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

TitleComparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
Authors
Issue Date2001
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic 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.
Persistent Identifierhttp://hdl.handle.net/10722/44365
ISSN
2014 Impact Factor: 9.112
2014 SCImago Journal Rankings: 6.160
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWilson, MDen_HK
dc.contributor.authorRiemer, Cen_HK
dc.contributor.authorMartindale, DWen_HK
dc.contributor.authorSchnupf, Pen_HK
dc.contributor.authorBoright, APen_HK
dc.contributor.authorCheung, TLen_HK
dc.contributor.authorHardy, DMen_HK
dc.contributor.authorSchwartz, Sen_HK
dc.contributor.authorScherer, SWen_HK
dc.contributor.authorTsui, LCen_HK
dc.contributor.authorMiller, Wen_HK
dc.contributor.authorKoop, BFen_HK
dc.date.accessioned2007-09-12T03:52:10Z-
dc.date.available2007-09-12T03:52:10Z-
dc.date.issued2001en_HK
dc.identifier.citationNucleic Acids Research, 2001, v. 29 n. 6, p. 1352-1365en_HK
dc.identifier.issn0305-1048en_HK
dc.identifier.urihttp://hdl.handle.net/10722/44365-
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.en_HK
dc.languageengen_HK
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/en_HK
dc.relation.ispartofNucleic Acids Researchen_HK
dc.subject.meshPhysical chromosome mappingen_HK
dc.subject.meshReceptors, transferrin - geneticsen_HK
dc.subject.meshChromosomes, human, pair 7 - geneticsen_HK
dc.subject.meshDna - chemistry - geneticsen_HK
dc.subject.meshAcetylcholinesterase - geneticsen_HK
dc.titleComparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5en_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0305-1048&volume=29&issue=6&spage=1352&epage=65&date=2001&atitle=Comparative+analysis+of+the+gene-dense+ACHE/TFR2+region+on+human+chromosome+7q22+with+the+orthologous+region+on+mouse+chromosome+5en_HK
dc.identifier.emailTsui, LC: tsuilc@hkucc.hku.hken_HK
dc.identifier.authorityTsui, LC=rp00058en_HK
dc.description.naturelink_to_OA_fulltexten_HK
dc.identifier.pmid11239002en_HK
dc.identifier.pmcidPMC29746-
dc.identifier.scopuseid_2-s2.0-0035869121en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0035869121&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume29en_HK
dc.identifier.issue6en_HK
dc.identifier.spage1352en_HK
dc.identifier.epage1365en_HK
dc.identifier.isiWOS:000167529200012-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWilson, MD=7408666439en_HK
dc.identifier.scopusauthoridRiemer, C=7003529042en_HK
dc.identifier.scopusauthoridMartindale, DW=7003588061en_HK
dc.identifier.scopusauthoridSchnupf, P=8973555200en_HK
dc.identifier.scopusauthoridBoright, AP=6603298498en_HK
dc.identifier.scopusauthoridCheung, TL=7103334554en_HK
dc.identifier.scopusauthoridHardy, DM=7202621609en_HK
dc.identifier.scopusauthoridSchwartz, S=7403605322en_HK
dc.identifier.scopusauthoridScherer, SW=35374654500en_HK
dc.identifier.scopusauthoridTsui, LC=7102754167en_HK
dc.identifier.scopusauthoridMiller, W=7406059331en_HK
dc.identifier.scopusauthoridKoop, BF=7006161280en_HK

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