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Example sentences for: krc-selected
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For example, the KRC/ZAS-C consensus sequence "ATTTTGTGG" matches completely with 6 nucleotides of the RSS nonamer and 3 flanking nucleotides of the human IgH D1, D2, D3 and D4 gene segments [ 35 ] . Furthermore, the MAST search identified KRC-selected motifs near two chromosomal breakpoints: between a t(11:14) translocation of the Ig DH2-2 gene segment and the B cell lymphoma 1 ( BCL-1 ) gene in a mantle cell lymphoma [ 36 ] , and at a t(11:19) translocation of the myeloid lymphoid leukemia ( MLL ) gene and the ENL/MLLT1/LTG19 gene in a T-cell acute lymphoblastic leukemia [ 37 ] . The other hits were derived from loci of cellular genes, pseduogenes, or DNA fragments [ 41 42 43 44 ] . The expression of those genes has not been shown to be regulated by KRC or other family members, therefore, the biological significance of those MAST results is unknown.
After cloning and DNA sequencing, the KRC-selected sequence datasets were analyzed by the computer program Multiple Expectation Maximum for Motif Elicitation (MEME version 3.0) to generate sets of position specific scoring matrices (PSSMs) or motifs [ 30 ] . When the program was set to identify wider sequences (= 9 nucleotides) the PSSMs were homologous to Sb [ 29 ] , the κB motif [ 31 ] , and the canonical heptamer and nonamer elements of the RSS [ 32 ] . However, shortening the width of the motifs to 5 nucleotides, the target length for the C 2 H 2 zinc finger pairs of the tramtrack [ 33 ] , the ZAS-N dataset yielded two motifs, "GGTAT" and "T(T/C)TT(T/G)G" and the ZAS-C dataset yielded a single motif, "TGTGG".
The computer program Multiple Alignment Sequence Tool (MAST version 3.0) [ 34 ] was used to search human and mouse genome databases for DNA elements matching the KRC-selected PSSMs.
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