Article: Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5

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TitleComparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
AuthorsWilson, MD2
Riemer, C1
Martindale, DW2
Schnupf, P2
Boright, AP4
Cheung, TL3
Hardy, DM3
Schwartz, S1
Scherer, SW4
Tsui, LC4
Miller, W1
Koop, BF2
Issue Date2001
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
CitationNucleic Acids Research, 2001, v. 29 n. 6, p. 1352-1365 [How to Cite?]
AbstractChromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning Ache to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by Ache and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://web.uvic.ca/∼bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.
ISSN0305-1048
2011 Impact Factor: 8.026
2011 SCImago Journal Rankings: 1.542
ISI Accession Number IDWOS:000167529200012
PubMed Central IDPMC29746
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorWilson, MD
dc.contributor.authorRiemer, C
dc.contributor.authorMartindale, DW
dc.contributor.authorSchnupf, P
dc.contributor.authorBoright, AP
dc.contributor.authorCheung, TL
dc.contributor.authorHardy, DM
dc.contributor.authorSchwartz, S
dc.contributor.authorScherer, SW
dc.contributor.authorTsui, LC
dc.contributor.authorMiller, W
dc.contributor.authorKoop, BF
dc.date.accessioned2007-09-12T03:52:10Z
dc.date.available2007-09-12T03:52:10Z
dc.date.issued2001
dc.description.abstractChromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene-dense, GC-rich sub-region of 7q22 with the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes. A 296 kb segment from the physical map, spanning Ache to Tfr2, was compared with 267 kb of human sequence. We identified a conserved linkage of 12 genes including an open reading frame flanked by Ache and Asr2, a novel cation-chloride cotransporter interacting protein Cip1, Ephb4, Zan and Perq1. While some of these genes have been previously described, in each case we present new data derived from our comparative sequence analysis. Adjacent unfinished sequence data from the mouse contains an orthologous block of 10 additional genes including three novel cDNA sequences that we subsequently mapped to human 7q22. Methods for displaying comparative genomic information, including unfinished sequence data, are becoming increasingly important. We supplement our printed comparative analysis with a new, Web-based program called Laj (local alignments with java). Laj provides interactive access to archived pairwise sequence alignments via the WWW. It displays synchronized views of a dot-plot, a percent identity plot, a nucleotide-level local alignment and a variety of relevant annotations. Our mouse-human comparison can be viewed at http://web.uvic.ca/∼bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/, along with online documentation and additional examples of annotated genomic regions.
dc.description.naturelink_to_OA_fulltext
dc.identifier.citationNucleic Acids Research, 2001, v. 29 n. 6, p. 1352-1365 [How to Cite?]
dc.identifier.epage1365
dc.identifier.isiWOS:000167529200012
dc.identifier.issn0305-1048
2011 Impact Factor: 8.026
2011 SCImago Journal Rankings: 1.542
dc.identifier.issue6
dc.identifier.openurl
dc.identifier.pmcidPMC29746
dc.identifier.pmid11239002
dc.identifier.scopuseid_2-s2.0-0035869121
dc.identifier.spage1352
dc.identifier.urihttp://hdl.handle.net/10722/44365
dc.identifier.volume29
dc.languageeng
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
dc.publisher.placeUnited Kingdom
dc.relation.ispartofNucleic Acids Research
dc.relation.referencesReferences in Scopus
dc.subject.meshPhysical chromosome mapping
dc.subject.meshReceptors, transferrin - genetics
dc.subject.meshChromosomes, human, pair 7 - genetics
dc.subject.meshDna - chemistry - genetics
dc.subject.meshAcetylcholinesterase - genetics
dc.titleComparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
dc.typeArticle
Author Affiliations
  1. Pennsylvania State University
  2. University of Victoria
  3. Texas Tech University Health Sciences Center at Lubbock
  4. Hospital for Sick Children, Toronto