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  • vertebrate
  • The most exciting thing for me is that the ultra-conserved regions we have identified do represent evolutionary innovations that must have happened sometime during vertebrate development, because we see such large pieces that no longer match in fish, and almost nothing in sea squirt. (futurepundit.com)
  • Homozygotes for a V2A missense mutation in a conserved vertebrate sequence of HES7 resulted in kinked tails while heterozygotes for the mutation presented with moderately kinked tails. (wikipedia.org)
  • alignment
  • Conserved sequences are typically identified by bioinformatics approaches based on sequence alignment. (wikipedia.org)
  • This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. (pubmedcentralcanada.ca)
  • Each curated CDD alignment records conserved features within the family members in terms of 'blocks', the regions where every sequence is aligned without the gaps. (pubmedcentralcanada.ca)
  • Some of them align all sequences simultaneously ( 5 , 6 ), while others apply a progressive alignment strategy ( 7 - 10 ). (pubmedcentralcanada.ca)
  • Moreover, the final alignment strongly depends on the order of sequences being aligned. (pubmedcentralcanada.ca)
  • To overcome these flaws, iterative approaches have introduced the capacity to reconsider and realign previously aligned sequences at each iteration with the goal of improving the overall alignment score ( 7 , 12 - 19 ). (pubmedcentralcanada.ca)
  • Due to their different copy numbers, positions and/or orientations within the different enhancers, the conserved short sequence elements may otherwise go unnoticed by more conventional DNA alignment programs. (biomedcentral.com)
  • base pairs
  • CSBs that are over 10 base-pairs (bp) long are likely to be made up of adjacent or overlapping sequence-specific transcription factor DNA-binding sites. (biomedcentral.com)
  • Between the strand-biased microsatellite repeats and G:C mononucleotide repeats, all sequence variations retained one or two base pairs with A (purine) interrupting the pyrimidine-rich strand and T (pyrimidine) interrupting the purine-rich strand. (wikipedia.org)
  • genomic
  • The name "satellite DNA" refers to the phenomenon that repetitions of a short DNA sequence tend to produce a different frequency of the bases adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA - such that they form a second or 'satellite' band when genomic DNA is separated on a density gradient. (wikipedia.org)
  • Drosophila
  • Although transcription factor consensus DNA-binding sites are detected within CSBs, searches of 2,086 CSBs (27,996 total bp) curated from 35 mammalian and 99 Drosophila characterized enhancers reveal that well over half of the sequences do not correspond to known DNA-binding sites and, as yet, have no assigned function(s) (this paper). (biomedcentral.com)
  • The vasa gene, is essential for germ cell development and was first identified in Drosophila melanogaster, but has since been found to be conserved in a variety of vertebrates and invertebrates including humans. (wikipedia.org)
  • transcription factors
  • Non-coding sequences important for gene regulation, such as the binding or recognition sites of ribosomes and transcription factors, may be conserved within a genome. (wikipedia.org)
  • Tissue-specific coordinate gene expression requires multiple inputs that involve dynamic interactions between sequence specific DNA-binding transcription factors and their target DNAs. (biomedcentral.com)
  • DNA sequence comparisons of different co-regulating enhancers suggest that many may rely on different combinations of transcription factors to achieve coordinate gene regulation. (biomedcentral.com)
  • regions
  • Many functional sequences are also modular, containing regions which may be subject to independent selection pressures, such as protein domains. (wikipedia.org)
  • The first indication of the existence of ultra-conserved sequence regions was found in the initial comparison of the human and mouse genomes. (futurepundit.com)
  • According to Haussler, the researchers were launched on their analysis when initial studies hinted at major regions of conserved DNA sequences. (futurepundit.com)
  • In this study, DNA fragments encoding miR-BARTs and miR-BHRF1 were amplified by PCR from DNA samples extracted from EBV-positive lymphoma patients and were directly sequenced to determine the mutation, deletion, and/or insertion status of the regions encoding miRNAs. (biomedcentral.com)
  • His research focuses on developing new algorithms for the detection of functional regions in DNA sequences. (wikipedia.org)
  • His research focuses on developing computational methods for detecting functional regions in DNA sequences. (wikipedia.org)
  • The most prevalent repeated sequences in the embedded microsatellite regions were CCT:AGG, CTT:AAG, CTTT:AAAG, and CCCT:AGGG. (wikipedia.org)
  • Other regions of variability among cloned RU sequences were found adjacent to alternating purine and pyrimidine sequences with Z-DNA/stem-loop structures. (wikipedia.org)
  • findings
  • Our findings demonstrate that linkage of multiple variant sequences into a single recombinant construct overcomes the need to embed the variant sequences in foreign helix promoting flanking sequences for conformational stability, and demonstrates the viability of the polyvalent candidates as global S. pyogenes vaccine candidates. (edu.au)