An Integrated Computational and Laboratory Approach for Selective Amplification of mRNAs Containing the Adenylate Uridylate-Rich Element Consensus Sequence

Table 1.

Consensus Sequences of Initiation Context Sequences in Human ARE mRNAs

Aa BHDVMMAATGAV Ag BVRMAATGGV
Ca BSHMRVCATGAV Cg VVVVRSCATGGM
Ga HBVVRVGATGAD Gg BVVSRVGATGGM
Ta BDDVRHTATGAM Tg VDBHRBTATGGM
Ac HDDVRBAATGCD At DRBVRMAATGTY
Cc VRSVRMCATGCB Ct BVBMRYCATGTS
Gc SSBBRMGATGCB Gt VDBVRRGATGTY
Tc VBDWWRTATGCM Tt DVBVWDTATGTY

  • Truncated 5′ UTRs regions of 605 ARE mRNAs (a subset of ARED;Bakheet et al. 2001) were computationally extracted as explained in the Methods second. They included at least −7 bp, ATG, +2 bp sequence and subsequently stratified into 16 subsets based on the formula NATGN (underlined). The truncated 5′ UTR regions in each subset were aligned using PileUp (GCG program), and consensus sequences were obtained using Consensus program (GCG) at 75% certainty level at each position. Letter codes follow ambiguous DNA IUB codes, for example, N = A, C, G, or T.

  • UTR, untranslated region; ARED, AU-rich element-containing mRNA database.

This Article

  1. Published in Advance May 16, 2002, doi: 10.1101/gr.204902 Genome Res. 12: 985-995

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