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PERSPECTIVE: The mouse genome
- Jean Louis Guénet
Genome Res. December 2005 15: 1729-1740; doi:10.1101/gr.3728305
.... Sequence comparisons at high resolution, made by matching orthologous segments spanning a few tens of base pairs from each and scoring the number of nucleotide mismatches at variable stringency, reveal that, on average, 40% of the mouse sequence can be aligned to the human sequence ( Waterston et al. 2002...
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RESOURCE: Initial sequence and comparative analysis of the cat genome
- Joan U. Pontius,
- James C. Mullikin,
- Douglas R. Smith,
- Agencourt Sequencing Team,
- Kerstin Lindblad-Toh,
- Sante Gnerre,
- Michele Clamp,
- Jean Chang,
- Robert Stephens,
- Beena Neelam,
- Natalia Volfovsky,
- Alejandro A. Schäffer,
- Richa Agarwala,
- Kristina Narfström,
- William J. Murphy,
- Urs Giger,
- Alfred L. Roca,
- Agostinho Antunes,
- Marilyn Menotti-Raymond,
- Naoya Yuhki,
- Jill Pecon-Slattery,
- Warren E. Johnson,
- Guillaume Bourque,
- Glenn Tesler,
- NISC Comparative Sequencing Program,
- and Stephen J. O’Brien
Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
...% of cat MHC genes), the recapitulation of gene syntenic orthology, the recovery of 54% of BAC-based FLA genes with &gt;50% exonic sequences, plus the designation of 11,000 SNPs within FLA (see below) constitute an extensive annotation considering the light sequence coverage and the refractory nature...
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Chicken Special/Resources: Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
- Simon J. Hubbard,
- Darren V. Grafham,
- Kevin J. Beattie,
- Ian M. Overton,
- Stuart R. McLaren,
- Michael D.R. Croning,
- Paul E. Boardman,
- James K. Bonfield,
- Joan Burnside,
- Robert M. Davies,
- Elizabeth R. Farrell,
- Matthew D. Francis,
- Sam Griffiths-Jones,
- Sean J. Humphray,
- Christopher Hyland,
- Carol E. Scott,
- Haizhou Tang,
- Ruth G. Taylor,
- Cheryll Tickle,
- William R.A. Brown,
- Ewan Birney,
- Jane Rogers,
- and Stuart A. Wilson
Genome Res. January 2005 15: 174-183; Published in Advance December 8, 2004, doi:10.1101/gr.3011405
...to the sequence which we anticipate, together with the Bursal full-length cDNA collection, will greatly benefit the existing chicken scientific community. It is hoped that the easy identification of the chicken orthologs of other vertebrate genes and access to physical clones will encourage others to use chicken...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
...DNA sequences (notably the RIKEN/SALK and Ceres resources) such that 16,000 of the 29,000 predicted genes are supported by experimental evidence ( Wortman et al. 2003 ). Comparison of Arabidopsis sequences with genomic sequence from the closely related Brassica oleracea (Chinese cabbage) identified regions...
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ARTICLE: Comparative Genome Analysis of the Mouse Imprinted Gene Impact and Its Nonimprinted Human Homolog IMPACT: Toward the Structural Basis for Species-Specific Imprinting
- Kohji Okamura,
- Yuriko Hagiwara-Takeuchi,
- Tao Li,
- Thanh H. Vu,
- Momoki Hirai,
- Masahira Hattori,
- Yoshiyuki Sakaki,
- Andrew R. Hoffman,
- and Takashi Ito
Genome Res. December 1, 2000 10: 1878-1889; doi:10.1101/gr.139200
...from a paralog rather than the ortholog of Impact . However, the striking structural conservation observed not only in the ORF but also in the 3′ UTR, the syntenic localization, and the well-conserved exon–intron organization (see below) support our idea that IMPACT is the ortholog of Impact . Also...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...spliced between a TE and a genic exon. (B) Sashimi browser plots from the Integrative Genomics Viewer (IGV; Robinson et al. 2011; Thorvaldsdóttir et al. 2013) showing the splicing events in representative samples for prenatal enriched TcGT L2a:CTPS2 and the postnatal enriched LTR12C:SEMA4D. (C) Heatmap...
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Chicken Special/Letters: Structural and functional analysis of a 0.5-Mb chicken region orthologous to the imprinted mammalian Ascl2/Mash2–Igf2–H19 region
- Takaaki Yokomine,
- Hisao Shirohzu,
- Wahyu Purbowasito,
- Atsushi Toyoda,
- Hisakazu Iwama,
- Kazuho Ikeo,
- Tetsuya Hori,
- Shigeki Mizuno,
- Masaoki Tsudzuki,
- Yoh-ichi Matsuda,
- Masahira Hattori,
- Yoshiyuki Sakaki,
- and Hiroyuki Sasaki
Genome Res. January 2005 15: 154-165; Published in Advance December 8, 2004, doi:10.1101/gr.2609605
...). The chicken gene consisted of 11 exons as the mammalian ortholog. The 5′-end of the gene was tentatively assigned based on an expressed sequence tag (EST) sequence (riken1 8h20r1), which was assumed to be a full-length cDNA, from the BursaEst Database ( http://swallow.gsf.de/dt40est.html ). Exons 10 and 11...
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Research: Noncoding origins of anthropoid traits and a new null model of transposon functionalization
- Ricardo C.H. del Rosario,
- Nirmala Arul Rayan,
- and Shyam Prabhakar
Genome Res. September 2014 24: 1469-1484; Published in Advance July 20, 2014, doi:10.1101/gr.168963.113
...) Illustrative example: Sequence alignment of ASC19060 shows constraint in anthropoids and unconstrained divergence among nonprimatemammals. Dots represent identical nucleotides. (C ) Derived allele frequency spectra of African (AFR) SNPs from the 1000 Genomes Project. SNPs within ASCs are shifted to lower...
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Research: Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
- Stephen N. Sansom,
- Noriko Shikama-Dorn,
- Saule Zhanybekova,
- Gretel Nusspaumer,
- Iain C. Macaulay,
- Mary E. Deadman,
- Andreas Heger,
- Chris P. Ponting,
- and Georg A. Holländer
Genome Res. December 2014 24: 1918-1931; Published in Advance September 15, 2014, doi:10.1101/gr.171645.113
...and expression of APS-1 autoantigen ortholog Sox10 and Polr2f encoding a RNA Pol II subunit in mature mTEC. Sansom et al. 1926 Genome Research www..org the periphery (Ernst et al. 1999). While we detect similar numbers of expressed genes in cTEC and inAire-negativemTEC (Fig. 2B), the promiscuous expression...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...regions of interest and the first coding exon of the KIT gene.The 1000 Bull Genomes Project generated a substantial amount of short-read sequencing data for three breeds (Simmental, Hereford, and Braunvieh) included in our pan. Two of these breeds exhibit white heads, whereas one has a colored head...

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