–49b

108–110b

114–116b

171–173b

183–185b

213–215b

231–233b

DNA polymerase a pause site core sequence

5'-GAG-3'

51–53

DRB1*0439

121–123

246–251 (2×)

268–270

5'-ACG-3'

2–4

115–117

116–118b

Deletion hotspot

5'-YYYTG-3'

7–11

177–181b

DRB1*0705

187–191

DRB1*1374


Only the motifs present in at least an (almost) entire allelic family are presented; some less common motifs are presented in the text. 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.

amotif ± 1 bp

b motif in non-coding strand corresponding to these bases in the coding strand.

von Salomé and Kukkonen BMC Genomics 2008 9:228   doi:10.1186/1471-2164-9-228

Open Data