Mammalian comparative sequence analysis of the Agrp locus. by Christopher B Kaelin, Gregory M Cooper, Arend Sidow, Gregory S Barsh

“…Our analysis reveals a symmetrical organization of conserved sequences upstream of Agrp, which cluster into two inverted repeat elements. …”
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Comparative genomics / by Bergman, Nicholas H.

“…Genome visualization and annotation ; Sequence alignments ; Identification of conserved sequences and biases in codon usage ; Identification and structural characterization of noncoding RNAs -- v. 2. …”

Evolution of conserved secondary structures and their function in transcriptional regulation networks by Irwin David M, Xie Hai-Bing, Zhang Ya-Ping

“…The density of SNPs in conserved secondary structures is about 65% of that of their flanking, non-conserved, sequences. Classification of sites as stems or as loops/bulges revealed that the density of SNPs in stems is about 62% of that found in loops/bulges. …”
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Sequence conservation and combinatorial complexity of <it>Drosophila </it>neural precursor cell enhancers by Kuzin Alexander, Baler Kevin, Rasband Wayne, Brody Thomas, Kundu Mukta, Odenwald Ward F

“…<p>Abstract</p> <p>Background</p> <p>The presence of highly conserved sequences within <it>cis</it>-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. …”
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A general pipeline for the development of anchor markers for comparative genomics in plants by Stougaard Jens, Sandal Niels, Bertioli David, Nielsen Anna, Hougaard Birgit K, Madsen Lene H, Fredslund Jakob, Schauser Leif

“…The key features are the identification of evolutionarily conserved sequences followed by automated design of intron-flanking Polymerase Chain Reaction (PCR) primer pairs. …”
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Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy by Dubchak Inna, Kurz Thorsten, Tan Zheng, Schneider Daniel H, Donfack Joseph, Frazer Kelly A, Ober Carole

“…<p>Abstract</p> <p>Background</p> <p>Evolutionarily conserved sequences likely have biological function.</p> <p>Methods</p> <p>To determine whether variation in conserved sequences in non-coding DNA contributes to risk for human disease, we studied six conserved non-coding elements in the Th2 cytokine cluster on human chromosome 5q31 in a large Hutterite pedigree and in samples of outbred European American and African American asthma cases and controls.…”
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The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns by Gil Loewenthal, Elya Wygoda, Natan Nagar, Lior Glick, Itay Mayrose, Tal Pupko

“…We show that when accounting for the occurrence of short conserved sequences within introns, we reproduce the main features, including the presence of long introns and the multimodality of intron distribution.…”
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Conservation and variability of West Nile virus proteins. by Qi Ying Koo, Asif M Khan, Keun-Ok Jung, Shweta Ramdas, Olivo Miotto, Tin Wee Tan, Vladimir Brusic, Jerome Salmon, J Thomas August

“…Of the 88 completely conserved sequences, 67 are also present in other flaviviruses, and several have been associated with the functional and structural properties of viral proteins. …”
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Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm. by Cheng-Hong Yang, Hsueh-Wei Chang, Chang-Hsuan Ho, Yii-Cheng Chou, Li-Yeh Chuang

“…We introduce ClustalW to generate the multiple sequence alignment needed to find the conserved sequences in closely-related species. These conserved sequences are suitable for designing the common primers for the entire mtDNA. …”
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Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact? by Meyer Axel, Hoegg Simone

“…We analyzed the intergenic regions of <it>KCNA </it>clusters in vertebrates and found that there are only a few conserved sequences shared between tetrapods and teleosts or between paralogous clusters. …”
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Oligonucleotide Probe Design for the Study of Cellulolytic and Solventogenic Genes in Colombian Clostridiumsp. strains (Clostridiaceae) by José David Montoya Solano, Zulma Rocío Suárez Moreno, Diego Mauricio Riaño Pachón, Dolly Montoya Castaño, Fabio Ancízar Aristizábal Gutiérrez

