The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Transcript catalogs of human chromosome 21 and orthologous chimpanzee and mouse regions
Abstract
A comprehensive representation of the gene content of the long arm of human chromosome 21 (Hsa21q) remains of interest for the study of Down syndrome, its associated phenotypic features, and mouse models. Here we compare transcript catalogs for Hsa21q, chimpanzee chromosome 21 (Ptr21q), and orthologous regions of mouse chromosomes 16, 17, and 10 for open reading frame (ORF) characteristics and conservation. The Hsa21q and mouse catalogs contain 552 and 444 gene models, respectively, of which only 162 are highly conserved. Hsa21q transcripts were used to identify orthologous exons in Ptr21q and assemble 533 putative transcripts. Transcript catalogs for all three organisms are searchable for nucleotide and amino acid sequence features of ORF length, repeat content, experimental support, gene structure, and conservation. For human and mouse comparisons, three additional summaries are provided: (1) the chromosomal distribution of novel ORF transcripts versus potential functional RNAs, (2) the distribution of species-specific transcripts within Hsa21q and mouse models of Down syndrome, and (3) the organization of sense-antisense and putative sense-antisense structures defining potential regulatory mechanisms. Catalogs, summaries, and nucleotide and amino acid sequences of all composite transcripts are available and searchable at http://gfuncpathdb.ucdenver.edu/iddrc/chr21/home.php. These data sets provide comprehensive information useful for evaluation of candidate genes and mouse models of Down syndrome and for identification of potential functional RNA genes and novel regulatory mechanisms involving Hsa21q genes. These catalogs and search tools complement and extend information available from other gene annotation projects.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Of 500 genes on chromosome 21, 18 genes influence gene expression, and more than 20 genes are involved in metabolic functioning (Sturgeon and Gardiner 2011).”
From Reactive Oxygen Species, Toxicity, Oxidative Stress, and Antioxidants: Chronic Diseases and Aging (2023) · cites this paper as Sturgeon and Gardiner 2011
Citations
Cites
1 retracted
Kuhn, D. E., Nuovo, G. J., Terry, A. V., Martin, M. M., Malana, G. E., Sansom, S. E., Pleister, A. P., Beck, W. D., Head, E., Feldman, D. S., et al. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.033407 · Cited by 121
RetractedLong non-coding RNAs: insights into functions
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2521 · Cited by 5,654
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
The DNA sequence of human chromosome 21
Hattori, M., Fujiyama, A., Taylor, T. D., Watanabe, H., Yada, T., Park, H.-S., Toyoda, A., Ishii, K., Totoki, Y., Choi, D., et al. (2000) · Nature · doi:10.1038/35012518 · Cited by 1,475
Self-citationTranscriptome analysis by strand-specific sequencing of complementary DNA
Parkhomchuk, D., Borodina, T. A., Amstislavskiy, V. S., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H. R., & Солдатов, А. В. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp596 · Cited by 934
Regulatory roles of natural antisense transcripts
Faghihi, M. A., & Wahlestedt, C. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2738 · Cited by 737
Genome-wide transcription and the implications for genomic organization
Kapranov, P., Willingham, A. T., & Gingeras, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2083 · Cited by 735
GENCODE: producing a reference annotation for ENCODE
Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.-K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., et al. (2006) · Genome Biology · doi:10.1186/gb-2006-7-s1-s4 · Cited by 648
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities
Dinger, M. E., Pang, K. C., Mercer, T. R., & Mattick, J. S. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000176 · Cited by 538
Cognitive deficits and associated neurological complications in individuals with Down's syndrome
Lott, I. T., & Dierssen, M. (2010) · The Lancet Neurology · doi:10.1016/s1474-4422(10)70112-5 · Cited by 484
Research works printed but not linked: 1
- CDC (Centers for Disease Control, Prevention) (2006) Improved National Prevalence Estimates for 18 Major Birth Defects. MMWR Morb Mortal Wkly Rep 54:6–12
Cited by
Sorted by citations
Reactive Oxygen Species, Toxicity, Oxidative Stress, and Antioxidants: Chronic Diseases and Aging
Jomova, K., Raptova, R., Alomar, S. Y., Alwasel, S. H., Nepovimova, E., Kuca, K., & Valko, M. (2023) · Archives of Toxicology · doi:10.1007/s00204-023-03562-9 · Cited by 2,638
Down syndrome and Alzheimer's disease: common pathways, common goals
Hartley, D., Blumenthal, T., Carrillo, M., DiPaolo, G., Esralew, L., Gardiner, K., Granholm, A.-C., Iqbal, K., Krams, M., Lemere, C., et al. (2015) · Alzheimer's & Dementia · doi:10.1016/j.jalz.2014.10.007 · Cited by 290
“Of the several DSmouse models that have been generated, the most widely used is the Ts65Dn model for studying DS, which is trisomic for 88 of 161 of the ortholog protein coding genes on human chromosome 21 [51].”
MethodSelf-citationDown syndrome: the brain in trisomic mode
Dierssen, M. (2012) · Nature reviews. Neuroscience · doi:10.1038/nrn3314 · Cited by 288
Glutamate Synapses in Human Cognitive Disorders
Volk, L. J., Chiu, S., Sharma, K., & Huganir, R. L. (2015) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-071714-033821 · Cited by 256
Trisomy 21 and early brain development
Haydar, T. F., & Reeves, R. H. (2012) · Trends in Neurosciences · doi:10.1016/j.tins.2011.11.001 · Cited by 200
“[117], and a recent meta-analysis of expression data in trisomy [118]).”
Background
Metadata
- Authors
- Sturgeon, X., & Gardiner, K. J.
- Affiliations
- University of Colorado Denver (US)
- Corresponding author
- Gardiner, Katheleen J.
- Venue
- Mammalian Genome
- Published
- 2011-03-13
- Volume
- 22
- Issue
- 5-6
- Pages
- 261-271
- ISSN
- 0938-8990 (ISSN-L)
- 1432-1777
- OpenAlex
- W2128527424
- Cited by
- 117
- References
- 38
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 6 · 2023: 5 · 2022: 4 · 2021: 5 · 2020: 5 · 2019: 6 · 2018: 9 · 2017: 8 · 2016: 10 · 2015: 9 · 2014: 12 · 2013: 10 · 2012: 13
- FWCI
- 13.20
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Mammalian Genome (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Anna and John J. Sie Foundation
- National Institutes of Health (5r01hd056235-05)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD056235, R01-HD056235)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Down syndrome and intellectual disability research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- chromosome 21, Down syndrome, orthologous regions, mouse chromosomes, open reading frames, genetic conservation, functional RNA, mouse models of Down syndrome, genome annotation
- MeSH terms
- Animals, Pan troglodytes, Chromosomes, Human, Pair 21, Down Syndrome, Genes, Humans, Species Specificity, Open Reading Frames, Conserved Sequence, DNA, Complementary, Gene Expression Profiling, Regulatory Elements, Transcriptional, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
