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The UCSC Genome Browser Database: update 2006

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Hinrichs, A. S.·2006·Nucleic Acids Research
DOI 10.1093/nar/gkj144PMC PMC1347506
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Abstract

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

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  • Chromosome 21 is one of five human acrocentric chromosomes (13, 14, 15, 21, and 22) that exhibit high sequence conservation and are characterized by an abundance of repetitive elements within their short arms.

    “Chromosome 21 is one of five human acrocentric chromosomes (13, 14, 15, 21, and 22) that exhibit high sequence conservation and are characterized by an abundance of repetitive elements within their short arms (99, 100).”

    From Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex (2026) · cites this paper as [99]

    Our copy’s Chromosome ideogram section describes a display feature, and its Conservation section describes multi-species alignment scores; neither addresses acrocentric chromosomes. Searches for chromosomes 13, 14, 15, 21, and 22 and for repetitive elements in their short arms found no passage supporting the claim. The supplied passages have no page numbers. (LLM, conf=0.75)

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Research works printed but not linked: 49

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Authors
Hinrichs, A. S.
Affiliations
University of California, Santa Cruz (US)
Corresponding author
Hinrichs, A. S.
ORCID
Hinrichs, A. S.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2006-01-01
Volume
34
Issue
90001
Pages
D590-D598
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkj144
PMC
PMC1347506
OpenAlex
W2915985519
Cited by
1,646
References
4
Citations by year
2026: 184 · 2025: 221 · 2024: 172 · 2023: 133 · 2022: 116 · 2021: 104 · 2020: 95 · 2019: 89 · 2018: 61 · 2017: 33 · 2016: 37 · 2015: 38 · 2014: 40 · 2013: 35 · 2012: 19
FWCI
22.17
Type
journal article
Language
en
Open access
Licence
other-oa
Locations
  • Nucleic Acids Research (publishedVersion, other-oa)
  • Europe PMC (PubMed Central) (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
Funders
  • University of California, Santa Cruz
  • National Institutes of Health
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
UCSC Genome Browser, genome annotation, vertebrate genomes, model organisms, genome assembly, gene prediction, comparative genomics, gene expression, genetic variation, blat, in silico PCR
MeSH terms
Amino Acid Sequence, Animals, California, Computer Graphics, Dogs, Genes, Humans, Proteins, Software, User-Computer Interface, Gene Expression, Sequence Alignment, Internet, Polymorphism, Single Nucleotide, Genomics, Databases, Genetic, Proteomics, Mice, Rats

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