Searching journal content for articles similar to Sopko and Andrews 16 (3): 314.

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  1. Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
    • Ursula Oggenfuss,
    • Robert T. Todd,
    • Natthapon Soisangwan,
    • Bailey Kemp,
    • Alison Guyer,
    • Annette Beach,
    • and Anna Selmecki
    Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
    ...reading frames (ORFs) close to SVs and TEs: Color indicates the percentage of ORFs that either overlap with at least one SV or TE, or that have at least one SV or TE in a 500 bp window upstream or downstream from the ORF. Gray indicates that no SV or TE is present. Color by SV type or TE: (TE...
  2. Method: Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time
    • Andreas Reicher,
    • Anna Koren,
    • and Stefan Kubicek
    Genome Res. December 2020 30: 1846-1855; Published in Advance November 17, 2020, doi:10.1101/gr.261503.120
    ...genes comprising all classic metabolic enzymes (Birsoy et al. 2015; Corcoran et al. 2017) and epigenetic modifiers. For the 2387 genes from this set that harbor targetable introns in the selected reading frame, we designed a library comprising 14,049 sgRNAs targeting 11,614 introns (Fig. 1B...
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  3. Method: ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
    • Riccardo Sangermano,
    • Mubeen Khan,
    • Stéphanie S. Cornelis,
    • Valerie Richelle,
    • Silvia Albert,
    • Alejandro Garanto,
    • Duaa Elmelik,
    • Raheel Qamar,
    • Dorien Lugtenberg,
    • L. Ingeborgh van den Born,
    • Rob W.J. Collin,
    • and Frans P.M. Cremers
    Genome Res. January 2018 28: 100-110; Published in Advance November 21, 2017, doi:10.1101/gr.226621.117
    ...-PCR encompassing RHO exons 3 and 5 was performed, which yielded a wild-type band of 472 bp for BA4 and a 35-nt elongation of exon 6 for c.768G>T (Fig. 3G,H), explained by the presence of a cryptic splice donor site 36-nt downstream (Fig. 3I). The reading frame shift results in a predicted truncated protein, p...
  4. Research: Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution
    • Herwig Bachmann,
    • Marjo J.C. Starrenburg,
    • Douwe Molenaar,
    • Michiel Kleerebezem,
    • and Johan E.T. van Hylckama Vlieg
    Genome Res. January 2012 22: 115-124; Published in Advance November 11, 2011, doi:10.1101/gr.121285.111
    ...ABC transporter, substrate-binding protein G213D 63 1 2,409,303 x A>G LLKF_2364 Zinc ABC transporter, substrate-binding protein T278T 175 0.99 2,471,411 x C>T LLKF_2414 Glucose-6-phosphate isomerase Upstream 37 1 21 4 6 aIndicates in which strain the mutation was detected. bOpen reading frames...
  5. LETTER: Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
    • Byung-Kwan Cho,
    • Eric M. Knight,
    • Christian L. Barrett,
    • and Bernhard Ø. Palsson
    Genome Res. June 2008 18: 900-910; Published in Advance March 13, 2008, doi:10.1101/gr.070276.107
    ...-resolution whole genome-tiling microarrays. We identified 894 Fis-associated regions across the E. coli genome. A significant number of these binding sites were found within open reading frames (33%) and between divergently transcribed transcripts (5%). Analysis indicates that A-tracts and AT...
  6. LETTER: Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families
    • Thomas Wicker and
    • Beat Keller
    Genome Res. July 2007 17: 1072-1081; Published in Advance June 7, 2007, doi:10.1101/gr.6214107
    ...reading frame (ORF), because frameshifts and stop codons are usually the result of mutations in one specific copy and are eliminated in the consensus sequence. For single-copy elements, the hypothetical protein sequences were deduced by comparison with proteins from similar copia elements, and frameshifts...
  7. LETTER: Construction of an ∼700-kb Transcript Map Around the Familial Mediterranean Fever Locus on Human Chromosome 16p13.3
    • Michael Centola,
    • Xiaoguang Chen,
    • Raman Sood,
    • Zuoming Deng,
    • Ivona Aksentijevich,
    • Trevor Blake,
    • Darrell O. Ricke,
    • Xiang Chen,
    • Geryl Wood,
    • Nurit Zaks,
    • Neil Richards,
    • David Krizman,
    • Elizabeth Mansfield,
    • Sinoula Apostolou,
    • Jingmei Liu,
    • Neta Shafran,
    • Anil Vedula,
    • Melanie Hamon,
    • Andrea Cercek,
    • Tanaz Kahan,
    • Deborah Gumucio,
    • David F. Callen,
    • Robert I. Richards,
    • Robert K. Moyzis,
    • Norman A. Doggett,
    • Francis S. Collins,
    • P. Paul Liu,
    • Nathan Fischel-Ghodsian,
    • and Daniel L. Kastner
    Genome Res. November 1, 1998 8: 1172-1191; doi:10.1101/gr.8.11.1172
    ...reading frame is colinear with the entire 310 amino acids of the mouse gene olf3–MUS , and thus is likely to encode an olfactory receptor of the 2C class, of which olf3–MUS is a prototypic member ( Lancet and Ben-Arie 1993 ). View larger version: In this window In a new window Figure 5. Olfactory receptor...
  8. ARTICLE: Caenorhabditis elegans Has Scores of hedgehogRelated Genes: Sequence and Expression Analysis
    • Gudrun Aspöck,
    • Hiroshi Kagoshima,
    • Gisela Niklaus,
    • and Thomas R. Bürglin
    Genome Res. October 1, 1999 9: 909-923; doi:10.1101/gr.9.10.909
    ...the amino terminus—marked with a small x—to line up all the residues; Y69A2A.x has also some problems with extending the ORF over the conserved region, although this YAC sequence is still unfinished. ( D ) Alignment of the Ground-like domains. Secondary structure predictions as for C . The reading frame...
  9. ARTICLES: The human obese (OB) gene: RNA expression pattern and mapping on the physical, cytogenetic, and genetic maps of chromosome 7.
    • E D Green,
    • M Maffei,
    • V V Braden,
    • R Proenca,
    • U DeSilva,
    • Y Zhang,
    • S C Chua,
    • R L Leibel,
    • J Weissenbach,
    • and J M Friedman
    Genome Res. August 1995 5: 5-12; doi:10.1101/gr.5.1.5
    ...gene. The mouse ob RNA is -4.5 kb in size and encodes a 167-amino-acid open reading frame, with the predicted amino acid sequence being 84% iden- tical in mouse and human. This protein appears to be secreted from adipose tissue and likely func- tions as part of a signaling pathway involved...
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