Table 3

Fully conserved stretches of a minimum of 3 bp in all DRB1-e2 sequences

Position

Sequence (underlined letters corresponding to motif in table 2)

Corresponding motif in Table 2


4–8

5'-

    GTTTC
-3'

Polypyrimidine tract

30–32

5'-TGT-3'

36–43

5'-T

    TCTTCA
A-3'

5'-

    TTCTTC
AA-3'

Deletion hotspot consensus sequence (5'-TGAAGA-3') in non-coding strand

Polypyrimidine tract (5'-TTCTTC-3')

47–49

5'-GAC-3'

51–54

5'-GAGC-3'

56–60

5'-GGTGC-3'

107–119

5'-CGACAGCGACGTG-3'

121–124

5'-

    GGGA
-3'

Polypurine tract

142–145

5'-

    AGCT
-3'

Part of the immunoglobulin heavy chain class switch repeat (5'-G

    AGCT
-3')a

5'-A

    GCT
-3'

Part of the chi-like sequence (5'-

    GCT
GGGG-3')a

147–149

5'-

    GGG
-3'

Part of deletion hotspot consensus sequence (5'-TG

    RRK
M-3')a

5'-

    GGG
-3'

Part of the chi-like sequence (5'-GCTG

    GGG
-3')a

167–174

5'-CTGGAACA-3'

179–182

5'-GAAG-3'

210–215

5'-GTGGAC-3'

222–227

5'-TGCAGA-3'

229–235

5'-ACAACTA-3'

246–250

5'-

    GAGAG
-3'

Polypurine trac

248–250

5'-

    GAG
-3'

Part of the immunoglobulin heavy chain class switch repeat (5'-

    GAG
CT-3')a

252–256

5'-

    TTCA
C-3'

Deletion hotspot consensus sequence

261–263

5'-CAG-3'

267–269

5'-CGA-3'


athe full motif as in Table 2

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

Open Data