“…Ninetyfour conserved sequences were obtained with an average 24nucleotide length, 65.8ºC average Tm and a (G+C) content between 14.3% and 60.0%. …”
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Conservation and variability of West Nile virus proteins. by Koo, Q, Khan, A, Jung, K, Ramdas, S, Miotto, O, Tan, T, Brusic, V, Salmon, J, August, J

“…Of the 88 completely conserved sequences, 67 are also present in other flaviviruses, and several have been associated with the functional and structural properties of viral proteins. …”

Conservation of the OmpC Porin Among Typhoidal and Non-Typhoidal Salmonella Serovars by Valero-Pacheco, N, Blight, J, Aldapa-Vega, G, Kemlo, P, Pérez-Toledo, M, Wong-Baeza, I, Kurioka, A, Perez-Shibayama, C, Gil-Cruz, C, Sánchez-Torres, LE, Pastelin-Palacios, R, Isibasi, A, Reyes-Sandoval, A, Klenerman, P, López-Macías, C

“…Collectively, these findings suggest that these highly conserved sequences may be used for the rational design of an effective broad-spectrum vaccine against Salmonella.…”

Asymmetrical distribution of non-conserved regulatory sequences at <it>PHOX2B </it>is reflected at the ENCODE loci and illuminates a possible genome-wide trend by McCallion Andrew S, Vinton Ryan M, Huynh Jimmy L, Stine Zachary E, McGaughey David M

“…Additionally, analysis of non-conserved sequences scattered over 135 kb 5' to <it>PHOX2B</it>, provides evidence of non-conserved regulatory elements positively biased with close proximity to the gene. …”
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Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach by Manjula Algama, Edward Tasker, Caitlin Williams, Adam C. Parslow, Robert J. Bryson-Richardson, Jonathan M. Keith

“…However, in contrast to previous studies which suggest the majority of conserved sequences are regulatory factor binding sites, the majority of conserved sequences identified using our approach contain evidence of conserved RNA secondary structures, and our laboratory results suggest most are expressed. …”
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NOX family NADPH oxidases in mammals: Evolutionary conservation and isoform-defining sequences by Bahareh Nazari, Vincent Jaquet, Karl-Heinz Krause

“…We also investigated amino acid sequence conservation among given NOX isoforms. Highly conserved sequences were observed for most isoforms except for NOX5. …”
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Phylogenetic analysis of promoter regions of human Dolichol kinase (DOLK) and orthologous genes using bioinformatics tools by Farooqi Nadia, Rahman Ataur, Ali Yasir, Ali Kishwar, Khan Muhammad Ezaz Hasan, Jones David Aaron, Abdelkarim Mouadh, Ullah Farman, Jalil Fazal

“…Conserved non-coding sequences (CNS) and motifs in promoter regions were found by analyzing upstream promoter sequences of Homo sapiens DOLK and its orthologous genes in other organisms. Conserved sequences were predicted in the promoter regions in CNS1 and CNS2. …”
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Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts by Daniel Dar, Rotem Sorek

“…A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. …”
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Rapid, simple, and sensitive detection of the <it>ompB</it> gene of spotted fever group rickettsiae by loop-mediated isothermal amplification by Pan Lei, Zhang Lijuan, Wang Guiqiang, Liu Qinghui

“…The LAMP assay was negative to typhus group rickettsiae including <it>R. prowazekii</it> and <it>R. typhi</it> for no available conserved sequences of <it>ompB</it> was obtained for designing primers.…”
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Conserved TCR beta chain usage in reactive arthritis; evidence for selection by a putative HLA-B27-associated autoantigen. by May, E, Dulphy, N, Frauendorf, E, Duchmann, R, Bowness, P, Lopez de Castro, J, Toubert, A, Märker-Hermann, E

“…All but one patient-derived conserved sequences originated from acute stage ReA-patients, and were not present among approximately 3800 other human TCRB sequences in the database. …”